PRIME EDITOR DELIVERY BY AAV RELATED APPLICATIONS [0001] This application claims priority under 35 U.S.C. § 119(e) to U.S. Provisional Application, U.S.S.N.63/426,336, filed on November 17, 2022, entitled “Prime editor delivery by AAV,” by David R. Liu et al. and to U.S. Provisional Application, U.S.S.N. 63/491,013, filed on March 17, 2023, entitled, “Prime editor delivery by AAV,” by David R. Liu et al., both of which are incorporated herein by reference in their entirety REFERENCE TO AN ELECTRONIC SEQUENCE LISTING [0002] The contents of the electronic sequence listing (B119570173WO00-SEQ- JQM.xml; Size: 596,955 bytes; and Date of Creation: November 16, 2023) is herein incorporated by reference in its entirety. GOVERNMENT FUNDING [0003] This invention was made with government support under UG3AI150551, U01AI142756, R35GM118062, and RM1HG009490 awarded by US National Institutes of Health (NIH). The government has certain rights in the invention. FIELD [0004] The present disclosure generally relates to genome editing and, in particular, to the in vivo delivery of genome editors using adeno associated virus (AAVs). BACKGROUND [0005] Precise genome targeting technologies using the CRISPR/Cas9 system have recently been explored in a wide range of applications, including gene therapy. A major limitation to the application of Cas9 and Cas9-based genome-editing agents, including the prime editing systems, in gene therapy is the size of Cas9 (>4 kb), impeding its efficient delivery via recombinant adeno-associated virus (rAAV). SUMMARY [0006] Described herein are systems, compositions, kits, and methods for delivering a prime editor to cells, e.g., via recombinant adeno-associated virus vectors (herein AAV). In some embodiments, the prime editor comprises a fusion protein of a nucleic acid programmable DNA binding protein (herein napDNAbp) and a polymerase (e.g., a reverse transcriptase), optionally connected via a linker. Typically, a prime editor is “split” into an N-terminal portion and a C-terminal portion because the full-length prime editor, which is encoded by a polynucleotide of ~6.3kb, exceeds the packaging limit of rAAV (~4.9 kb). The prime editor comprises a napDNAbp domain, an optional linker, and a polymerase domain. In certain embodiments, the napDNAbp comprises a SpCas9. In certain embodiments the SpCas9 of the prime editor is split into two fragments at a split site located approximately midway through the sequence of the prime editor. In certain embodiments, the split site is located within loop sites that can accommodate fusion to the intein halves with minimal disruption to function of the prime editor. In certain embodiments, the split site is located between residues 844 and 845 or between residues 1024 and 1025 (SEQ ID NOs: 118-124). The N-terminal portion and C-terminal portion of the prime editor may each be fused to one member of the intein system, respectively. For example, the N-terminal portion of the prime editor fused to a C-terminal intein and the C-terminal portion of the prime editor fused to a N-terminal intein. When delivered on separate vectors (e.g., separate rAAV vectors) into one cell and co-expressed, the N-terminal portion of the prime editor fused to a C-terminal intein and the C-terminal portion of the prime editor fused to a N-terminal intein may be joined to form a complete and functional prime editor (e.g., via intein-mediated protein splicing). Further provided herein are empirical testing of regulatory elements in the delivery vectors for high expression levels of the split prime editor. [0007] In certain embodiments, compositions comprising a first nucleotide sequence encoding a N-terminal portion of a prime editor fused at its C-terminus to an intein-N are described. In certain embodiments, compositions comprising a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of the primer editor are described. In some embodiments, compositions comprising a first nucleotide sequence encoding a N-terminal portion of a prime editor fused at its C-terminus to an intein-N and a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of the primer editor are described. The split site, in some cases, may be selected so that the N-terminal portion of the prime editor comprises a portion of any one of SEQ ID NOs: 14, 17, 19, 24-53, 55-65, 67-82, 84 that corresponds to amino acids 1-844 or 1-1024 of SEQ ID NO: 14. In some embodiments, the three N-terminal amino acids of the C-terminal extein may be mutated from the native residues to a consensus Cys-Phe-Asn extein sequence (herein referred to as the 844-CFN split and 1024-CFN split respectively). In other embodiments, zero, one, or two of the three N-terminal amino acids of the C-terminal extein may be mutated to the corresponding residues of the consensus Cys-Phe-Asn sequence; for example, the 844-SFL split, and 844-SFN split, and the 1024-SEQ split, 1024-SFQ split, 1024-SFN split, and 1024-SEN split, where the native residues for the three N-terminal amino acids of the C-terminal extein are SFL for residues 845-847 and SEQ for residues 1025-1027 in the native SpCas9 of the prime editor. [0008] In certain embodiments, compositions comprising a rAAV particle comprising a first nucleotide sequence encoding a N-terminal portion of a prime editor fused at its C- terminus to an intein-N are described. In certain embodiments, compositions comprising a second rAAV particle comprising a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of the prime editor are also described. In other embodiments, compositions comprising a rAAV particle comprising a first nucleotide sequence encoding a N-terminal portion of a prime editor fused at its C-terminus to an intein- N and a second rAAV particle comprising a second nucleotide sequence encoding a intein-C fused to the N-terminus of a C-terminal portion of the prime editor is also described. [0009] The split site, in some cases, may be selected so that the N-terminal portion of the prime editor comprises a portion of any one of SEQ ID NO: 14, 17, 19, 24-53, 55-65, 67-82, 84 that corresponds to amino acids 1-844 or 1-1024 of SEQ ID NO: 14. In some embodiments, the three N-terminal amino acids of the C-terminal extein may be mutated from the native residues to a consensus Cys-Phe-Asn extein sequence (herein referred to as the 844-CFN split and 1024-CFN split respectively). In other embodiments, zero, one, or two of the three N-terminal amino acids of the C-terminal extein may be mutated to the corresponding residues of the consensus Cys-Phe-Asn sequence; for example, the 844-SFL split, and 844-SFN split, and the 1024-SEQ split, 1024-SFQ split, 1024-SFN split, and 1024- SEN split, where the native residues for the three N-terminal amino acids of the C-terminal extein are SFL for residues 845-847 and SEQ for residues 1025-1027 in the native SpCas9 of the prime editor. [0010] In some cases, the first or second nucleotide sequence of the composition may further comprise a nucleotide sequence encoding a prime editing guide RNA (herein pegRNA) operably linked to a promoter. In other cases, the composition further comprises a third nucleotide sequence that encodes a pegRNA operably linked to a promoter. In some embodiments, the pegRNA comprises a 3′ stabilizing motif. In some embodiments, the pegRNA encodes one or more edits configured to natively evade an MMR pathway. [0011] Aspects of the present disclosure relate to compositions comprising a first rAAV particle comprising a first nucleotide sequence encoding a N-terminal portion of a prime editor fused at its C-terminus to an intein-N and a second rAAV particle comprising a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of the prime editor. The composition, in some cases, may further comprise a nucleotide sequence encoding a pegRNA operably linked to a promoter. In some embodiments, the pegRNA comprises a 3′ stabilizing motif. In some embodiments, the pegRNA encodes one or more edits configured to natively evade an MMR pathway. [0012] Other aspects of the present disclosure relate to a first nucleotide sequence encoding a N-terminal portion of a prime editor fused edits C-terminus to an intein-N and a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of the prime editor. In some embodiments, the first nucleotide sequence or the second nucleotide sequence further comprise a nucleotide encoding a pegRNA operably linked to a promoter. In some embodiments, the prime editor comprises a MMLV reverse transcriptase. In some embodiments the MMLV reverse transcriptase is codon optimized for expression in a mammalian cell. [0013] Other embodiments of the present disclosure relate to a first rAAV particle comprising a first nucleotide sequence encoding a N-terminal portion of a prime editor fused at its C-terminus to an intein-N and a second rAAV particle comprising a second nucleotide sequence encoding and intein-C fused to the N-terminus of a C-terminal portion of the prime editor. In some embodiments the first nucleotide sequence or the second nucleotide sequence further comprise a nucleotide encoding a peg RNA operably linked to a promoter. In some embodiments, the prime editor comprises a MMLV reverse transcriptase. In some embodiments, the MMLV reverse transcriptase is codon optimized for expression in a mammalian cell. [0014] Other aspects of the present disclosure relate to a triple rAAV system. For example, in some embodiments, a composition comprises a first nucleotide sequence encoding a N-terminal portion of a prime editor fused at its C-terminus to an intein-N and a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of the prime editor and third nucleotide sequence encoding a pegRNA and a sgRNA. [0015] In some aspects, the present disclosure relates to a first rAAV particle comprising a first nucleotide sequence encoding a N-terminal portion of the prime editor fused at its C- terminus to an intein-N and a second rAAV particle comprising a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of the prime editor and third rAAV particle comprising third nucleotide sequence encoding a pegRNA and a sgRNA. [0016] Aspects of the present disclosure further relate to a composition comprising a first nucleotide sequence encoding a N-terminal portion of a prime editor fused at its C-terminus to an intein-N and a second nucleotide sequence encoding an intein-C fused to the N- terminus of a C-terminal portion of the prime editor. In some embodiments, the prime editor further comprises a truncated MMLV reverse transcriptase with at least 80%, 85%, 90%, 95%, 99%, or 99.5% sequence identity to SEQ ID NO: 98. [0017] In some embodiments, a first rAAV particle comprises a first nucleotide sequence encoding a N-terminal portion of a prime editor fused at its C-terminus to an intein-N and a second rAAV particle comprises a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of the prime editor. In some embodiments, the prime editor further comprises a truncated MMLV reverse transcriptase with at least 80%, 85%, 90%, 95%, 99%, or 99.5% sequence identity to SEQ ID NO: 98. [0018] Other aspects of the present disclosure relate to cells with the polynucleotides described herein, the vectors described herein, cells with the prime editors described herein, cells with a portion of the prime editor (spliced or not spliced), and cells with one or more rAAVs described herein. [0019] The present disclosure also relates to a protein encoded by a first nucleotide sequence encoding a N-terminal portion of a prime editor fused at its C-terminus to an intein- N. The present disclosure also relates to a protein encoded by a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of the primer editor. The present disclosure also relates to the proteins encoded by a first nucleotide sequence encoding a N-terminal portion of a prime editor fused at its C-terminus to an intein-N and a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of the primer editor. [0020] The present disclosure also relates to vectors for the delivery of a first nucleotide sequence encoding a N-terminal portion of a prime editor fused at its C-terminus to an intein- N to cells. The present disclosure further relates to vectors for the delivery of a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of the primer editor to cells. The present disclosure also relates to vectors for the delivery of a first nucleotide sequence encoding a N-terminal portion of a prime editor fused at its C- terminus to an intein-N and a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of the primer editor to cells. [0021] The present disclosure further describes compositions comprising a first nucleotide sequence encoding a N-terminal portion of a prime editor fused at its C-terminus to an intein-N encapsulated with an LNP or VLP. In certain embodiments, compositions comprising a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of the primer editor encapsulated with an LNP or VLP are described. In some embodiments, compositions comprising a first nucleotide sequence encoding a N- terminal portion of a prime editor fused at its C-terminus to an intein-N and a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of the primer editor encapsulated with an LNP or VLP are described. [0022] The present disclosure further describes pharmaceutical compositions comprising a first nucleotide sequence encoding a N-terminal portion of a prime editor fused at its C- terminus to an intein-N and one or more pharmaceutically acceptable excipients. The present disclosure further describes pharmaceutical compositions comprising a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of the primer editor and one or more pharmaceutically acceptable excipients. The present disclosure further describes pharmaceutical compositions comprising a first nucleotide sequence encoding a N-terminal portion of a prime editor fused at its C-terminus to an intein-N and a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of the primer editor and one or more pharmaceutically acceptable excipients. The present disclosure further describes pharmaceutical compositions comprising a protein encoding a N-terminal portion of a prime editor fused at its C-terminus to an intein-N and one or more pharmaceutically acceptable excipients. The present disclosure further describes pharmaceutical compositions comprising a protein encoding an intein-C fused to the N- terminus of a C-terminal portion of the primer editor and one or more pharmaceutically acceptable excipients. The present disclosure further describes pharmaceutical compositions comprising proteins encoding a N-terminal portion of a prime editor fused at its C-terminus to an intein-N and an intein-C fused to the N-terminus of a C-terminal portion of the primer editor and one or more pharmaceutically acceptable excipients. [0023] Other aspects of the present disclosure relate to kits comprising anyone of the compositions and/or cells described herein. [0024] Additional aspects of the present disclosure relate to methods of using the compositions, cells, and kits described herein. For example, in some cases, the present disclosure relates to a method for the systemic delivery of prime editors to the central nervous system (CNS) of a subject in need thereof. In some embodiments, the method comprises administering to the subject any one of the compositions, cells, or kits described herein. In some cases, the method comprises the use of rAAV particles capable of crossing the blood- brain barrier (e.g., AAV PHP.eB). [0025] In some aspects, the disclosure relates to a method of editing an organ in a subject. In some embodiments, the method comprises administering to the subject a first nucleotide sequence encoding a N-terminal portion of a prime editor fused at its C-terminus to an intein- N; and a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C- terminal portion of the prime editor. In some embodiments, the second nucleotide sequence comprises a pegRNA and sgRNA. In some embodiment the pegRNA comprises a 3’ stabilizing motif. In some embodiments, the pegRNA encodes one or more edits configured to natively evade an MMR pathway. In some embodiments, the prime editor comprises a truncated MMLV reverse transcriptase. [0026] In other aspects, the present disclosure relates to a method of contacting a cell with any one of the compositions or rAAV particles described herein. In some embodiments, contacting results in the delivery of the first nucleotide sequence and the second nucleotide sequence, and optionally third nucleotide sequence, into the cell. Once inside the cell the N- terminal portion of the prime editor and the C-terminal portion of the prime editor are joined to form a prime editor. [0027] Additional aspects of the present disclosure relate to a method comprising administering to a subject in need thereof a therapeutically effective amount of any one of the compositions or rAAV particles described and a pharmaceutically acceptable [0028] It should be appreciated that the foregoing concepts, and additional concepts discussed below, may be arranged in any suitable combination, as the present disclosure is not limited in this respect. Further, other advantages and novel features of the present disclosure will become apparent from the following detailed description of various non- limiting embodiments when considered in conjunction with the accompanying figures. BRIEF DESCRIPTION OF THE DRAWINGS [0029] Non-limiting embodiments of the present disclosure will be described by way of example with reference to the accompanying figures, which are schematic and are not intended to be drawn to scale. In the figures, each identical or nearly identical component illustrated is typically represented by a single numeral. For purposes of clarity, not every component is labeled in every figure, nor is every component of each embodiment of the disclosure shown where illustration is not necessary to allow those of ordinary skill in the art to understand the disclosure. In the figures: [0030] FIGs.1A-1C. Initial development of a split prime editor in tissue culture and for AAV mediated in vivo prime editing a, Editing performance at three genomic loci of intein- split PE3 variants normalized to that of unsplit, canonical PE3 when delivered by plasmid transfection in HEK293T cells. The split site in SpCas9 and the identity of the three most N- terminal residues of the C-terminal extein are indicated below each bar. (FIG.1A) sub- optimal amount of editor plasmid was used in order to avoid saturating editing efficiencies. Dots represent values normalized to canonical PE3 activity and error bars represent mean±SEM of n= 3 biological replicates at three genomic loci. (FIG.1B) Schematic of v1 PE3-AAV architecture. (FIG.1C) In vivo editing activity of v1 PE3-AAV9 with pegRNA encoding the Dnmt1 +5 G-to-T edit delivered to neonatal C57BL/6 pups by P0 ICV injection at a dose of 1×10 ¹¹ vg total (5×10 ¹⁰ vg per half). Cortex (neocortex and hippocampus) was harvested, nuclei were isolated and sorted by FACS into bulk and GFP+ populations, and genomic DNA was harvested and analyzed by high-throughput screening (HTS). For c, dots represent individual mice and error bars represent mean±SEM of n=3-5 mice. [0031] FIGs.2A-2C. AAV-mediated in vivo prime editing efficiency is dependent on the type of edit. (FIG.2A) Editing activity of PE2 and PE4 in N2a cells by plasmid transfection for four different edits at Dnmt1. N2a cells were transfected with either PE2 and pegRNA or PE4 (PE2 + MLH1dn) and pegRNA. Three days later, genomic DNA was harvested and analyzed by HTS. Dots represent values and error bars represent mean±SEM of n= 2 biological replicates. (FIG.2B), In vivo editing activity of v1 AAV9 PE3 delivered to neonatal C57BL/6 pups on P0 by ICV at a total dose of 1×10 ¹¹ vg (5×10 ¹⁰ vg per half). Cortex (neocortex and hippocampus) was harvested, nuclei were isolated and sorted by FACS into bulk and GFP+ populations, and genomic DNA was analyzed by HTS. (FIG.2C) In vivo editing activity of PE3 delivered via v1 PE3-AAV9 by RO injection to 6- to 8- week-old C57BL/6 mice at a total dose of 1×10 ¹² vg. Three weeks after injection, bulk tissues were harvested and genomic DNA was isolated and analyzed by HTS. For (FIG.2B) and (FIG. 2C), dots represent individual mice and error bars represent mean±SEM of n=3-4 mice. [0032] FIGs.3A-3E. Evaluation of factors limiting systemic prime editing efficiency. (FIG.3A) Comparison of unmodified pegRNA or epegRNA installing a +2 G-to-C edit in bulk liver. v1 PE3-AAV9 was delivered by RO injection to 6- to 8- week-old C57BL/6 mice at a dose of 1×10 ¹² vg (5×10 ¹¹ vg per N- and C-terminal AAVs). Bulk tissue was harvested three weeks after injection and genomic DNA was isolated and analyzed by HTS. (FIG.3B) Comparison of unmodified pegRNA or epegRNA installing a +1 C-to-G edit in cortical tissue. v1 PE3-AAV9 was delivered via P0 ICV injection at a total dose of 1×10 ¹¹ vg. Neocortex was harvested three weeks after injection. Nuclei were isolated and GFP+ subpopulations were isolated by FACS. Genomic DNA was extracted and analyzed by HTS. (FIG.3C) Schematic of v2 PE3-AAV. (FIG.3D) C57BL/6 mice were injected retro-orbitally with 1.25×10 ¹² vg total of either v2 AAV9-PE3 (5×10 ¹¹ vg each N- & C- terminal AAVs encoding PEmax plus 2.5×10 ¹¹ vg epegRNA/sgRNA AAV encoding the Dnmt1+2 G-to-C edit), or architecture-matched v2 Cas9 nuclease AAV9 (5×10 ¹¹ vg each N- & C- terminal AAVs encoding Cas9 nuclease plus 2.5×10 ¹¹ vg sgRNA AAV). Bulk liver, heart, and muscle tissues were harvested three weeks after injection and genomic DNA was analyzed by HTS. (FIG.3E), Comparison of PE3 and PE3max by v2 AAV9 PE at Dnmt1 installing the +1 C-to- G edit. For (FIG.3A), (FIG.3B), (FIG.3D), and (FIG.3E), dots represent individual mice and error bars represent mean±SEM of n=3 mice. [0033] FIGs.4A-4E. Development of a dual-AAV system for efficient in vivo prime editing. The liver, heart, or brain. (FIG.4A), C57BL/6 mice were injected retro-orbitally with 1.25×10 ¹² vg total of v2em PE3-AAV9 (5×10 ¹¹ vg each N & C terminal AAVs plus 2.5×10 ¹¹ vg epegRNA/sgRNA AAV) encoding PE3max with its native full- length RT, or PE3max with one of two truncated ∆RNaseH reverse transcriptases to install a Dnmt1 +1 C-to-G edit. Three weeks after injection, liver, heart, and muscle tissues were harvested and analyzed by HTS. (FIG.4B) C57BL/6 pups were injected on P0 by ICV injection of a total of 5.7×10 ¹⁰ vg total of v2em PE3-AAV (2.3×10 ¹⁰ vg each N & C terminal AAVs plus 1.1×10 ¹⁰ vg epegRNA/sgRNA AAV) encoding PE3max with full-length RT or PE3max with a truncated ∆RNaseH RT to install the Dnmt1 +2 G-to-C edit. Three weeks post injection, mice were harvested, neocortex was dissected, and nuclei were isolated and sorted by FACS. The bulk population (all nuclei) and a GFP-positive subpopulation were lysed and genomic DNA was analyzed by HTS. (FIG.4C) Schematic of v3em PE3max AAV. (FIG.4D) C57BL/6 mice were injected retro-orbitally with either 1.25×10 ¹² vg total of v2em PE3 ∆RNaseH AAV9 (5×10 ¹¹ vg each N & C terminal AAVs plus 2.5×10 ¹¹ vg epegRNA/sgRNA AAV) or 1×10 ¹² vg total of v3em PE3-AAV9 (5×10 ¹¹ vg each N & C terminal AAVs), both installing the Dnmt1 +1 C-to-G edit. Three weeks after injection, liver, heart, and muscle tissues were harvested and analyzed by HTS. (FIG.4E) prime editing efficiency in bulk liver of v1em or v3em PE3-AAV9 following a single injection of AAV at two different doses. C57BL/6 mice were injected retro-orbitally with 1×10 ¹¹ vg or 1×10 ¹² vg total of either v1em or v3em PE3- AAV9 containing an epegRNA encoding the Dnmt1 +2 G-to-C edit. Three weeks after injection, liver tissue was harvested and analyzed by HTS. For (FIG.4A), (FIG.4B), (FIG. 4D), and (FIG.4E) dots represent individual mice and error bars represent mean±SEM of n=2-5 mice. [0034] FIGs.5A-5D. Improved prime editing in the mouse CNS. Comparison of prime editing from v1em and v3em PEmax AAVs in the CNS via direct injection in neonatal mice, or systemic injection in adult mice. (FIG.5A) Percent GFP-positive nuclei of capsid-, promoter-, and terminator- matched EGFP:KASH used for enrichment. (FIG.5B) Either v1em or v3em PE3-AAV9 encoding the +1 C-to-G edit at Dnmt1 was delivered via P0 ICV injection at a dose of 1×10 ¹¹ vg. Neocortex was harvested after three weeks and nuclei were isolated. GFP-positive subpopulations were sorted by FACS. Genomic DNA from bulk or GFP-positive nuclei was extracted and analyzed by HTS. (FIG.5C) Adult 6- to 8- weeks old were injected retro-orbitally with a total dose of 1×10 ¹² vg AAV PHP.eB with either v1em or v3em PE3-AAV encoding the +2 G-to-C edit at Dnmt1. Neocortex was harvested after three weeks and nuclei were isolated. GFP-positive subpopulations were sorted by FACS. Genomic DNA from bulk or GFP-positive nuclei was extracted and analyzed by HTS. (FIG.5D) Installation of APOE3 R136S (APOE Christchurch) in humanized APOE3 mice.1×10 ¹¹ vg v3em PE3-AAV9 was administered by ICV injection to mice on postnatal day P1 or P3. Genomic DNA or total RNA was isolated from neocortex and hippocampus (matched hemispheres). RNA was converted to cDNA and both genomic DNA and cDNA were analyzed by HTS. For (FIG.5A)-( FIG.5C) dots represent individual mice and error bars represent mean±SEM of n=2-4 mice. [0035] FIGs.6A-6F. In vivo prime editing to install Pcsk9 Q152H and its effect on plasma cholesterol levels. (FIG.6A) Timing of injections of v3em PE3-AAV9, evaluation of prime editing, and plasma analysis. (FIG.6B) Bulk liver editing efficiencies for installation of Pcsk9 Q152H. (FIG.6C, FIG.6D) Plasma total cholesterol and plasma LDL cholesterol in mice treated with prime editing AAV normalized to untreated mice at the same age. Data are shown as mean±SEM for n=8 mice (4 male and 4 female), *P < 0.05. Significance was calculated using two-way repeated measures ANOVA with Sidak multiple comparisons, and is shown for the eight weeks timepoint. (FIG.6E, FIG.6F) Off-target prime editing for 10 CIRCLE-seq-nominated off-target loci (Off1- Off10) for pegRNA and nicking sgRNA from the livers of v3em PE3-AAV treated and untreated mice. For (FIG.6B), (FIG.6E) and (FIG. 6F), dots represent individual mice and error bars represent mean±SEM of n=8 mice (4 male and 4 female). [0036] FIGs.7A, 7B. Efficiencies of various prime edits at Dnmt1 and the effect of transient MMR inhibition . (FIG.7A) Mouse N2A cells were transfected with plasmids encoding PE2, a +53 nicking sgRNA, and one pegRNA encoding the edit indicated below each bar. (FIG.7B) The impact of MMR recognition of the installed edit on editing efficiency was assessed by installing one of four edits (Dnmt1 +5 G to T, Dnmt1 +1 CCC insertion, Dnmt1 +1 C to G, or Dnmt1 +2 G to C) as PE2, PE3, PE4 (PE2 + MLH1dn), or PE5 (PE3 + MLH1dn). Data are shown as individual data points and mean±SEM for n=2-3 independent biological replicates. [0037] FIG.8. Effect of incubation time on systemic in vivo prime editing efficiency. v1 PE-AAV9 was administered at a dose of 1x1012 vg total (5x1011 vg per half) by RO injection to 6- to 8-week-old C57BL/6 mice and three weeks after, bulk tissues were harvested and isolated genomic DNA was analyzed by HTS. Dots represent individual mice and error bars represent mean±SEM of n=3 different mice. [0038] FIGs.9A, 9B. Incorporation of epegRNAs and PEmax together substantially enhance prime editing in CNS. (FIG.9A, FIG.9B) PE3-AAVs encoding a Dnmt1 +1 C to G edit were delivered as v1, v1e, or v1em architecture at a dose of 1x10 ¹¹ vg (5x10 ¹⁰ vg each N- and C- terminal AAVs) with 1x10 ¹⁰ vg promoter-matched AAV9 EGFP:KASH. At three weeks, nuclei from neocortex were isolated and sorted by FACS to either all nuclei (bulk) or GFP+ populations. Genomic DNA was extracted and analyzed by HTS. While improvement from incorporation of epegRNA alone did not reach statistical significance (P=0.17), incorporation of epegRNA and PEmax (v1em) yielded highly statistically significant improvement in prime editing over v1 (for both bulk and GFP+ populations, P<0.0001). Significance was calculated by unpaired t-test with correction for multiple comparisons. Dots represent individual data points and error bars represent mean±SEM for n=3 different mice. [0039] FIG.10. Activity of full-length and intein-split SaPE2 by plasmid transfection in HEK293T cells with a pegRNA encoding the HEK3 +6 G-to-T edit. An intein split at previously validated position 740 ¹ was assessed to maintain on-target editing efficiency compared to full-length (SaPE2). The three N-terminal residues of the C-terminal extein are indicated, with ‘SMP’ being the native residues to SaCas9, and CFN as the consensus residues of Npu intein. Dots represent individual data points and error bars represent mean±SEM for n=3 independent biological replicates. [0040] FIG.11. PE ∆RNaseH maintains prime editing activity in cultured cells across a variety of edits. HEK293T cells were transfected with plasmids encoding PE2 or PE2 ∆RNaseH and pegRNA (PE2) or pegRNA and nicking sgRNA (PE3). Genomic DNA was harvested after three days and analyzed by HTS. Dots represent individual data points and error bars represent mean±SEM for n=3 independent biological replicates. [0041] FIGs.12A, 12B. Transduction and RNA expression of PE-AAVs in liver. (FIG. 12A) In vivo comparison of viral genomes per diploid genome by promoter and dose in liver tissue. prime editors were expressed from either the v3em (Cbh promoter) or v1em (EFS promoter) architecture at the doses indicated. Isolated DNA was quantified by ddPCR using primers and a probe specific to either the N- or C-terminal half of SpCas9. Viral genome concentrations were normalized to Gapdh. (FIG.12B) In vivo comparison of PE transcript levels by promoter and dose in liver tissue. prime editors were expressed from either the v3em (Cbh promoter) or v1em (EFS promoter) architecture at the doses indicated. Mature mRNA transcripts were reverse transcribed, and PE transcript quantities from the resulting cDNA were measured by droplet digital PCR (ddPCR) using primers and a probe specific to either the N- or C-terminal half of SpCas9. Transcript concentrations were normalized to Gapdh. For (FIG.12A) and (FIG.12B), dots represent individual mice and error bars represent mean±SEM of n=4 different mice. [0042] FIG.13. Comparison of v3em PE3-AAV split at two different positions.6- to 8- week-old C57BL/6 mice were injected with 1x10 ¹² vg total of v3em PE3-AAV9 (5x10 ¹¹ vg each N & C terminal AAVs) using the intein-split indicated (residue 1024 or 844, in both cases with extein residues mutated to CFN) installing a Dnmt1 +1 C-to-G edit. Dots represent individual mice and error bars represent mean±SEM of n=3-5 mice. [0043] FIG.14. Comparison of PE2 and PE3 in vivo. v1em AAV9 with an epegRNA encoding a +1 C-to-G edit or +2 G-to-C edit at Dnmt1 was delivered via P0 ICV injection at a dose of 1x10 ¹¹ vg (5x10 ¹⁰ vg each N- and C-terminal AAVs) with 1x10 ¹⁰ vg promoter- matched AAV9 EGFP:KASH. At three weeks, nuclei from neocortex were isolated and sorted by FACS to either all nuclei (bulk) or GFP+ populations. Genomic DNA was extracted and analyzed by HTS. Dots represent individual mice and error bars represent mean±SEM of n=2-4 mice. [0044] FIGs.15A-15D. PE-mediated installation of protective APOE3 R136S Christchurch allele. (FIGs.15A-15C) Screening of pegRNAs with various PBS length (8-nt, 10-nt and 12-nt) and RTT (15-nt, 17-nt, 18-nt, 19-nt and 23-nt) along with three nicking guides (+25, +53 and +83) in HEK293T cells. Data are shown as mean±SEM for n=3 biological replicates. (FIG.15D) PE3 and PE5 (PE3 + MLH1dn) installation of protective APOE3 R136S Christchurch allele in immortalized mouse astrocytes. Data are shown as mean±SEM for n=3 biological replicates. [0045] FIGs.16A-16D. PE-mediated installation of Pcsk9 Q155H. (FIG.16A, FIG.16B) Screening of pegRNAs with various two protospacers, multiple PBS lengths (8-nt, 9-nt, 10- nt, 11-nt, 12-nt, 13-nt, 14-nt and 15-nt) and RTT lengths (13-nt, 17-nt and 20-nt) in Neuro-2a cells. (FIG.16C) Screening of nicking guides (-45, -66, +30, +42, +63 and +101) in in Neuro-2a cells. (FIG.16D) Further improvements in prime editing efficiencies from using engineered pegRNAs, making a silent PAM edit, and installing silent MMR-evading edits with +64 nicking sgRNA. Data are shown as mean±SEM for n=3 biological replicates. [0046] FIG.17. Installation of Pcsk9 Q155H in vivo. v3em PE3-AAV9 was injected into 6- to 8-week-old C57BL/6 mice and liver was harvested eight weeks post injection to assess bulk editing. Dots represent individual mice and error bars represent mean±SEM for n=4 mice. [0047] FIGs.18A-18E. prime editing and plasma analytes (normalized to untreated) data of either untreated or v3em PE3-AAV9 treated male and female C57BL/6 mice. (FIG.18A) Installation of Pcsk9 Q152H in mouse liver using v3em PE AAV9. Dots represent individual mice and error bars represent mean±SEM for n=4 mice. (FIG.18B, FIG.18C) Total plasma cholesterol in C57BL/6 male mice (FIG.18B) and female mice (FIG.18C) normalized to untreated. (FIG.18 D, FIG.18E) Plasma LDL cholesterol levels from C57BL/6 mice male mice (FIG.18D) and female mice (FIG.18E) normalized to untreated. Data are shown as mean±SEM for n=4 mice. [0048] FIGs.19A-19D. Raw (unnormalized) levels of plasma analytes of male and female mice treated with either v3em PE3-AAV9 installing Pcsk9 Q152H mutation or untreated. (FIG.19A, FIG.19B) Total plasma cholesterol in C57BL/6 mice male mice a and female mice b. (FIG.19C, FIG.19D) Plasma LDL cholesterol levels from C57BL/6 mice male mice c and female mice (FIG.19D). Data are shown as mean±SEM for n=4 mice. [0049] FIGs.20A, 20B. Assessment of LDL receptor expression. (FIG.20A) Western blot evaluating LDL receptor expression on liver extracts of untreated, v3em PE-AAV9 Pcsk9 Q155H treated, Ldlr ^–/– and Pcsk9 ^–/– mice. Ldlr ^–/– and Pcsk9 ^–/– mice samples were used as negative and positive control, respectively. Raw, uncropped membrane images are shown in FIG.23. (FIG.20B) Densitometry-based quantification of LDL receptor expression from western blots. Data are normalized to untreated and shown as individual data points and mean±SEM for n=3-4 mice. [0050] FIGs.21A-21D. Assessment of liver toxicity following systemic v3em PE-AAV8 injection. Adult mice were systemically injected v3em PE-AAV8 along with dose- and serotype- matched AAV8 encoding EGFP to control for toxicity induced by the AAV vector, dose- and serotype-matched Cas9 nickase to control for toxicity caused by Cas9 nickase and sgRNA portion of the prime editor, and a fourth cohort injected with saline alone. (FIG.21A) Histopathological assessment by hematoxylin and eosin staining of livers at eight weeks post- injection of saline or 1x10 ¹² vg total AAV8 encoding either EGFP, Cas9 nuclease, or prime editor. Scale bars, 50 μm, representative images from two separate mice shown per condition. (FIG.21B, FIG.21C) Plasma aspartate transaminase (AST) and alanine transaminase (ALT) levels. Data are shown as mean±SEM for n=4 mice. The dotted lines mark the upper limit of normal physiological range for AST and ALT in adult C57BL/6 mice. (FIG.21D) Installation of Pcsk9 Q155H in vivo for liver toxicity study. v3em PE3- AAV8 was injected into 6- to 8- week old adult C57BL/6 mice at a dose of 1x10 ¹² vg total by retro-orbital injection and liver was harvested eight weeks post injection to assess bulk editing. Dots represent individual mice and error bars represent mean±SEM for n=4 mice. [0051] FIG.22. FACS gating strategy for brain nuclei. Nuclei were isolated from fresh or previously frozen brain tissue stained with DyeCycle Ruby. Gates were drawn around nuclei based on forward and side scatter area, then gated on singlets based on DyeCycle Ruby intensity, then sorted based on GFP fluorescence into a “bulk” population containing all nuclei regardless of GFP positivity, and a GFP+ population. [0052] FIG.23. Raw western blot images. Uncropped images for LDL receptor (top) and ^-Actin (bottom) from liver extracts of v3em PE-AAV9 Pcsk9 Q155H treated, Ldlr ^–/– and Pcsk9 ^–/– mice. Ldlr ^–/– and Pcsk9 ^–/– mice samples were used as negative and positive control, respectively. [0053] FIG.24. Dependence on splicing of split-intein PE2 activity. Full-length or intein-split PE2 were transfected into HEK239T cells with epegRNA and nicking sgRNA then analyzed by HTS three days after transfection. Splicing-inactive inteins contained a Cys1→Ala mutation in NpuN. A sub-optimal amount of editor plasmid was used to avoid saturating editing efficiencies. Two sites per condition are shown (HEK327bp insertion and RNF2 +1 C to A). Dots represent values and error bars represent mean+/-SEM of n= 3 biological replicates at two genomic loci. [0054] FIG.25. In vivo comparison of higher ratio of N-terminal v3em PE-AAV to C- terminal half v3em PE-AAV. v3em PE3-AAV9 encoding the Dnmt +2 G to C edit was delivered at a total dose of 1×10 ¹² vg at the ratio indicated: either a ratio of 1:1 (5×10 ¹¹ vg each N- and C-terminal halves) or a ratio of 2.5:1 (7.1×10 ¹¹ vg N-terminal half and 2.9×10 ¹¹ vg C-terminal half) and bulk tissues were analyzed three weeks post injection by HTS. Dots represent individual mice and error bars represent mean +/- SEM of n=3-4 different mice. BRIEF DESCRIPTION OF THE SEQUENCES

Cas9 variants with modified PAM specificities [0137] In a particular embodiment, the Cas9 variant having expanded PAM capabilities is SpCas9 (H840A) VRQR (SEQ ID NO: 80), which has the following amino acid sequence (with the V, R, Q, R substitutions relative to the SpCas9 (H840A) of SEQ ID NO: 47 being show in bold underline. In addition, the methionine residue in SpCas9 (H840) was removed for SpCas9 (H840A) VRQR):

[0138] In another particular embodiment, the Cas9 variant having expanded PAM capabilities is SpCas9 (H840A) VRER, which has the following amino acid sequence (with the V, R, E, R substitutions relative to the SpCas9 (H840A) of SEQ ID NO: 47 being shown in bold underline . In addition, the methionine residue in SpCas9 (H840) was removed for SpCas9 (H840A) VRER):

) [0139] For example, a napDNAbp domain with altered PAM specificity, such as a domain with at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity with wild type Francisella novicida Cpf1 (D917, E1006, and D1255) (SEQ ID NO: 82), which has the following amino acid sequence: [0140] An additional napDNAbp domain with altered PAM specificity, such as a domain having at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity with wild type Geobacillus thermodenitrificans Cas9 (SEQ ID NO: 34), which has the following amino acid sequence: [0141] The disclosed fusion proteins may comprise a napDNAbp domain having at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity with wild type Natronobacterium gregoryi Argonaute (SEQ ID NO: 84), which has the following amino acid sequence:

Wild Type Polymerases [0143] Reverse transcriptase (M-MLV RT) wild type moloney murine leukemia virus Used in PE1 (prime editor 1 fusion protein disclosed herein)

AAV Sequences [0197] Sequence of N-term v1em PE3-AAV (5' to 3'), 4915 bp ITR-EFS promoter-N-term PEmax (start codon-SV40NLS-SpCAS9)NpuN-SV40NLS-W3- bGH polyA-sgRNA (protospacer in bold)-human U6-ITR (Underlined sequences contain restriction sites for cloning; EFS promoter is in bold, N-term PEmax (start codon-SV40NLS-SpCAS9)NpuN is italicized; SV40NLS is bolded and underlined, W3-bGH polyA is italicized and underlined, sgRNA is bolded and italicized, and human U6 is underlined with dotted line).

[0198] Sequence of C-term v1em PE3-AAV (5' to 3'), 4,880 bp ITR-EFS promoter- SV40NLS- NpuC-C-term PEmax (SpCas9-RT-SV40NLS)-W3-bGH polyA-epegRNA (protospacer in bold)-human U6-ITR (Underlined sequences contain restriction sites for cloning; EFS promoter is in bold, C-term PEmax (SpCas9-RT-SV40NLS) is italicized; NpuC is squiggle underlined; SV40NLS is bolded and underlined, W3-bGH polyA is italicized and underlined, epegRNA is bolded and italicized, and human U6 is underlined with dotted line). [0199] Sequence of N-term v2em PE3-AAV (5' to 3'), 5083 bp ITR-Cbh promoter-N-term PEmax (start codon-SV40NLS-SpCas9)-NpuN-SV40NLS-W3- bGH polyA-ITR (Underlined sequences contain restriction sites for cloning; Cbh promoter is in bold, N-term PEmax (start codon-SV40NLS-SpCas9 is italicized; NpuN is squiggle underlined; SV40NLS is bolded and underlined, W3-bGH polyA is italicized and underlined). ) [0200] Sequence of C-term v2em PE3-AAV (5' to 3'), 4978 bp ITR-Cbh promoter-SV40NLS-NpuC-C-term PEmax (SpCas9-RT-SV40NLS)-W3- bGHpolyA- ITR (Underlined sequences contain restriction sites for cloning; Cbh promoter is in bold, C-term PEmax (SpCas9-RT-SV40NLS) is italicized; NpuC is squiggle underlined; SV40NLS is bolded and underlined, W3-bGH polyA is italicized and underlined)

) [0201] Sequence of v2em EGFP:KASH pegRNA/sgRNA (5' to 3'), 3438 bp ITR-Cbh promoter-EGFP:KASH -sgRNA -mouse U6-epegRNA -human U6-ITR (Underlined sequences contain restriction sites for cloning; Cbh promoter is in bold, EGFP:KASH is italicized; sgRNA is bolded and underlined, epegRNA is italicized and underlined, mouse U6 is squiggle underlined, and human U6 is italicized and bolded).

[0202] Sequence of N-term v3em PE3-AAV (5' to 3'), 4,740 bp ITR-Cbh promoter-N-term PEmax (start codon-SV40NLS-SpCas9)-NpuN-SV40NLS-SV40 late polyA-ITR (Sequences in grey contain restriction sites for cloning) (Underlined sequences contain restriction sites for cloning; Cbh promoter is in bold, N-term PEmax (start codon-SV40NLS-SpCas9) is italicized; NpuN is squiggle underlined; SV40NLS is bolded and underlined, SV40 late polyA is italicized and underlined). [0203] Sequence of C-term v3em PE3-AAV (5' to 3'), 4,968 bp ITR-Cbh promoter-SV40NLS-NpuC-C-term PEmax (SpCas9-RT-SV40NLS)-SV40 late polyA-sgRNA (protospacer in bold)-mouse U6-epegRNA (protospacer in bold)-human U6- ITR (Underlined sequences contain restriction sites for cloning; Cbh promoter is in bold (SEQ ID NO: 436), C-term PEmax (SpCas9-RT-SV40NLS) is italicized (SEQ ID NO: 437); NpuC is squiggle underlined (SEQ ID NO: 438); SV40NLS is bolded and underlined (SEQ ID NO: 439), SV40 late polyA is italicized and underlined (SEQ ID NO: 440), epegRNA is bolded and squiggle underlined (SEQ ID NO: 441), sgRNA is dotted underlined (SEQ ID NO: 442), mouse U6 is double underlined (SEQ ID NO: 443), and human U6 is double underline and italicized(SEQ ID NO: 444)). LINKERS [0225] In some other embodiments, the linker comprises the amino acid sequence (GGGGS)n (SEQ ID NO: 141), (G)n (SEQ ID NO: 142), (EAAAK)n (SEQ ID NO: 143), (GGS)n (SEQ ID NO: 144), (SGGS)n (SEQ ID NO: 145), (XP)n (SEQ ID NO: 146), or any combination thereof, wherein n is independently an integer between 1 and 30, and wherein X is any amino acid. In some embodiments, the linker comprises the amino acid sequence (GGS)n (SEQ ID NO: 144), wherein n is 1, 3, or 7. In some embodiments, the linker comprises the amino acid sequence SGSETPGTSESATPES (SEQ ID NO: 147). In some embodiments, the linker comprises the amino acid sequence SGGSSGGSSGSETPGTSESATPESSGGSSGGS (SEQ ID NO: 148). In some embodiments, the linker comprises the amino acid sequence SGGSGGSGGS (SEQ ID NO: 149). In some embodiments, the linker comprises the amino acid sequence SGGS (SEQ ID NO: 150). In other embodiments, the linker comprises the amino acid sequence SGGSSGGSSGSETPGTSESATPESAGSYPYDVPDYAGSAAPAAKKKKLDGSGSGGSS GGS (SEQ ID NO: 151, 60AA). [0226] In particular, the following linkers can be used in various embodiments to join prime editor domains with one another: Nuclear Localization Sequences [0233] PKKKRKV (SEQ ID NO: 156) [0234] MDSLLMNRRKFLYQFKNVRWAKGRRETYLC (SEQ ID NO: 157) [0235] Bipartite NLS typically contains two clusters of basic amino acids, separated by a spacer of about 10 amino acids. One non-limiting example of a bipartite NLS is the NLS of nucleoplasmin, KRPAATKKAGQAKKKK (SEQ ID NO: 158) (spacer underlined). [0236] SV40 bipartite NLS [0237] KRTADGSEFESPKKKRKV (SEQ ID NO: 159), e.g., as described in Hodel et al., J Biol Chem.2001 Jan 12;276(2):1317-25, incorporated herein by reference) [0238] Kanadaptin bipartite NLS [0239] KKTELQTTNAENKTKKL (SEQ ID NO: 160), e.g., as described in Hubner et al., Biochem J.2002 Jan 15;361(Pt 2):287-96, incorporated herein by reference); [0240] influenza A nucleoprotein bipartite NLS [0241] KRGINDRNFWRGENGRKTR (SEQ ID NO: 161), e.g., as described in Ketha et al., BMC Cell Biology.2008;9:22, incorporated herein by reference) [0242] ZO-2 bipartite NLS [0243] RKSGKIAAIVVKRPRK (SEQ ID NO: 162), e.g., as described in Quiros et al., Nusrat A, ed. Molecular Biology of the Cell.2013;24(16):2528-2543, incorporated herein by reference).

[0296] In some embodiments, N-terminal amino acids at positions 1-3 (e.g., SEQ) of SEQ ID NO: 456 can be mutated to SFQ, SFN, SEN, or CFN. RNA-protein interaction domain Sequences [0297] The nucleotide sequence of the MS2 hairpin (or equivalently referred to as the “MS2 aptamer”) is: GCCAACATGAGGATCACCCATGTCTGCAGGGCC (SEQ ID NO: 192) Additional PE elements [0300] Exemplary glycosylases are provided below. The catalytically inactivated variants of any of these glycosylase domains are iBERs that may be fused to the napDNAbp or polymerase domain of the prime editors provided in this disclosure. pegRNAs [0305] For the S. pyogenes Cas9 target site of the form: MMMMMMMMNNNNNNNNNNNNXGG (SEQ ID NO: 198), where NNNNNNNNNNNNXGG (SEQ ID NO: 199) (N is A, G, T, or C; and X can be anything) [0306] For the S. pyogenes Cas9 target site of the form MMMMMMMMMNNNNNNNNNNNXGG (SEQ ID NO: 200), where NNNNNNNNNNNXGG (SEQ ID NO: 201) (N is A, G, T, or C; and X can be anything). [0307] For the S. thermophilus CRISPR1Cas9, a unique target sequence in a genome may include a Cas9 target site of the form MMMMMMMMNNNNNNNNNNNNXXAGAAW (SEQ ID NO: 202), where NNNNNNNNNNNNXXAGAAW (SEQ ID NO: 203) (N is A, G, T, or C; X can be anything; and W is A or T). [0308] A unique target sequence in a genome may include an S. thermophilus CRISPR 1 Cas9 target site of the form MMMMMMMMMNNNNNNNNNNNXXAGAAW (SEQ ID NO: 204), where NNNNNNNNNNNXXAGAAW (SEQ ID NO: 205) (N is A, G, T, or C; X can be anything; and W is A or T). [0309] For the S. pyogenes Cas9, a unique target sequence in a genome may include a Cas9 target site of the form MMMMMMMMNNNNNNNNNNNNXGGXG (SEQ ID NO: 206) where NNNNNNNNNNNNXGGXG (SEQ ID NO: 207) (N is A, G, T, or C; and X can be anything). [0310] A unique target sequence in a genome may include an S. pyogenes Cas9 target site of the form MMMMMMMMMNNNNNNNNNNNXGGXG (SEQ ID NO: 208) where NNNNNNNNNNNXGGXG (SEQ ID NO: 209) (N is A, G, T, or C; and X can be anything). [0311] In each of the above sequences “M” may be A, G, T, or C, and need not be considered in identifying a sequence as unique. listed 5′ to 3′ “N” represents a base of a guide sequence, the first block of lower case letters represent the tracr mate sequence, and the second block of lower case letters represent the tracr sequence, and the final poly-T sequence represents the transcription terminator. [0312] NNNNNNNNgtttttgtactctcaagatttaGAAAtaaatcttgcagaagctacaaagata aggcttcatgccg aaatcaacaccctgtcattttatggcagggtgttttcgttatttaaTTTTTT (SEQ ID NO: 210) [0313] listed 5′ to 3′ [0314] “N” represents a base of a guide sequence, the first block of lower case letters represent the tracr mate sequence, and the second block of lower case letters represent the tracr sequence, and the final poly-T sequence represents the transcription terminator. [0315] NNNNNNNNNNNNNNNNNNgtttttgtactctcaGAAAtgcagaagctacaaagataaggc ttcat gccgaaatcaacaccctgtcattttatggcagggtgttttcgttatttaaTTTTTT (SEQ ID NO: 211) [0316] listed 5′ to 3′ [0317] “N” represents a base of a guide sequence, the first block of lower case letters represent the tracr mate sequence, and the second block of lower case letters represent the tracr sequence, and the final poly-T sequence represents the transcription terminator. [0318] NNNNNNNNNNNNNNNNNNNNgtttttgtactctcaGAAAtgcagaagctacaaagataag gct tcatgccgaaatcaacaccctgtcattttatggcagggtgtTTTTT (SEQ ID NO: 212) [0319] listed 5′ to 3′ [0320] “N” represents a base of a guide sequence, the first block of lower case letters represent the tracr mate sequence, and the second block of lower case letters represent the tracr sequence, and the final poly-T sequence represents the transcription terminator. [0321] NNNNNNNNNNNNNNNNNNNNgttttagagctaGAAAtagcaagttaaaataaggctagtc cg ttatcaacttgaaaaagtggcaccgagtcggtgcTTTTTT (SEQ ID NO: 213) [0322] listed 5′ to 3′ [0323] “N” represents a base of a guide sequence, the first block of lower case letters represent the tracr mate sequence, and the second block of lower case letters represent the tracr sequence, and the final poly-T sequence represents the transcription terminator. [0324] NNNNNNNNNNNNNNNNNNNNgttttagagctaGAAATAGcaagttaaaataaggctagtc cgttatcaacttgaaaaagtgTTTTTTT (SEQ ID NO: 214) [0325] listed 5′ to 3′ [0326] “N” represents a base of a guide sequence, the first block of lower case letters represent the tracr mate sequence, and the second block of lower case letters represent the tracr sequence, and the final poly-T sequence represents the transcription terminator. [0327] NNNNNNNNNNNNNNNNNNNNgttttagagctagAAATAGcaagttaaaataaggctagtc c gttatcaTTTTTTTT (SEQ ID NO: 215) [0328] 5ʹ-[guide sequence]- guuuuagagcuagaaauagcaaguuaaaauaaaggcuaguccguuaucaacuugaaaaag uggcaccgagucggugcuu uuu-3ʹ (SEQ ID NO: 216) [0329] PEgRNA expression platform consisting of pCMV, Csy4 hairpin, the PEgRNA, and MALAT1 ENE DEFINITIONS [0339] As used herein and in the claims, the singular forms “a,” “an,” and “the” include the singular and the plural reference unless the context clearly indicates otherwise. Thus, for example, a reference to “an agent” includes a single agent and a plurality of such agents. A subject in need thereof [0340] “A subject in need thereof” refers to an individual who has a disease, a sign and/or symptom of a disease, or a predisposition toward a disease, with the purpose to cure, heal, alleviate, relieve, alter, remedy, ameliorate, improve, or affect the disease, the symptom of the disease, or the predisposition toward the disease. In some embodiments, the subject is a mammal. In some embodiments, the subject is a non-human primate. In some embodiments, the subject is human. In some embodiments, the mammal is a rodent. In some embodiments, the rodent is a mouse. In some embodiments, the rodent is a rat. In some embodiments, the mammal is a companion animal. A “companion animal” refers to pets and other domestic animals. Non-limiting examples of companion animals include dogs and cats; livestock, such as horses, cattle, pigs, sheep, goats, and chickens; and other animals, such as mice, rats, guinea pigs, and hamsters. Adeno-associated virus (AAV) [0341] An “adeno-associated virus” or “AAV” is a virus which infects humans and some other primate species. The wild-type AAV genome is a single-stranded deoxyribonucleic acid (ssDNA), either positive- or negative-sensed. The genome comprises two inverted terminal repeats (ITRs), one at each end of the DNA strand, and two open reading frames (ORFs): rep and cap between the ITRs. The rep ORF comprises four overlapping genes encoding Rep proteins required for the AAV life cycle. The cap ORF comprises overlapping genes encoding capsid proteins: VP1, VP2 and VP3, which interact together to form the viral capsid. VP1, VP2 and VP3 are translated from one mRNA transcript, which can be spliced in two different manners: either a longer or shorter intron can be excised resulting in the formation of two isoforms of mRNAs: a ~2.3 kb- and a ~2.6 kb-long mRNA isoform. The capsid forms a supramolecular assembly of approximately 60 individual capsid protein subunits into a non-enveloped, T-1 icosahedral lattice capable of protecting the AAV genome. The mature capsid is composed of VP1, VP2, and VP3 (molecular masses of approximately 87, 73, and 62 kDa respectively) in a ratio of about 1:1:10. [0342] rAAV particles may comprise a nucleic acid vector (e.g., a recombinant genome), which may comprise at a minimum: (a) one or more heterologous nucleic acid regions comprising a sequence encoding a protein or polypeptide of interest (e.g., a split prime editor) or an RNA of interest (e.g., a gRNA), or one or more nucleic acid regions comprising a sequence encoding a Rep protein; and (b) one or more regions comprising inverted terminal repeat (ITR) sequences (e.g., wild-type ITR sequences or engineered ITR sequences) flanking the one or more nucleic acid regions (e.g., heterologous nucleic acid regions). In some embodiments, the nucleic acid vector is between 4 kb and 5 kb in size (e.g., 4.2 to 4.7 kb in size). In some embodiments, the nucleic acid vector further comprises a region encoding a Rep protein. In some embodiments, the nucleic acid vector is circular. In some embodiments, the nucleic acid vector is single-stranded. In some embodiments, the nucleic acid vector is double-stranded. In some embodiments, a double-stranded nucleic acid vector may be, for example, a self-complimentary vector that contains a region of the nucleic acid vector that is complementary to another region of the nucleic acid vector, initiating the formation of the double-strandedness of the nucleic acid vector. Cas9 [0343] As used herein, the term “Cas9,” “Cas9 protein,” or “Cas9 nuclease” refers to an RNA-guided nuclease comprising a Cas9 protein (e.g., Cas9 nucleases from a variety of bacterial species), a fragment, a variant (e.g., a catalytically inactive Cas9 or a Cas9 nickase), or a fusion protein (e.g., a Cas9 fused to another protein domain) thereof. A Cas9 nuclease is also referred to sometimes as a casn1 nuclease or a CRISPR (clustered regularly interspaced short palindromic repeat)-associated nuclease. CRISPR is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements, and conjugative plasmids). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and a Cas9 protein. The tracrRNA serves as a guide for ribonuclease 3- aided processing of pre-crRNA. Subsequently, Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer. In nature, DNA- binding and cleavage typically requires protein and both RNAs. However, single guide RNAs (“sgRNA”, or simply “gNRA”) can be engineered so as to incorporate aspects of both the crRNA and tracrRNA into a single RNA species. Non-limiting examples of Cas9 proteins and their respective amino acid sequence are provided in Example 1. [0344] A nuclease-inactive Cas9 protein may interchangeably be referred to as a “dCas9” protein (for nuclease-“dead” Cas9). Methods for generating a Cas9 protein (or a fragment thereof) having an inactive DNA cleavage domain are known (See, e.g., Jinek et al., Science. 337:816-821(2012); Qi et al., (2013) Cell.28;152(5):1173-83, incorporated herein by reference). For example, the DNA cleavage domain of Cas9 is known to include two subdomains, the HNH nuclease subdomain and the RuvC1 subdomain. The HNH subdomain cleaves the strand complementary to the gRNA, whereas the RuvC1 subdomain cleaves the non-complementary strand. Mutations within these subdomains can silence the nuclease activity of Cas9. For example, the mutations D10A and H840A completely inactivate the nuclease activity of S. pyogenes Cas9 (Jinek et al., Science.337:816-821(2012); Qi et al., Cell.28;152(5):1173-83 (2013). Additional suitable nuclease-inactive dCas9 domains will be apparent to those of skill in the art based on this disclosure and knowledge in the field, and are within the scope of this disclosure. Such additional exemplary suitable nuclease-inactive Cas9 domains include, but are not limited to, D10A/H840A, D10A/D839A/H840A, and D10A/D839A/H840A/N863A mutant domains (See, e.g., Prashant et al., Nature Biotechnology.2013; 31(9):833-838, incorporated herein by reference). [0345] A Cas9 nickase is able to cleave one strand of the double strand DNA. A Cas9 nickase may be generated by introducing an inactivating mutation into either the HNH domain or the RuvC1 domain. For example, an inactivating mutation (D10A) may be introduced in the RuvC1 domain of the S. pyogenes Cas9, while the HNH domain remains active, i.e., the residue at position 840 remains a histidine. Such Cas9 variants are able to generate a single-strand DNA break (nick) at a specific location based on the gRNA-defined target sequence. One skilled in the art is able to identify the catalytic residues in the RuvC1 and HNH domains of any known Cas9 proteins and introduce inactivating mutations to generate a corresponding dCas9 or nCas9. CRISPR [0346] CRISPR is a family of DNA sequences (i.e., CRISPR clusters) in bacteria and archaea that represent snippets of prior infections by a virus that have invaded the prokaryote. The snippets of DNA are used by the prokaryotic cell to detect and destroy DNA from subsequent attacks by similar viruses and effectively compose, along with an array of CRISPR-associated proteins (including Cas9 and homologs thereof) and CRISPR-associated RNA, a prokaryotic immune defense system. In nature, CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). In certain types of CRISPR systems (e.g., type II CRISPR systems), correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and a Cas9 protein. The tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA. Subsequently, Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the RNA. Specifically, the target strand not complementary to crRNA is first cut endonucleolytically, then trimmed 3´-5′ exonucleolytically. In nature, DNA-binding and cleavage typically requires protein and both RNAs. However, single guide RNAs (“sgRNA”, or simply “gNRA”) can be engineered so as to incorporate aspects of both the crRNA and tracrRNA into a single RNA species – the guide RNA. See, e.g., Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J.A., Charpentier E. Science 337:816-821(2012), the entire contents of which is hereby incorporated by reference. Cas9 recognizes a short motif in the CRISPR repeat sequences (the PAM or protospacer adjacent motif) to help distinguish self versus non-self. CRISPR biology, as well as Cas9 nuclease sequences and structures are well known to those of skill in the art (see, e.g., “Complete genome sequence of an M1 strain of Streptococcus pyogenes.” Ferretti et al., J.J., McShan W.M., Ajdic D.J., Savic D.J., Savic G., Lyon K., primeaux C., Sezate S., Suvorov A.N., Kenton S., Lai H.S., Lin S.P., Qian Y., Jia H.G., Najar F.Z., Ren Q., Zhu H., Song L., White J., Yuan X., Clifton S.W., Roe B.A., McLaughlin R.E., Proc. Natl. Acad. Sci. U.S.A.98:4658-4663(2001); “CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III.” Deltcheva E., Chylinski K., Sharma C.M., Gonzales K., Chao Y., Pirzada Z.A., Eckert M.R., Vogel J., Charpentier E., Nature 471:602-607(2011); and “A programmable dual-RNA- guided DNA endonuclease in adaptive bacterial immunity.” Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J.A., Charpentier E. Science 337:816-821(2012), the entire contents of each of which are incorporated herein by reference). Cas9 orthologs have been described in various species, including, but not limited to, S. pyogenes and S. thermophilus. Additional suitable Cas9 nucleases and sequences will be apparent to those of skill in the art based on this disclosure, and such Cas9 nucleases and sequences include Cas9 sequences from the organisms and loci disclosed in Chylinski, Rhun, and Charpentier, “The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems” (2013) RNA Biology 10:5, 726-737; the entire contents of which are incorporated herein by reference. [0347] In certain types of CRISPR systems (e.g., type II CRISPR systems), correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc), and a Cas9 protein. The tracrRNA serves as a guide for ribonuclease 3- aided processing of pre-crRNA. Subsequently, Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular nucleic acid target complementary to the RNA. Specifically, the target strand not complementary to crRNA is first cut endonucleolytically, then trimmed 3′-5′ exonucleolytically. In nature, DNA-binding and cleavage typically requires protein and both RNAs. However, single guide RNAs (“sgRNA”, or simply “gRNA”) can be engineered so as to incorporate embodiments of both the crRNA and tracrRNA into a single RNA species— the guide RNA. [0348] In general, a “CRISPR system” refers collectively to transcripts and other elements involved in the expression of or directing the activity of CRISPR-associated (“Cas”) genes, including sequences encoding a Cas gene, a tracr (trans-activating CRISPR) sequence (e.g. tracrRNA or an active partial tracrRNA), a tracr mate sequence (encompassing a “direct repeat” and a tracrRNA-processed partial direct repeat in the context of an endogenous CRISPR system), a guide sequence (also referred to as a “spacer” in the context of an endogenous CRISPR system), or other sequences and transcripts from a CRISPR locus. The tracrRNA of the system is complementary (fully or partially) to the tracr mate sequence present on the guide RNA. Downstream [0349] As used herein, the terms “upstream” and “downstream” are terms of relativity that define the linear position of at least two elements located in a nucleic acid molecule (whether single or double-stranded) that is orientated in a 5ʹ-to-3ʹ direction. In particular, a first element is upstream of a second element in a nucleic acid molecule where the first element is positioned somewhere that is 5’ to the second element. For example, a SNP is upstream of a Cas9-induced nick site if the SNP is on the 5’ side of the nick site. Conversely, a first element is downstream of a second element in a nucleic acid molecule where the first element is positioned somewhere that is 3’ to the second element. For example, a SNP is downstream of a Cas9-induced nick site if the SNP is on the 3’ side of the nick site. The nucleic acid molecule can be a DNA (double or single stranded). RNA (double or single stranded), or a hybrid of DNA and RNA. The analysis is the same for single strand nucleic acid molecule and a double strand molecule since the terms upstream and downstream are in reference to only a single strand of a nucleic acid molecule, except that one needs to select which strand of the double stranded molecule is being considered. Often, the strand of a double stranded DNA which can be used to determine the positional relativity of at least two elements is the “sense” or “coding” strand. In genetics, a “sense” strand is the segment within double-stranded DNA that runs from 5' to 3', and which is complementary to the antisense strand of DNA, or template strand, which runs from 3' to 5'. Thus, as an example, a SNP nucleobase is “downstream” of a promoter sequence in a genomic DNA (which is double-stranded) if the SNP nucleobase is on the 3' side of the promoter on the sense or coding strand. Error-prone reverse transcriptase [0350] As used herein, the term “error-prone” reverse transcriptase (or more broadly, any polymerase) refers to a reverse transcriptase (or more broadly, any polymerase) that occurs naturally or which has been derived from another reverse transcriptase (e.g., a wild type M- MLV reverse transcriptase) which has an error rate that is less than the error rate of wild type M-MLV reverse transcriptase. The error rate of wild type M-MLV reverse transcriptase is reported to be in the range of one error in 15,000 (higher) to 27,000 (lower). An error rate of 1 in 15,000 corresponds with an error rate of 6.7 x 10 ^-5 . An error rate of 1 in 27,000 corresponds with an error rate of 3.7 x 10 ^-5 . See Boutabout et al. (2001) “DNA synthesis fidelity by the reverse transcriptase of the yeast retrotransposon Ty1,” Nucleic Acids Res 29(11):2217–2222, which is incorporated herein by reference. Thus, for purposes of this application, the term “error prone” refers to those RT that have an error rate that is greater than one error in 15,000 nucleobase incorporation (6.7 x 10 ^-5 or higher), e.g., 1 error in 14,000 nucleobases (7.14 x 10 ^-5 or higher), 1 error in 13,000 nucleobases or fewer (7.7 x 10 ^-5 or higher), 1 error in 12,000 nucleobases or fewer (7.7 x 10 ^-5 or higher), 1 error in 11,000 nucleobases or fewer (9.1 x 10 ^-5 or higher), 1 error in 10,000 nucleobases or fewer (1 x 10 ^-4 or 0.0001 or higher), 1 error in 9,000 nucleobases or fewer (0.00011 or higher), 1 error in 8,000 nucleobases or fewer (0.00013 or higher) 1 error in 7,000 nucleobases or fewer (0.00014 or higher), 1 error in 6,000 nucleobases or fewer (0.00016 or higher), 1 error in 5,000 nucleobases or fewer (0.0002 or higher), 1 error in 4,000 nucleobases or fewer (0.00025 or higher), 1 error in 3,000 nucleobases or fewer (0.00033 or higher), 1 error in 2,000 nucleobase or fewer (0.00050 or higher), or 1 error in 1,000 nucleobases or fewer (0.001 or higher), or 1 error in 500 nucleobases or fewer (0.002 or higher), or 1 error in 250 nucleobases or fewer (0.004 or higher). Extein [0351] The term “extein,” as used herein, refers to an polypeptide sequence that is flanked by an intein and is ligated to another extein during the process of protein splicing to form a mature, spliced protein. Typically, an intein is flanked by two extein sequences that are ligated together when the intein catalyzes its own excision. Exteins, accordingly, are the protein analog to exons found in mRNA. For example, a polypeptide comprising an intein may be of the structure extein(N) – intein – extein(C). After excision of the intein and splicing of the two exteins, the resulting structures are extein(N) – extein(C) and a free intein. In various configurations, the exteins may be separate proteins (e.g., half of a Cas9 or PE fusion protein), each fused to a split-intein, wherein the excision of the split inteins causes the splicing together of the extein sequences. Extension arm [0352] The term “extension arm” refers to a nucleotide sequence component of a PEgRNA which provides several functions, including a primer binding site and an edit template for reverse transcriptase. In some embodiments, the extension arm is located at the 3ʹ end of the guide RNA. In other embodiments, the extension arm is located at the 5ʹ end of the guide RNA. In some embodiments, the extension arm also includes a homology arm. In various embodiments, the extension arm comprises the following components in a 5ʹ to 3ʹ direction: the homology arm, the edit template, and the primer binding site. Since polymerization activity of the reverse transcriptase is in the 5ʹ to 3ʹ direction, the preferred arrangement of the homology arm, edit template, and primer binding site is in the 5ʹ to 3ʹ direction such that the reverse transcriptase, once primed by an annealed primer sequence, polymerases a single strand of DNA using the edit template as a complementary template strand. Further details, such as the length of the extension arm, are described elsewhere herein. [0353] The extension arm may also be described as comprising generally two regions: a primer binding site (PBS) and a DNA synthesis template, for instance. The primer binding site binds to the primer sequence that is formed from the endogenous DNA strand of the target site when it becomes nicked by the prime editor complex, thereby exposing a 3ʹ end on the endogenous nicked strand. As explained herein, the binding of the primer sequence to the primer binding site on the extension arm of the PEgRNA creates a duplex region with an exposed 3ʹ end (i.e., the 3ʹ of the primer sequence), which then provides a substrate for a polymerase to begin polymerizing a single strand of DNA from the exposed 3ʹ end along the length of the DNA synthesis template. The sequence of the single strand DNA product is the complement of the DNA synthesis template. Polymerization continues towards the 5ʹ of the DNA synthesis template (or extension arm) until polymerization terminates. Thus, the DNA synthesis template represents the portion of the extension arm that is encoded into a single strand DNA product (i.e., the 3ʹ single strand DNA flap containing the desired genetic edit information) by the polymerase of the prime editor complex and which ultimately replaces the corresponding endogenous DNA strand of the target site that sits immediate downstream of the PE-induced nick site. Without being bound by theory, polymerization of the DNA synthesis template continues towards the 5ʹ end of the extension arm until a termination event. Polymerization may terminate in a variety of ways, including, but not limited to (a) reaching a 5ʹ terminus of the PEgRNA (e.g., in the case of the 5ʹ extension arm wherein the DNA polymerase simply runs out of template), (b) reaching an impassable RNA secondary structure (e.g., hairpin or stem/loop), or (c) reaching a replication termination signal, e.g., a specific nucleotide sequence that blocks or inhibits the polymerase, or a nucleic acid topological signal, such as, supercoiled DNA or RNA. Fusion Protein [0354] Two proteins or protein domains are considered to be “fused” when a peptide bond is formed linking the two proteins or two protein domains. In some embodiments, a linker (e.g., a peptide linker) is present between the two proteins or two protein domains. The term “linker,” as used herein, refers to a chemical group or a molecule linking two molecules or moieties, e.g., two domains of a fusion protein, such as, for example, a nuclease-inactive Cas9 domain and a nucleic acid editing domain (e.g., a recombinase domain). Typically, the linker is positioned between, or flanked by, two groups, molecules, or other moieties and connected to each one via a covalent bond, thus connecting the two. In some embodiments, the linker is an amino acid or a plurality of amino acids (e.g., a peptide or protein). In some embodiments, the linker is an organic molecule, group, polymer, or chemical moiety. In some embodiments, the linker is 5-100 amino acids in length, for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 30-35, 35-40, 40-45, 45-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100-150, or 150-200 amino acids in length. Longer or shorter linkers are also contemplated. Gene of interest (GOI) [0355] The term “gene of interest” or “GOI” refers to a gene that encodes a biomolecule of interest (e.g., a protein or an RNA molecule). A protein of interest can include any intracellular protein, membrane protein, or extracellular protein, e.g., a nuclear protein, transcription factor, nuclear membrane transporter, intracellular organelle associated protein, a membrane receptor, a catalytic protein, and enzyme, a therapeutic protein, a membrane protein, a membrane transport protein, a signal transduction protein, or an immunological protein (e.g., an IgG or other antibody protein), etc. The gene of interest may also encode an RNA molecule, including, but not limited to, messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), small nuclear RNA (snRNA), antisense RNA, guide RNA, microRNA (miRNA), small interfering RNA (siRNA), and cell-free RNA (cfRNA). Genetic Elements [0356] Nucleic acids of the present disclosure may include one or more genetic elements. A “genetic element” refers to a particular nucleotide sequence that has a role in nucleic acid expression (e.g., promoter, enhancer, terminator) or encodes a discrete product of an engineered nucleic acid (e.g., a nucleotide sequence encoding a guide RNA, a protein and/or an RNA interference molecule). [0357] A “promoter” refers to a control region of a nucleic acid sequence at which initiation and rate of transcription of the remainder of a nucleic acid sequence are controlled. A promoter may also contain sub-regions at which regulatory proteins and molecules may bind, such as RNA polymerase and other transcription factors. Promoters may be constitutive, inducible, activatable, repressible, tissue-specific, or any combination thereof. A promoter drives expression or drives transcription of the nucleic acid sequence that it regulates. Herein, a promoter is considered to be “operably linked” when it is in a correct functional location and orientation in relation to a nucleic acid sequence it regulates to control (“drive”) transcriptional initiation and/or expression of that sequence. [0358] A promoter may be one naturally associated with a gene or sequence, as may be obtained by isolating the 5' non-coding sequences located upstream of the coding segment of a given gene or sequence. Such a promoter is referred to as an “endogenous promoter.” In some embodiments, a coding nucleic acid sequence may be positioned under the control of a recombinant or heterologous promoter, which refers to a promoter that is not normally associated with the encoded sequence in its natural environment. Such promoters may include promoters of other genes; promoters isolated from any other cell; and synthetic promoters or enhancers that are not “naturally occurring” such as, for example, those that contain different elements of different transcriptional regulatory regions and/or mutations that alter expression through methods of genetic engineering that are known in the art. In addition to producing nucleic acid sequences of promoters and enhancers synthetically, sequences may be produced using recombinant cloning and/or nucleic acid amplification technology, including polymerase chain reaction (PCR). [0359] In some embodiments, promoters used in accordance with the present disclosure are “inducible promoters,” which are promoters that are characterized by regulating (e.g., initiating or activating) transcriptional activity when in the presence of, influenced by or contacted by an inducer signal. An inducer signal may be endogenous or a normally exogenous condition (e.g., light), compound (e.g., chemical or non-chemical compound) or protein that contacts an inducible promoter in such a way as to be active in regulating transcriptional activity from the inducible promoter. Thus, a “signal that regulates transcription” of a nucleic acid refers to an inducer signal that acts on an inducible promoter. A signal that regulates transcription may activate or inactivate transcription, depending on the regulatory system used. Activation of transcription may involve directly acting on a promoter to drive transcription or indirectly acting on a promoter by inactivation a repressor that is preventing the promoter from driving transcription. Conversely, deactivation of transcription may involve directly acting on a promoter to prevent transcription or indirectly acting on a promoter by activating a repressor that then acts on the promoter. [0360] A “transcriptional terminator” is a nucleic acid sequence that causes transcription to stop. A transcriptional terminator may be unidirectional or bidirectional. It is comprised of a DNA sequence involved in specific termination of an RNA transcript by an RNA polymerase. A transcriptional terminator sequence prevents transcriptional activation of downstream nucleic acid sequences by upstream promoters. A transcriptional terminator may be necessary in vivo to achieve desirable expression levels or to avoid transcription of certain sequences. A transcriptional terminator is considered to be “operably linked to” a nucleotide sequence when it is able to terminate the transcription of the sequence it is linked to. [0361] The most commonly used type of terminator is a forward terminator. When placed downstream of a nucleic acid sequence that is usually transcribed, a forward transcriptional terminator will cause transcription to abort. In some embodiments, bidirectional transcriptional terminators are provided, which usually cause transcription to terminate on both the forward and reverse strand. In some embodiments, reverse transcriptional terminators are provided, which usually terminate transcription on the reverse strand only. [0362] In prokaryotic systems, terminators usually fall into two categories (1) rho- independent terminators and (2) rho-dependent terminators. Rho-independent terminators are generally composed of palindromic sequence that forms a stem loop rich in G-C base pairs followed by several T bases. Without wishing to be bound by theory, the conventional model of transcriptional termination is that the stem loop causes RNA polymerase to pause, and transcription of the poly-A tail causes the RNA:DNA duplex to unwind and dissociate from RNA polymerase. [0363] In eukaryotic systems, the terminator region may comprise specific DNA sequences that permit site-specific cleavage of the new transcript so as to expose a polyadenylation site. This signals a specialized endogenous polymerase to add a stretch of about 200 A residues (polyA) to the 3' end of the transcript. RNA molecules modified with this polyA tail appear to more stable and are translated more efficiently. Thus, in some embodiments involving eukaryotes, a terminator may comprise a signal for the cleavage of the RNA. In some embodiments, the terminator signal promotes polyadenylation of the message. The terminator and/or polyadenylation site elements may serve to enhance output nucleic acid levels and/or to minimize read through between nucleic acids. [0364] Terminators for use in accordance with the present disclosure include any terminator of transcription described herein or known to one of ordinary skill in the art. Examples of terminators include, without limitation, the termination sequences of genes such as, for example, the bovine growth hormone terminator, and viral termination sequences such as, for example, the SV40 terminator, spy, yejM, secG-leuU, thrLABC, rrnB T1, hisLGDCBHAFI, metZWV, rrnC, xapR, aspA and arcA terminator. In some embodiments, the termination signal may be a sequence that cannot be transcribed or translated, such as those resulting from a sequence truncation. [0365] A “Woodchuck Hepatitis Virus (WHP) Posttranscriptional Regulatory Element (WPRE)” is a DNA sequence that, when transcribed creates a tertiary structure enhancing expression. Commonly used in molecular biology to increase expression of genes delivered by viral vectors. WPRE is a tripartite regulatory element with gamma, alpha, and beta components. WPRE sequence listing is in the Description of the Sequences Section. Guide RNA (gRNA) [0366] A gRNA is a component of the CRISPR/Cas system. A “gRNA” (guide ribonucleic acid) herein refers to a fusion of a CRISPR-targeting RNA (crRNA) and a trans- activation crRNA (tracrRNA), providing both targeting specificity and scaffolding/binding ability for Cas9 nuclease. A “crRNA” is a bacterial RNA that confers target specificity and requires tracrRNA to bind to Cas9. A “tracrRNA” is a bacterial RNA that links the crRNA to the Cas9 nuclease and typically can bind any crRNA. The sequence specificity of a Cas DNA-binding protein is determined by gRNAs, which have nucleotide base-pairing complementarity to target DNA sequences. The native gRNA comprises a 20 nucleotide (nt) Specificity Determining Sequence (SDS), which specifies the DNA sequence to be targeted, and is immediately followed by a 80 nt scaffold sequence, which associates the gRNA with Cas9. In some embodiments, an SDS of the present disclosure has a length of 15 to 100 nucleotides, or more. For example, an SDS may have a length of 15 to 90, 15 to 85, 15 to 80, 15 to 75, 15 to 70, 15 to 65, 15 to 60, 15 to 55, 15 to 50, 15 to 45, 15 to 40, 15 to 35, 15 to 30, or 15 to 20 nucleotides. In some embodiments, the SDS is 20 nucleotides long. For example, the SDS may be 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides long. At least a portion of the target DNA sequence is complementary to the SDS of the gRNA. For Cas9 to successfully bind to the DNA target sequence, a region of the target sequence is complementary to the SDS of the gRNA sequence and is immediately followed by the correct protospacer adjacent motif (PAM) sequence (e.g., NGG for Cas9 and TTN, TTTN, or YTN for Cpf1). In some embodiments, an SDS is 100% complementary to its target sequence. In some embodiments, the SDS sequence is less than 100% complementary to its target sequence and is, thus, considered to be partially complementary to its target sequence. For example, a targeting sequence may be 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% complementary to its target sequence. In some embodiments, the SDS of template DNA or target DNA may differ from a complementary region of a gRNA by 1, 2, 3, 4 or 5 nucleotides. [0367] In addition to the SDS, the gRNA comprises a scaffold sequence (corresponding to the tracrRNA in the native CRISPR/Cas system) that is required for its association with Cas9 (referred to herein as the “gRNA handle”). In some embodiments, the gRNA comprises a structure 5′-[SDS] -[gRNA handle]-3′. In some embodiments, the scaffold sequence comprises the nucleotide sequence of 5′-guuuuagagcuagaaauagcaaguuaaaauaaaggcuaguc cguuaucaacuugaaaaaguggcaccgagucggugcuuuuu-3′ (SEQ ID NO: 216). Other non-limiting, suitable gRNA handle sequences that may be used in accordance with the present disclosure are listed in the Description of the Sequences. [0368] In some embodiments, the guide RNA is about 15-120 nucleotides long and comprises a sequence of at least 10 contiguous nucleotides that is complementary to a target sequence. In some embodiments, the guide RNA is 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, or 120 nucleotides long. In some embodiments, the guide RNA comprises a sequence of 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more contiguous nucleotides that is complementary to a target sequence. Sequence complementarity refers to distinct interactions between adenine and thymine (DNA) or uracil (RNA), and between guanine and cytosine. Homology arm [0369] The term “homology arm” refers to a portion of the extension arm that encodes a portion of the resulting reverse transcriptase-encoded single strand DNA flap that is to be integrated into the target DNA site by replacing the endogenous strand. The portion of the single strand DNA flap encoded by the homology arm is complementary to the non-edited strand of the target DNA sequence, which facilitates the displacement of the endogenous strand and annealing of the single strand DNA flap in its place, thereby installing the edit. This component is further defined elsewhere. The homology arm is part of the DNA synthesis template since it is by definition encoded by the polymerase of the prime editors described herein. Host cell [0370] The term “host cell,” as used herein, refers to a cell that can host, replicate, and express a vector described herein, e.g., a vector comprising a nucleic acid molecule encoding a fusion protein comprising a Cas9 or Cas9 equivalent and a reverse transcriptase. Intein [0371] An “intein” is a segment of a protein that is able to excise itself and join the remaining portions (the exteins) with a peptide bond in a process known as protein splicing. Inteins are also referred to as “protein introns.” The process of an intein excising itself and joining the remaining portions of the protein is herein termed “protein splicing” or “intein-mediated protein splicing.” In some embodiments, an intein of a precursor protein (an intein containing protein prior to intein-mediated protein splicing) comes from two genes. Such intein is referred to herein as a split intein. For example, in cyanobacteria, DnaE, the catalytic subunit α of DNA polymerase III, is encoded by two separate genes, dnaE-n and dnaE-c. The intein encoded by the dnaE-n gene is herein referred as “intein-N.” The intein encoded by the dnaE-c gene is herein referred as “intein-C.” [0372] Other intein systems may also be used. For example, a synthetic intein based on the dnaE intein, the Cfa-N and Cfa-C intein pair, has been described (e.g., in Stevens et al., J Am Chem Soc.2016 Feb 24;138(7):2162-5, incorporated herein by reference). Non-limiting examples of intein pairs that may be used in accordance with the present disclosure include: Cfa DnaE intein, Ssp GyrB intein, Ssp DnaX intein, Ter DnaE3 intein, Ter ThyX intein, Rma DnaB intein and Cne Prp8 intein (e.g., as described in US Patent 8,394,604, incorporated herein by reference. [0373] Intein-N and intein-C may be fused to the N-terminal portion of the split prime editor and the C-terminal portion of the split prime editor, respectively, for the joining of the N-terminal portion of the split prime editor and the C-terminal portion of the split prime editor. For example, in some embodiments, an intein-N is fused to the C-terminus of the N- terminal portion of the split prime editor, i.e., to form a structure of N-[N-terminal portion of the split prime editor]-[intein-N]-C. In some embodiments, an intein-C is fused to the N- terminus of the C-terminal portion of the split prime editor, i.e., to form a structure of N- [intein-C]-[C-terminal portion of the split prime editor]-C. The mechanism of intein-mediated protein splicing for joining the proteins the inteins are fused to (e.g., split prime editor) is known in the art, e.g., as described in Shah et al., Chem Sci.2014; 5(1):446–461, incorporated herein by reference. Ligand-dependent intein [0374] The term “ligand-dependent intein,” as used herein refers to an intein that comprises a ligand-binding domain. Typically, the ligand-binding domain is inserted into the amino acid sequence of the intein, resulting in a structure intein (N) – ligand-binding domain – intein (C). Typically, ligand-dependent inteins exhibit no or only minimal protein splicing activity in the absence of an appropriate ligand, and a marked increase of protein splicing activity in the presence of the ligand. In some embodiments, the ligand-dependent intein does not exhibit observable splicing activity in the absence of ligand but does exhibit splicing activity in the presence of the ligand. In some embodiments, the ligand-dependent intein exhibits an observable protein splicing activity in the absence of the ligand, and a protein splicing activity in the presence of an appropriate ligand that is at least 5 times, at least 10 times, at least 50 times, at least 100 times, at least 150 times, at least 200 times, at least 250 times, at least 500 times, at least 1000 times, at least 1500 times, at least 2000 times, at least 2500 times, at least 5000 times, at least 10000 times, at least 20000 times, at least 25000 times, at least 50000 times, at least 100000 times, at least 500000 times, or at least 1000000 times greater than the activity observed in the absence of the ligand. In some embodiments, the increase in activity is dose dependent over at least 1 order of magnitude, at least 2 orders of magnitude, at least 3 orders of magnitude, at least 4 orders of magnitude, or at least 5 orders of magnitude, allowing for fine-tuning of intein activity by adjusting the concentration of the ligand. Suitable ligand-dependent inteins are known in the art, and in include those provided below and those described in published U.S. Patent Application U.S.2014/0065711 A1; Mootz et al., “Protein splicing triggered by a small molecule.” J. Am. Chem. Soc.2002; 124, 9044–9045; Mootz et al., “Conditional protein splicing: a new tool to control protein structure and function in vitro and in vivo.” J. Am. Chem. Soc.2003; 125, 10561–10569; Buskirk et al., Proc. Natl. Acad. Sci. USA.2004; 101, 10505-10510); Skretas & Wood, “Regulation of protein activity with small-molecule-controlled inteins.” Protein Sci.2005; 14, 523-532; Schwartz, et al., “Post-translational enzyme activation in an animal via optimized conditional protein splicing.” Nat. Chem. Biol.2007; 3, 50-54; Peck et al., Chem. Biol.2011; 18 (5), 619-630; the entire contents of each are hereby incorporated by reference. Exemplary sequences are listed in the Description of the Sequences section. Linker [0375] The term “linker,” as used herein, refers to a molecule linking two other molecules or moieties. The linker can be an amino acid sequence in the case of a linker joining two fusion proteins. For example, a Cas9 can be fused to a reverse transcriptase by an amino acid linker sequence. The linker can also be a nucleotide sequence in the case of joining two nucleotide sequences together. For example, in the instant case, the traditional guide RNA is linked via a spacer or linker nucleotide sequence to the RNA extension of a prime editing guide RNA which may comprise a RT template sequence and an RT primer binding site. In other embodiments, the linker is an organic molecule, group, polymer, or chemical moiety. In some embodiments, the linker is 5-100 amino acids in length, for example, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 30-35, 35-40, 40-45, 45-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100-150, or 150-200 amino acids in length. Longer or shorter linkers are also contemplated. napDNAbp [0376] As used herein, the term “nucleic acid programmable DNA binding protein” or “napDNAbp,” of which Cas9 is an example, refer to a proteins which use RNA:DNA hybridization to target and bind to specific sequences in a DNA molecule. Each napDNAbp is associated with at least one guide nucleic acid (e.g., guide RNA), which localizes the napDNAbp to a DNA sequence that comprises a DNA strand (i.e., a target strand) that is complementary to the guide nucleic acid, or a portion thereof (e.g., the protospacer of a guide RNA). In other words, the guide nucleic-acid “programs” the napDNAbp (e.g., Cas9 or equivalent) to localize and bind to a complementary sequence. [0377] Without being bound by theory, the binding mechanism of a napDNAbp – guide RNA complex, in general, includes the step of forming an R-loop whereby the napDNAbp induces the unwinding of a double-strand DNA target, thereby separating the strands in the region bound by the napDNAbp. The guide RNA protospacer then hybridizes to the “target strand.” This displaces a “non-target strand” that is complementary to the target strand, which forms the single strand region of the R-loop. In some embodiments, the napDNAbp includes one or more nuclease activities, which then cut the DNA leaving various types of lesions. For example, the napDNAbp may comprises a nuclease activity that cuts the non- target strand at a first location, and/ or cuts the target strand at a second location. Depending on the nuclease activity, the target DNA can be cut to form a “double-stranded break” whereby both strands are cut. In other embodiments, the target DNA can be cut at only a single site, i.e., the DNA is “nicked” on one strand. Exemplary napDNAbp with different nuclease activities include “Cas9 nickase” (“nCas9”) and a deactivated Cas9 having no nuclease activities (“dead Cas9” or “dCas9”). Exemplary sequences for these and other napDNAbp are provided herein. Nickase [0378] The term “nickase” refers to a Cas9 with one of the two nuclease domains inactivated. This enzyme is capable of cleaving only one strand of a target DNA. Nucleic Acid [0379] The terms “nucleic acid,” and “polynucleotide,” as used herein, refer to a compound comprising a nucleobase and an acidic moiety, e.g., a nucleotide, or a polymer of nucleotides. Typically, polymeric nucleic acids, e.g., nucleic acid molecules comprising three or more nucleotides are linear molecules, in which adjacent nucleotides are linked to each other via a phosphodiester linkage. In some embodiments, “nucleic acid” refers to individual nucleic acid residues (e.g. nucleotides and/or nucleosides). In some embodiments, “nucleic acid” refers to an oligonucleotide chain comprising three or more individual nucleotide residues. As used herein, the terms “oligonucleotide” and “polynucleotide” can be used interchangeably to refer to a polymer of nucleotides (e.g., a string of at least three nucleotides). In some embodiments, “nucleic acid” encompasses RNA as well as single and/or double-stranded DNA. Nucleic acids may be naturally occurring, for example, in the context of a genome, a transcript, an mRNA, tRNA, rRNA, siRNA, snRNA, a plasmid, cosmid, chromosome, chromatid, or other naturally occurring nucleic acid molecule. On the other hand, a nucleic acid molecule may be a non-naturally occurring molecule, e.g., a recombinant DNA or RNA, an artificial chromosome, an engineered genome (e.g., an engineered viral vector), an engineered vector, or fragment thereof, or a synthetic DNA, RNA, or DNA/RNA hybrid, optionally including non-naturally occurring nucleotides or nucleosides. Furthermore, the terms “nucleic acid,” “DNA,” “RNA,” and/or similar terms include nucleic acid analogs, e.g., analogs having other than a phosphodiester backbone. Nucleic acids can be purified from natural sources, produced using recombinant expression systems and optionally purified, chemically synthesized, etc. Where appropriate, e.g., in the case of chemically synthesized molecules, nucleic acids can comprise nucleoside analogs such as analogs having chemically modified bases or sugars, and backbone modifications. A nucleic acid sequence is presented in the 5′ to 3′ direction unless otherwise indicated. In some embodiments, a nucleic acid is or comprises natural nucleosides (e.g. adenosine, thymidine, guanosine, cytidine, uridine, deoxyadenosine, deoxythymidine, deoxyguanosine, and deoxycytidine); nucleoside analogs (e.g., 2-aminoadenosine, 2-thiothymidine, inosine, pyrrolo-pyrimidine, 3-methyl adenosine, 5-methylcytidine, 2-aminoadenosine, C5- bromouridine, C5-fluorouridine, C5-iodouridine, C5-propynyl-uridine, C5-propynyl-cytidine, C5-methylcytidine, 2-aminoadenosine, 7-deazaadenosine, 7-deazaguanosine, 8- oxoadenosine, 8-oxoguanosine, O(6)-methylguanine, and 2-thiocytidine); chemically modified bases; biologically modified bases (e.g., methylated bases); intercalated bases; modified sugars (e.g., 2′-fluororibose, ribose, 2′-deoxyribose, arabinose, and hexose); and/or modified phosphate groups (e.g., phosphorothioates and 5′-N-phosphoramidite linkages). Nuclear Localization Signal (NLS) [0380] A “nuclear localization signal” or “NLS” refers to as an amino acid sequence that “tags” a protein for import into the cell nucleus by nuclear transport. Typically, this signal consists of one or more short sequences of positively charged lysines or arginines exposed on the protein surface. One or more NLS may be added to the N- or C-terminus of a protein, or internally (e.g., between two protein domains). For example, one or more NLS may be added to the N- or C-terminus of a prime editor, or between the napDNAbp and the polymerase in a prime editor. In some embodiments, 1, 2, 3, 4, 5, or more NLS may be added. Nuclear localization sequences are known in the art and would be apparent to the skilled artisan. For example, NLS sequences are described in Plank et al., PCT/EP2000/011690, filed November 23, 2000, the contents of which are incorporated herein by reference for its disclosure of exemplary nuclear localization sequences. [0381] The nucleotide sequence encoding an NLS is “operably linked” to the nucleotide sequence encoding a protein to which the NLS is fused (e.g., a prime editor) when two coding sequences are “in-frame with each other” and are translated as a single polypeptide fusing two sequences. PegRNAs [0382] As used herein, the terms “prime editing guide RNA” or “PEgRNA” or “extended guide RNA” refers to a specialized form of a guide RNA that has been modified to include one or more additional sequences for implementing the prime editing methods and compositions described herein. As described herein, the prime editing guide RNA comprise one or more “extended regions” of nucleic acid sequence. The extended regions may comprise, but are not limited to, single-stranded RNA or DNA. Further, the extended regions may occur at the 3´ end of a traditional guide RNA. In other arrangements, the extended regions may occur at the 5´ end of a traditional guide RNA. In still other arrangements, the extended region may occur at an intramolecular region of the traditional guide RNA, for example, in the gRNA core region which associates and/or binds to the napDNAbp. The extended region comprises a “DNA synthesis template” which encodes (by the polymerase of the prime editor) a single-stranded DNA which, in turn, has been designed to be (a) homologous with the endogenous target DNA to be edited, and (b) which comprises at least one desired nucleotide change (e.g., a transition, a transversion, a deletion, or an insertion) to be introduced or integrated into the endogenous target DNA. The extended region may also comprise other functional sequence elements, such as, but not limited to, a “primer binding site” and a “spacer or linker” sequence, or other structural elements, such as, but not limited to aptamers, stem loops, hairpins, toe loops (e.g., a 3’ toeloop), or an RNA- protein recruitment domain (e.g., MS2 hairpin). As used herein the “primer binding site” comprises a sequence that hybridizes to a single-strand DNA sequence having a 3´ end generated from the nicked DNA of the R-loop. [0383] In certain embodiments, the PEgRNAs are represented by a 5ʹ extension arm, a spacer, and a gRNA core. The 5ʹ extension further comprises in the 5ʹ to 3ʹ direction a reverse transcriptase template, a primer binding site, and a linker. As shown, the reverse transcriptase template may also be referred to more broadly as the “DNA synthesis template” where the polymerase of a prime editor described herein is not an RT, but another type of polymerase. [0384] In certain other embodiments, the PEgRNAs are represented by a 5ʹ extension arm, a spacer, and a gRNA core. The 5ʹ extension further comprises in the 5ʹ to 3ʹ direction a reverse transcriptase template, a primer binding site, and a linker. As shown, the reverse transcriptase template may also be referred to more broadly as the “DNA synthesis template” where the polymerase of a prime editor described herein is not an RT, but another type of polymerase. [0385] In still other embodiments, the PEgRNAs are represented having in the 5ʹ to 3ʹ direction a spacer (1), a gRNA core (2), and an extension arm (3). The extension arm (3) is at the 3ʹ end of the PEgRNA. The extension arm (3) further comprises in the 5ʹ to 3ʹ direction a “primer binding site” (A), an “edit template” (B), and a “homology arm” (C). The extension arm (3) may also comprise an optional modifier region at the 3ʹ and 5ʹ ends, which may be the same sequences or different sequences. In addition, the 3ʹ end of the PEgRNA may comprise a transcriptional terminator sequence. These sequence elements of the PEgRNAs are further described and defined herein. [0386] In still other embodiments, the PEgRNAs are represented by having in the 5ʹ to 3ʹ direction an extension arm (3), a spacer (1), and a gRNA core (2). The extension arm (3) is at the 5ʹ end of the PEgRNA. The extension arm (3) further comprises in the 3ʹ to 5ʹ direction a “primer binding site” (A), an “edit template” (B), and a “homology arm” (C). The extension arm (3) may also comprise an optional modifier region at the 3ʹ and 5ʹ ends, which may be the same sequences or different sequences. The PEgRNAs may also comprise a transcriptional terminator sequence at the 3ʹ end. These sequence elements of the PEgRNAs are further described and defined herein. PE1 [0387] As used herein, “PE1” refers to a PE complex comprising a fusion protein comprising Cas9(H840A) and a wild type MMLV RT having the following structure: [NLS]- [Cas9(H840A)]-[linker]-[MMLV_RT(wt)] + a desired PEgRNA, wherein the PE fusion has the amino acid sequence of SEQ ID NO: 125 (See Description of Sequences) PE2 [0388] As used herein, “PE2” refers to a PE complex comprising a fusion protein comprising Cas9(H840A) and a variant MMLV RT having the following structure: [NLS]- [Cas9(H840A)]-[linker]-[MMLV_RT(D200N)(T330P)(L603W)(T306K)( W313F)] + a desired PEgRNA, wherein the PE fusion has the amino acid sequence of SEQ ID NO: 129 (See Description of Sequences) PE3 [0389] As used herein, “PE3” refers to PE2 plus a second-strand nicking guide RNA that complexes with the PE2 and introduces a nick in the non-edited DNA strand in order to induce preferential replacement of the edited strand. PE3b [0390] As used herein, “PE3b” refers to PE3 but wherein the second-strand nicking guide RNA is designed for temporal control such that the second strand nick is not introduced until after the installation of the desired edit. This is achieved by designing a gRNA with a spacer sequence that matches only the edited strand, but not the original allele. Using this strategy, referred to hereafter as PE3b, mismatches between the protospacer and the unedited allele should disfavor nicking by the sgRNA until after the editing event on the PAM strand takes place. PE-short [0391] As used herein, “PE-short” refers to a PE construct that is fused to a C-terminally truncated reverse transcriptase, and has the following SEQ ID NO: 130 (See Description of Sequences) Peptide tag [0392] The term “peptide tag” refers to a peptide amino acid sequence that is genetically fused to a protein sequence to impart one or more functions onto the proteins that facilitate the manipulation of the protein for various purposes, such as, visualization, purification, solubilization, and separation, etc. Peptide tags can include various types of tags categorized by purpose or function, which may include “affinity tags” (to facilitate protein purification), “solubilization tags” (to assist in proper folding of proteins), “chromatography tags” (to alter chromatographic properties of proteins), “epitope tags” (to bind to high affinity antibodies), “fluorescence tags” (to facilitate visualization of proteins in a cell or in vitro). Polymerase [0393] As used herein, the term “polymerase” refers to an enzyme that synthesizes a nucleotide strand and which may be used in connection with the prime editor systems described herein. The polymerase can be a “template-dependent” polymerase (i.e., a polymerase which synthesizes a nucleotide strand based on the order of nucleotide bases of a template strand). The polymerase can also be a “template-independent” polymerase (i.e., a polymerase which synthesizes a nucleotide strand without the requirement of a template strand). A polymerase may also be further categorized as a “DNA polymerase” or an “RNA polymerase.” In various embodiments, the prime editor system comprises a DNA polymerase. In various embodiments, the DNA polymerase can be a “DNA-dependent DNA polymerase” (i.e., whereby the template molecule is a strand of DNA). In such cases, the DNA template molecule can be a PEgRNA, wherein the extension arm comprises a strand of DNA. In such cases, the PEgRNA may be referred to as a chimeric or hybrid PEgRNA which comprises an RNA portion (i.e., the guide RNA components, including the spacer and the gRNA core) and a DNA portion (i.e., the extension arm). In various other embodiments, the DNA polymerase can be an “RNA-dependent DNA polymerase” (i.e., whereby the template molecule is a strand of RNA). In such cases, the PEgRNA is RNA, i.e., including an RNA extension. The term “polymerase” may also refer to an enzyme that catalyzes the polymerization of nucleotide (i.e., the polymerase activity). Generally, the enzyme will initiate synthesis at the 3'-end of a primer annealed to a polynucleotide template sequence (e.g., such as a primer sequence annealed to the primer binding site of a PEgRNA), and will proceed toward the 5' end of the template strand. A “DNA polymerase” catalyzes the polymerization of deoxynucleotides. As used herein in reference to a DNA polymerase, the term DNA polymerase includes a “functional fragment thereof”. A “functional fragment thereof” refers to any portion of a wild-type or mutant DNA polymerase that encompasses less than the entire amino acid sequence of the polymerase and which retains the ability, under at least one set of conditions, to catalyze the polymerization of a polynucleotide. Such a functional fragment may exist as a separate entity, or it may be a constituent of a larger polypeptide, such as a fusion protein. Pharmaceutically acceptable Carrier [0394] The term “pharmaceutically-acceptable carrier” means a pharmaceutically- acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, manufacturing aid (e.g., lubricant, talc magnesium, calcium or zinc stearate, or steric acid), or solvent encapsulating material, involved in carrying or transporting the compound from one site (e.g., the delivery site) of the body, to another site (e.g., organ, tissue or portion of the body). A pharmaceutically acceptable carrier is “acceptable” in the sense of being compatible with the other ingredients of the formulation and not injurious to the tissue of the subject (e.g., physiologically compatible, sterile, physiologic pH, etc.). prime editing [0395] As used herein, the term “prime editing” refers to a novel approach for gene editing using napDNAbps, a polymerase (e.g., a reverse transcriptase), and specialized guide RNAs that include a DNA synthesis template for encoding desired new genetic information (or deleting genetic information) that is then incorporated into a target DNA sequence. [0396] prime editing represents an entirely new platform for genome editing that is a versatile and precise genome editing method that directly writes new genetic information into a specified DNA site using a nucleic acid programmable DNA binding protein (“napDNAbp”) working in association with a polymerase (i.e., in the form of a fusion protein or otherwise provided in trans with the napDNAbp), wherein the prime editing system is programmed with a prime editing (PE) guide RNA (“PEgRNA”) that both specifies the target site and templates the synthesis of the desired edit in the form of a replacement DNA strand by way of an extension (either DNA or RNA) engineered onto a guide RNA (e.g., at the 5ʹ or 3ʹ end, or at an internal portion of a guide RNA). The replacement strand containing the desired edit (e.g., a single nucleobase substitution) shares the same (or is homologous to) sequence as the endogenous strand (immediately downstream of the nick site) of the target site to be edited (with the exception that it includes the desired edit). Through DNA repair and/or replication machinery, the endogenous strand downstream of the nick site is replaced by the newly synthesized replacement strand containing the desired edit. In some cases, prime editing may be thought of as a “search-and-replace” genome editing technology since the prime editors, as described herein, not only search and locate the desired target site to be edited, but at the same time, encode a replacement strand containing a desired edit which is installed in place of the corresponding target site endogenous DNA strand. The prime editors of the present disclosure relate, in part, to the discovery that the mechanism of target-primed reverse transcription (TPRT) or “prime editing” can be leveraged or adapted for conducting precision CRISPR/Cas-based genome editing with high efficiency and genetic flexibility. TPRT is naturally used by mobile DNA elements, such as mammalian non-LTR retrotransposons and bacterial Group II introns ^28,29 . The inventors have herein used Cas protein-reverse transcriptase fusions or related systems to target a specific DNA sequence with a guide RNA, generate a single strand nick at the target site, and use the nicked DNA as a primer for reverse transcription of an engineered reverse transcriptase template that is integrated with the guide RNA. However, while the concept begins with prime editors that use reverse transcriptase as the DNA polymerase component, the prime editors described herein are not limited to reverse transcriptases but may include the use of virtually any DNA polymerase. Indeed, while the application throughout may refer to prime editors with “reverse transcriptases,” it is set forth here that reverse transcriptases are only one type of DNA polymerase that may work with prime editing. Thus, where ever the specification mentions a “reverse transcriptase,” the person having ordinary skill in the art should appreciate that any suitable DNA polymerase may be used in place of the reverse transcriptase. Thus, in one aspect, the prime editors may comprise Cas9 (or an equivalent napDNAbp) which is programmed to target a DNA sequence by associating it with a specialized guide RNA (i.e., PEgRNA) containing a spacer sequence that anneals to a complementary protospacer in the target DNA. The specialized guide RNA also contains new genetic information in the form of an extension that encodes a replacement strand of DNA containing a desired genetic alteration which is used to replace a corresponding endogenous DNA strand at the target site. To transfer information from the PEgRNA to the target DNA, the mechanism of prime editing involves nicking the target site in one strand of the DNA to expose a 3′-hydroxyl group. The exposed 3′-hydroxyl group can then be used to prime the DNA polymerization of the edit-encoding extension on PEgRNA directly into the target site. In various embodiments, the extension—which provides the template for polymerization of the replacement strand containing the edit—can be formed from RNA or DNA. In the case of an RNA extension, the polymerase of the prime editor can be an RNA-dependent DNA polymerase (such as, a reverse transcriptase). In the case of a DNA extension, the polymerase of the prime editor may be a DNA-dependent DNA polymerase. The newly synthesized strand (i.e., the replacement DNA strand containing the desired edit) that is formed by the herein disclosed prime editors would be homologous to the genomic target sequence (i.e., have the same sequence as) except for the inclusion of a desired nucleotide change (e.g., a single nucleotide change, a deletion, or an insertion, or a combination thereof). The newly synthesized (or replacement) strand of DNA may also be referred to as a single strand DNA flap, which would compete for hybridization with the complementary homologous endogenous DNA strand, thereby displacing the corresponding endogenous strand. In certain embodiments, the system can be combined with the use of an error-prone reverse transcriptase enzyme (e.g., provided as a fusion protein with the Cas9 domain, or provided in trans to the Cas9 domain). The error-prone reverse transcriptase enzyme can introduce alterations during synthesis of the single strand DNA flap. Thus, in certain embodiments, error-prone reverse transcriptase can be utilized to introduce nucleotide changes to the target DNA. Depending on the error-prone reverse transcriptase that is used with the system, the changes can be random or non-random. Resolution of the hybridized intermediate (comprising the single strand DNA flap synthesized by the reverse transcriptase hybridized to the endogenous DNA strand) can include removal of the resulting displaced flap of endogenous DNA (e.g., with a 5ʹ end DNA flap endonuclease, FEN1), ligation of the synthesized single strand DNA flap to the target DNA, and assimilation of the desired nucleotide change as a result of cellular DNA repair and/or replication processes. Because templated DNA synthesis offers single nucleotide precision for the modification of any nucleotide, including insertions and deletions, the scope of this approach is very broad and could foreseeably be used for myriad applications in basic science and therapeutics. [0397] In various embodiments, prime editing operates by contacting a target DNA molecule (for which a change in the nucleotide sequence is desired to be introduced) with a nucleic acid programmable DNA binding protein (napDNAbp) complexed with a prime editing guide RNA (PEgRNA). In some embodiments, the prime editing guide RNA (PEgRNA) comprises an extension at the 3´ or 5´ end of the guide RNA, or at an intramolecular location in the guide RNA and encodes the desired nucleotide change (e.g., single nucleotide change, insertion, or deletion). In step (a), the napDNAbp/extended gRNA complex contacts the DNA molecule and the extended gRNA guides the napDNAbp to bind to a target locus. In step (b), a nick in one of the strands of DNA of the target locus is introduced (e.g., by a nuclease or chemical agent), thereby creating an available 3´ end in one of the strands of the target locus. In certain embodiments, the nick is created in the strand of DNA that corresponds to the R-loop strand, i.e., the strand that is not hybridized to the guide RNA sequence, i.e., the “non-target strand.” The nick, however, could be introduced in either of the strands. That is, the nick could be introduced into the R-loop “target strand” (i.e., the strand hybridized to the protospacer of the extended gRNA) or the “non-target strand” (i.e., the strand forming the single-stranded portion of the R-loop and which is complementary to the target strand). In step (c), the 3´ end of the DNA strand (formed by the nick) interacts with the extended portion of the guide RNA in order to prime reverse transcription (i.e., “target-primed RT”). In certain embodiments, the 3´ end DNA strand hybridizes to a specific RT priming sequence on the extended portion of the guide RNA, i.e., the “reverse transcriptase priming sequence” or “primer binding site” on the PEgRNA. In step (d), a reverse transcriptase (or other suitable DNA polymerase) is introduced which synthesizes a single strand of DNA from the 3´ end of the primed site towards the 5´ end of the prime editing guide RNA. The DNA polymerase (e.g., reverse transcriptase) can be fused to the napDNAbp or alternatively can be provided in trans to the napDNAbp. This forms a single-strand DNA flap comprising the desired nucleotide change (e.g., the single base change, insertion, or deletion, or a combination thereof) and which is otherwise homologous to the endogenous DNA at or adjacent to the nick site. In step (e), the napDNAbp and guide RNA are released. Steps (f) and (g) relate to the resolution of the single strand DNA flap such that the desired nucleotide change becomes incorporated into the target locus. This process can be driven towards the desired product formation by removing the corresponding 5´ endogenous DNA flap that forms once the 3´ single strand DNA flap invades and hybridizes to the endogenous DNA sequence. Without being bound by theory, the cells endogenous DNA repair and replication processes resolves the mismatched DNA to incorporate the nucleotide change(s) to form the desired altered product. The process can also be driven towards product formation with “second strand nicking” as is known in the art. This process may introduce at least one or more of the following genetic changes: transversions, transitions, deletions, and insertions. prime editor [0398] The term “prime editor” refers to the herein described fusion constructs comprising a napDNAbp (e.g., Cas9 nickase) and a reverse transcriptase and is capable of carrying out prime editing on a target nucleotide sequence in the presence of a PEgRNA (or “extended guide RNA”). The term “prime editor” may refer to the fusion protein or to the fusion protein complexed with a PEgRNA, and/or further complexed with a second-strand nicking sgRNA. In some embodiments, the prime editor may also refer to the complex comprising a fusion protein (reverse transcriptase fused to a napDNAbp), a PEgRNA, and a regular guide RNA capable of directing the second-site nicking step of the non-edited strand as described herein. In other embodiments, the reverse transcriptase component of the “primer editor” may be provided in trans. primer binding site [0399] The term “primer binding site” or “the PBS” refers to the nucleotide sequence located on a PEgRNA as component of the extension arm (typically at the 3ʹ end of the extension arm) and serves to bind to the primer sequence that is formed after Cas9 nicking of the target sequence by the prime editor. As detailed elsewhere, when the Cas9 nickase component of a prime editor nicks one strand of the target DNA sequence, a 3ʹ-ended ssDNA flap is formed, which serves a primer sequence that anneals to the primer binding site on the PEgRNA to prime reverse transcription. Protein, Peptide, and Polypeptides [0400] The terms “protein,” “peptide,” and “polypeptide” are used interchangeably herein, and refer to a polymer of amino acid residues linked together by peptide (amide) bonds. The terms refer to a protein, peptide, or polypeptide of any size, structure, or function. Typically, a protein, peptide, or polypeptide will be at least three amino acids long. A protein, peptide, or polypeptide may refer to an individual protein or a collection of proteins. One or more of the amino acids in a protein, peptide, or polypeptide may be modified, for example, by the addition of a chemical entity such as a carbohydrate group, a hydroxyl group, a phosphate group, a farnesyl group, an isofarnesyl group, a fatty acid group, a linker for conjugation, functionalization, or other modification, etc. A protein, peptide, or polypeptide may also be a single molecule or may be a multi-molecular complex. A protein, peptide, or polypeptide may be just a fragment of a naturally occurring protein or peptide. A protein, peptide, or polypeptide may be naturally occurring, recombinant, or synthetic, or any combination thereof. The term “fusion protein” as used herein refers to a hybrid polypeptide which comprises protein domains from at least two different proteins. One protein may be located at the amino-terminal (N-terminal) portion of the fusion protein or at the carboxy- terminal (C-terminal) protein thus forming an “amino-terminal fusion protein” or a “carboxy- terminal fusion protein,” respectively. A protein may comprise different domains, for example, a nucleic acid binding domain (e.g., the gRNA binding domain of Cas9 that directs the binding of the protein to a target site) and a nucleic acid cleavage domain or a catalytic domain of a nucleic-acid editing protein. In some embodiments, a protein is in a complex with, or is in association with, a nucleic acid, e.g., RNA or DNA. Any of the proteins provided herein may be produced by any method known in the art. For example, the proteins provided herein may be produced via recombinant protein expression and purification, which is especially suited for fusion proteins comprising a peptide linker. Methods for recombinant protein expression and purification are well known, and include those described by Green and Sambrook, Molecular Cloning: A Laboratory Manual (4 ^th ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2012)), which are incorporated herein by reference. Protospacer [0401] As used herein, the term “protospacer” refers to the sequence (~20 bp) in DNA adjacent to the PAM (protospacer adjacent motif) sequence. The protospacer shares the same sequence as the spacer sequence of the guide RNA. The guide RNA anneals to the complement of the protospacer sequence on the target DNA (specifically, one strand thereof, i.e., the “target strand” versus the “non-target strand” of the target DNA sequence). In order for Cas9 to function it also requires a specific protospacer adjacent motif (PAM) that varies depending on the bacterial species of the Cas9 gene. The most commonly used Cas9 nuclease, derived from S. pyogenes, recognizes a PAM sequence of NGG that is found directly downstream of the target sequence in the genomic DNA, on the non-target strand. The skilled person will appreciate that the literature in the state of the art sometimes refers to the “protospacer” as the ~20-nt target-specific guide sequence on the guide RNA itself, rather than referring to it as a “spacer.” Thus, in some cases, the term “protospacer” as used herein may be used interchangeably with the term “spacer.” The context of the description surrounding the appearance of either “protospacer” or “spacer” will help inform the reader as to whether the term is in reference to the gRNA or the DNA target. Protospacer adjacent motif (PAM) [0402] A “protospacer adjacent motif” (PAM) is typically a sequence of nucleotides located adjacent to (e.g., within 10, 9, 8, 7, 6, 5, 4, 3, 3, or 1 nucleotide(s) of a target sequence). A PAM sequence is “immediately adjacent to” a target sequence if the PAM sequence is contiguous with the target sequence (that is, if there are no nucleotides located between the PAM sequence and the target sequence). In some embodiments, a PAM sequence is a wild-type PAM sequence. Examples of PAM sequences include, without limitation, NGG, NGR, NNGRR(T/N), NNNNGATT, NNAGAAW, NGGAG, NAAAAC, AWG, and CC. In some embodiments, a PAM sequence is obtained from Streptococcus pyogenes (e.g., NGG or NGR). In some embodiments, a PAM sequence is obtained from Staphylococcus aureus (e.g., NNGRR(T/N)). In some embodiments, a PAM sequence is obtained from Neisseria meningitidis (e.g., NNNNGATT). In some embodiments, a PAM sequence is obtained from Streptococcus thermophilus (e.g., NNAGAAW or NGGAG). In some embodiments, a PAM sequence is obtained from Treponema denticola (e.g., NAAAAC). In some embodiments, a PAM sequence is obtained from Escherichia coli (e.g., AWG). In some embodiments, a PAM sequence is obtained from Pseudomonas auruginosa (e.g., CC). Other PAM sequences are contemplated. A PAM sequence is typically located downstream (i.e., 3′) from the target sequence, although in some embodiments a PAM sequence may be located upstream (i.e., 5′) from the target sequence. Protein splicing [0403] The term “protein splicing,” as used herein, refers to a process in which a sequence, an intein (or split inteins, as the case may be), is excised from within an amino acid sequence, and the remaining fragments of the amino acid sequence, the exteins, are ligated via an amide bond to form a continuous amino acid sequence. The term “trans” protein splicing refers to the specific case where the inteins are split inteins and they are located on different proteins. Recombinase [0404] The term “recombinase,” as used herein, refers to a site-specific enzyme that mediates the recombination of DNA between recombinase recognition sequences, which results in the excision, integration, inversion, or exchange (e.g., translocation) of DNA fragments between the recombinase recognition sequences. Recombinases can be classified into two distinct families: serine recombinases (e.g., resolvases and invertases) and tyrosine recombinases (e.g., integrases). Examples of serine recombinases include, without limitation, Hin, Gin, Tn3, β-six, CinH, ParA, γδ, Bxb1, ϕC31, TP901, TG1, φBT1, R4, φRV1, φFC1, MR11, A118, U153, and gp29. Examples of tyrosine recombinases include, without limitation, Cre, FLP, R, Lambda, HK101, HK022, and pSAM2. The serine and tyrosine recombinase names stem from the conserved nucleophilic amino acid residue that the recombinase uses to attack the DNA and which becomes covalently linked to the DNA during strand exchange. Recombinases have numerous applications, including the creation of gene knockouts/knock-ins and gene therapy applications. See, e.g., Brown et al., “Serine recombinases as tools for genome engineering.” Methods.2011;53(4):372-9; Hirano et al., “Site-specific recombinases as tools for heterologous gene integration.” Appl. Microbiol. Biotechnol.2011; 92(2):227-39; Chavez and Calos, “Therapeutic applications of the ΦC31 integrase system.” Curr. Gene Ther.2011;11(5):375-81; Turan and Bode, “Site-specific recombinases: from tag-and-target- to tag-and-exchange-based genomic modifications.” FASEB J.2011; 25(12):4088-107; Venken and Bellen, “Genome-wide manipulations of Drosophila melanogaster with transposons, Flp recombinase, and ΦC31 integrase.” Methods Mol. Biol.2012; 859:203-28; Murphy, “Phage recombinases and their applications.” Adv. Virus Res.2012; 83:367-414; Zhang et al., “Conditional gene manipulation: Cre-ating a new biological era.” J. Zhejiang Univ. Sci. B.2012; 13(7):511-24; Karpenshif and Bernstein, “From yeast to mammals: recent advances in genetic control of homologous recombination.” DNA Repair (Amst).2012; 1;11(10):781-8; the entire contents of each are hereby incorporated by reference in their entirety. The recombinases provided herein are not meant to be exclusive examples of recombinases that can be used in embodiments of the invention. The methods and compositions of the invention can be expanded by mining databases for new orthogonal recombinases or designing synthetic recombinases with defined DNA specificities (See, e.g., Groth et al., “Phage integrases: biology and applications.” J. Mol. Biol.2004; 335, 667-678; Gordley et al., “Synthesis of programmable integrases.” Proc. Natl. Acad. Sci. U S A.2009; 106, 5053-5058; the entire contents of each are hereby incorporated by reference in their entirety). Other examples of recombinases that are useful in the methods and compositions described herein are known to those of skill in the art, and any new recombinase that is discovered or generated is expected to be able to be used in the different embodiments of the invention. In some embodiments, the catalytic domains of a recombinase are fused to a nuclease-inactivated RNA-programmable nuclease (e.g., dCas9, or a fragment thereof), such that the recombinase domain does not comprise a nucleic acid binding domain or is unable to bind to a target nucleic acid (e.g., the recombinase domain is engineered such that it does not have specific DNA binding activity). Recombinases lacking DNA binding activity and methods for engineering such are known, and include those described by Klippel et al., “Isolation and characterisation of unusual gin mutants.” EMBO J.1988; 7: 3983–3989: Burke et al., “Activating mutations of Tn3 resolvase marking interfaces important in recombination catalysis and its regulation. Mol Microbiol.2004; 51: 937–948; Olorunniji et al., “Synapsis and catalysis by activated Tn3 resolvase mutants.” Nucleic Acids Res.2008; 36: 7181–7191; Rowland et al., “Regulatory mutations in Sin recombinase support a structure-based model of the synaptosome.” Mol Microbiol.2009; 74: 282–298; Akopian et al., “Chimeric recombinases with designed DNA sequence recognition.” Proc Natl Acad Sci USA.2003;100: 8688–8691; Gordley et al., “Evolution of programmable zinc finger-recombinases with activity in human cells. J Mol Biol.2007; 367: 802–813; Gordley et al., “Synthesis of programmable integrases.” Proc Natl Acad Sci USA. 2009;106: 5053–5058; Arnold et al., “Mutants of Tn3 resolvase which do not require accessory binding sites for recombination activity.” EMBO J.1999;18: 1407–1414; Gaj et al., “Structure-guided reprogramming of serine recombinase DNA sequence specificity.” Proc Natl Acad Sci USA.2011;108(2):498-503; and Proudfoot et al., “Zinc finger recombinases with adaptable DNA sequence specificity.” PLoS One.2011;6(4):e19537; the entire contents of each are hereby incorporated by reference. For example, serine recombinases of the resolvase-invertase group, e.g., Tn3 and γδ resolvases and the Hin and Gin invertases, have modular structures with autonomous catalytic and DNA-binding domains (See, e.g., Grindley et al., “Mechanism of site-specific recombination.” Ann Rev Biochem.2006; 75: 567–605, the entire contents of which are incorporated by reference). The catalytic domains of these recombinases are thus amenable to being recombined with nuclease-inactivated RNA-programmable nucleases (e.g., dCas9, or a fragment thereof) as described herein, e.g., following the isolation of ‘activated’ recombinase mutants which do not require any accessory factors (e.g., DNA binding activities) (See, e.g., Klippel et al., “Isolation and characterisation of unusual gin mutants.” EMBO J.1988; 7: 3983–3989: Burke et al., “Activating mutations of Tn3 resolvase marking interfaces important in recombination catalysis and its regulation. Mol Microbiol.2004; 51: 937–948; Olorunniji et al., “Synapsis and catalysis by activated Tn3 resolvase mutants.” Nucleic Acids Res.2008; 36: 7181–7191; Rowland et al., “Regulatory mutations in Sin recombinase support a structure-based model of the synaptosome.” Mol Microbiol.2009; 74: 282–298; Akopian et al., “Chimeric recombinases with designed DNA sequence recognition.” Proc Natl Acad Sci USA.2003;100: 8688–8691). Additionally, many other natural serine recombinases having an N-terminal catalytic domain and a C-terminal DNA binding domain are known (e.g., phiC31 integrase, TnpX transposase, IS607 transposase), and their catalytic domains can be co-opted to engineer programmable site-specific recombinases as described herein (See, e.g., Smith et al., “Diversity in the serine recombinases.” Mol Microbiol.2002;44: 299–307, the entire contents of which are incorporated by reference). Similarly, the core catalytic domains of tyrosine recombinases (e.g., Cre, λ integrase) are known, and can be similarly co-opted to engineer programmable site-specific recombinases as described herein (See, e.g., Guo et al., “Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse.” Nature.1997; 389:40–46; Hartung et al., “Cre mutants with altered DNA binding properties.” J Biol Chem 1998; 273:22884–22891; Shaikh et al., “Chimeras of the Flp and Cre recombinases: Tests of the mode of cleavage by Flp and Cre. J Mol Biol.2000; 302:27– 48; Rongrong et al., “Effect of deletion mutation on the recombination activity of Cre recombinase.” Acta Biochim Pol.2005; 52:541–544; Kilbride et al., “Determinants of product topology in a hybrid Cre-Tn3 resolvase site-specific recombination system.” J Mol Biol.2006; 355:185–195; Warren et al., “A chimeric cre recombinase with regulated directionality.” Proc Natl Acad Sci USA.2008105:18278–18283; Van Duyne, “Teaching Cre to follow directions.” Proc Natl Acad Sci USA.2009 Jan 6;106(1):4-5; Numrych et al., “A comparison of the effects of single-base and triple-base changes in the integrase arm-type binding sites on the site-specific recombination of bacteriophage λ.” Nucleic Acids Res. 1990; 18:3953–3959; Tirumalai et al., “The recognition of core-type DNA sites by λ integrase.” J Mol Biol.1998; 279:513–527; Aihara et al., “A conformational switch controls the DNA cleavage activity of λ integrase.” Mol Cell.2003; 12:187–198; Biswas et al., “A structural basis for allosteric control of DNA recombination by λ integrase.” Nature.2005; 435:1059–1066; and Warren et al., “Mutations in the amino-terminal domain of λ-integrase have differential effects on integrative and excisive recombination.” Mol Microbiol.2005; 55:1104–1112; the entire contents of each are incorporated by reference). Recombinase recognition sequence [0405] The term “recombinase recognition sequence”, or equivalently as “RRS” or “recombinase target sequence”, as used herein, refers to a nucleotide sequence target recognized by a recombinase and which undergoes strand exchange with another DNA molecule having a the RRS that results in excision, integration, inversion, or exchange of DNA fragments between the recombinase recognition sequences. Recombine or recombination [0406] The term “recombine,” or “recombination,” in the context of a nucleic acid modification (e.g., a genomic modification), is used to refer to the process by which two or more nucleic acid molecules, or two or more regions of a single nucleic acid molecule, are modified by the action of a recombinase protein (e.g., an inventive recombinase fusion protein provided herein). Recombination can result in, inter alia, the insertion, inversion, excision, or translocation of nucleic acids, e.g., in or between one or more nucleic acid molecules. recombinase recognition sequences Reverse transcriptase [0407] The term "reverse transcriptase" describes a class of polymerases characterized as RNA-dependent DNA polymerases. All known reverse transcriptases require a primer to synthesize a DNA transcript from an RNA template. Historically, reverse transcriptase has been used primarily to transcribe mRNA into cDNA which can then be cloned into a vector for further manipulation. Avian myoblastosis virus (AMV) reverse transcriptase was the first widely used RNA-dependent DNA polymerase (Verma, Biochim. Biophys. Acta 473:1 (1977)). The enzyme has 5ʹ-3ʹ RNA-directed DNA polymerase activity, 5ʹ-3ʹ DNA-directed DNA polymerase activity, and RNase H activity. RNase H is a processive 5ʹ and 3ʹ ribonuclease specific for the RNA strand for RNA-DNA hybrids (Perbal, A Practical Guide to Molecular Cloning, New York: Wiley & Sons (1984)). Errors in transcription cannot be corrected by reverse transcriptase because known viral reverse transcriptases lack the 3ʹ-5ʹ exonuclease activity necessary for proofreading (Saunders and Saunders, Microbial Genetics Applied to Biotechnology, London: Croom Helm (1987)). A detailed study of the activity of AMV reverse transcriptase and its associated RNase H activity has been presented by Berger et al., Biochemistry 22:2365-2372 (1983). Another reverse transcriptase which is used extensively in molecular biology is reverse transcriptase originating from Moloney murine leukemia virus (M-MLV). See, e.g., Gerard, G. R., DNA 5:271-279 (1986) and Kotewicz, M. L., et al., Gene 35:249-258 (1985). M-MLV reverse transcriptase substantially lacking in RNase H activity has also been described. See, e.g., U.S. Pat. No.5,244,797. The invention contemplates the use of any such reverse transcriptases, or variants or mutants thereof. [0408] In addition, the invention contemplates the use of reverse transcriptases which are error-prone, i.e., which may be referred to as error-prone reverse transcriptases or reverse transcriptases which do not support high fidelity incorporation of nucleotides during polymerization. During synthesis of the single-strand DNA flap based on the RT template integrated with the guide RNA, the error-prone reverse transcriptase can introduce one or more nucleotides which are mismatched with the RT template sequence, thereby introducing changes to the nucleotide sequence through erroneous polymerization of the single-strand DNA flap. These errors introduced during synthesis of the single strand DNA flap then become integrated into the double strand molecule through hybridization to the corresponding endogenous target strand, removal of the endogenous displaced strand, ligation, and then through one more round of endogenous DNA repair and/or sequencing processes. Reverse transcription [0409] As used herein, the term "reverse transcription" indicates the capability of enzyme to synthesize DNA strand (that is, complementary DNA or cDNA) using RNA as a template. In some embodiments, the reverse transcription can be “error-prone reverse transcription,” which refers to the properties of certain reverse transcriptase enzymes which are error-prone in their DNA polymerization activity. Recombinant [0410] The term “recombinant” as used herein in the context of proteins or nucleic acids refers to proteins or nucleic acids that do not occur in nature, but are the product of human engineering. For example, in some embodiments, a recombinant protein or nucleic acid molecule comprises an amino acid or nucleotide sequence that comprises at least one, at least two, at least three, at least four, at least five, at least six, or at least seven mutations as compared to any naturally occurring sequence. The fusion proteins (e.g., base editors) described herein are made recombinantly. Recombinant technology is familiar to those skilled in the art. Sense strand [0411] In genetics, a “sense” strand is the segment within double-stranded DNA that runs from 5' to 3', and which is complementary to the antisense strand of DNA, or template strand, which runs from 3' to 5'. In the case of a DNA segment that encodes a protein, the sense strand is the strand of DNA that has the same sequence as the mRNA, which takes the antisense strand as its template during transcription, and eventually undergoes (typically, not always) translation into a protein. The antisense strand is thus responsible for the RNA that is later translated to protein, while the sense strand possesses a nearly identical makeup to that of the mRNA. Note that for each segment of dsDNA, there will possibly be two sets of sense and antisense, depending on which direction one reads (since sense and antisense is relative to perspective). It is ultimately the gene product, or mRNA, that dictates which strand of one segment of dsDNA is referred to as sense or antisense. [0412] In the context of a PEgRNA, the first step is the synthesis of a single-strand complementary DNA (i.e., the 3ʹ ssDNA flap, which becomes incorporated) oriented in the 5ʹ to 3ʹ direction which is templated off of the PEgRNA extension arm. Whether the 3ʹ ssDNA flap should be regarded as a sense or antisense strand depends on the direction of transcription since it well accepted that both strands of DNA may serve as a template for transcription (but not at the same time). Thus, in some embodiments, the 3ʹ ssDNA flap (which overall runs in the 5ʹ to 3ʹ direction) will serve as the sense strand because it is the coding strand. In other embodiments, the 3ʹ ssDNA flap (which overall runs in the 5ʹ to 3ʹ direction) will serve as the antisense strand and thus, the template for transcription. Spacer sequence [0413] As used herein, the term “spacer sequence” in connection with a guide RNA or a PEgRNA refers to the portion of the guide RNA or PEgRNA of about 20 nucleotides which contains a nucleotide sequence that is complementary to the protospacer sequence in the target DNA sequence. The spacer sequence anneals to the protospacer sequence to form a ssRNA/ssDNA hybrid structure at the target site and a corresponding R loop ssDNA structure of the endogenous DNA strand that is complementary to the protospacer sequence. Split Cas9 [0414] A “split prime editor protein” or “split Cas9” refers to a fusion protein with a split site located within the Cas9 protein that is provided as an N-terminal portion (also referred to as an N-terminal half) and a C-terminal portion (also referred to as a C-terminal half) encoded by two separate nucleotide sequences. The polypeptides corresponding to the N- terminal portion and the C-terminal portion of the Cas9 protein may be combined (joined) to form a complete Cas9 protein. A Cas9 protein is known to consist of a bi-lobed structure linked by a disordered linker (e.g., as described in Nishimasu et al., Cell, Volume 156, Issue 5, pp.935–949, 2014, incorporated herein by reference). In some embodiments, the “split” occurs between the two lobes, generating two portions of a Cas9 protein, each containing one lobe. Split intein [0415] Although inteins are most frequently found as a contiguous domain, some exist in a naturally split form. In this case, the two fragments are expressed as separate polypeptides and must associate before splicing takes place, so-called protein trans-splicing. [0416] An exemplary split intein is the Ssp DnaE intein, which comprises two subunits, namely, DnaE-N and DnaE-C. The two different subunits are encoded by separate genes, namely dnaE-n and dnaE-c, which encode the DnaE-N and DnaE-C subunits, respectively. DnaE is a naturally occurring split intein in Synechocytis sp. PCC6803 and is capable of directing trans-splicing of two separate proteins, each comprising a fusion with either DnaE- N or DnaE-C. [0417] Additional naturally occurring or engineered split-intein sequences are known in the or can be made from whole-intein sequences described herein or those available in the art. Examples of split-intein sequences can be found in Stevens et al., “A promiscuous split intein with expanded protein engineering applications,” PNAS, 2017, Vol.114: 8538-8543; Iwai et al., “Highly efficient protein trans-splicing by a naturally split DnaE intein from Nostc punctiforme, FEBS Lett, 580: 1853-1858, each of which are incorporated herein by reference. Additional split intein sequences can be found, for example, in WO 2013/045632, WO 2014/055782, WO 2016/069774, and EP2877490, the contents each of which are incorporated herein by reference. [0418] In addition, protein splicing in trans has been described in vivo and in vitro (Shingledecker, et al., Gene 207:187 (1998), Southworth, et al., EMBO J.17:918 (1998); Mills, et al., Proc. Natl. Acad. Sci. USA, 95:3543-3548 (1998); Lew, et al., J. Biol. Chem., 273:15887-15890 (1998); Wu, et al., Biochim. Biophys. Acta 35732:1 (1998b), Yamazaki, et al., J. Am. Chem. Soc.120:5591 (1998), Evans, et al., J. Biol. Chem.275:9091 (2000); Otomo, et al., Biochemistry 38:16040-16044 (1999); Otomo, et al., J. Biolmol. NMR 14:105- 114 (1999); Scott, et al., Proc. Natl. Acad. Sci. USA 96:13638-13643 (1999)) and provides the opportunity to express a protein as to two inactive fragments that subsequently undergo ligation to form a functional product. Split prime Editor [0419] A “split prime editor” refers to a prime editor that is provided as an N-terminal portion (also referred to as a N-terminal half) and a C-terminal portion (also referred to as a C-terminal half) encoded by two separate nucleic acids. The polypeptides corresponding to the N-terminal portion and the C-terminal portion of the prime editor may be combined to form a complete prime editor. In some embodiments, for a prime editor that comprises a dCas9 or nCas9, the “split” is located in the dCas9 or nCas9 domain, at positions as described herein in the split prime editor. Accordingly, in some embodiments, the N-terminal portion of the prime editor contains the N-terminal portion of the split prime editor, and the C-terminal portion of the prime editor contains the C-terminal portion of the split prime editor. Similarly, intein-N or intein-C may be fused to the N-terminal portion or the C-terminal portion of the prime editor, respectively, for the joining of the N- and C-terminal portions of the prime editor to form a complete prime editor. Subject [0420] The term “subject,” as used herein, refers to an individual organism, for example, an individual mammal. In some embodiments, the subject is a human. In some embodiments, the subject is a non-human mammal. In some embodiments, the subject is a non-human primate. In some embodiments, the subject is a rodent (e.g., mouse, rat). In some embodiments, the subject is a domesticated animal. In some embodiments, the subject is a sheep, a goat, a cow, a cat, or a dog. In some embodiments, the subject is a research animal. In some embodiments, the subject is genetically engineered, e.g., a genetically engineered non-human subject. The subject may be of either sex and at any stage of development. Target site [0421] The term “target site” refers to a sequence within a nucleic acid molecule that is edited by a prime editor (PE) disclosed herein. The target site further refers to the sequence within a nucleic acid molecule to which a complex of the prime editor (PE) and gRNA binds. Transitions [0422] As used herein, “transitions” refer to the interchange of purine nucleobases (A ↔ G) or the interchange of pyrimidine nucleobases (C ↔ T). This class of interchanges involves nucleobases of similar shape. The compositions and methods disclosed herein are capable of inducing one or more transitions in a target DNA molecule. The compositions and methods disclosed herein are also capable of inducing both transitions and transversion in the same target DNA molecule. These changes involve A ↔ G, G ↔ A, C ↔ T, or T ↔ C. In the context of a double-strand DNA with Watson-Crick paired nucleobases, transversions refer to the following base pair exchanges: A:T ↔ G:C, G:G ↔ A:T, C:G ↔ T:A, or T:A↔ C:G. The compositions and methods disclosed herein are capable of inducing one or more transitions in a target DNA molecule. The compositions and methods disclosed herein are also capable of inducing both transitions and transversion in the same target DNA molecule, as well as other nucleotide changes, including deletions and insertions. Transversions [0423] As used herein, “transversions” refer to the interchange of purine nucleobases for pyrimidine nucleobases, or in the reverse and thus, involve the interchange of nucleobases with dissimilar shape. These changes involve T ↔ A, T↔ G, C ↔ G, C ↔ A, A ↔ T, A ↔ C, G ↔ C, and G ↔ T. In the context of a double-strand DNA with Watson-Crick paired nucleobases, transversions refer to the following base pair exchanges: T:A ↔ A:T, T:A ↔ G:C, C:G ↔ G:C, C:G ↔ A:T, A:T ↔ T:A, A:T ↔ C:G, G:C ↔ C:G, and G:C ↔ T:A. The compositions and methods disclosed herein are capable of inducing one or more transversions in a target DNA molecule. The compositions and methods disclosed herein are also capable of inducing both transitions and transversion in the same target DNA molecule, as well as other nucleotide changes, including deletions and insertions. Treatment, Treat, and Treating [0424] The terms “treatment,” “treat,” and “treating,” refer to a clinical intervention aimed to reverse, alleviate, delay the onset of, or inhibit the progress of a disease or disorder, or one or more symptoms thereof, as described herein. As used herein, the terms “treatment,” “treat,” and “treating” refer to a clinical intervention aimed to reverse, alleviate, delay the onset of, or inhibit the progress of a disease or disorder, or one or more symptoms thereof, as described herein. In some embodiments, treatment may be administered after one or more symptoms have developed and/or after a disease has been diagnosed. In other embodiments, treatment may be administered in the absence of symptoms, e.g., to prevent or delay onset of a symptom or inhibit onset or progression of a disease. For example, treatment may be administered to a susceptible individual prior to the onset of symptoms (e.g., in light of a history of symptoms and/or in light of genetic or other susceptibility factors). Treatment may also be continued after symptoms have resolved, for example, to prevent or delay their recurrence. Therapeutically-effective Amount [0425] “A therapeutically effective amount” as used herein refers to the amount of each therapeutic agent (e.g., prime editor, rAAV) described in the present disclosure required to confer therapeutic effect on the subject, either alone or in combination with one or more other therapeutic agents. Effective amounts vary, as recognized by those skilled in the art, depending on the particular condition being treated, the severity of the condition, the individual subject parameters including age, physical condition, size, gender, and weight, the duration of the treatment, the nature of concurrent therapy (if any), the specific route of administration and like factors within the knowledge and expertise of the health practitioner. These factors are well known to those of ordinary skill in the art and can be addressed with no more than routine experimentation. It is generally preferred that a maximum dose of the individual components or combinations thereof be used, that is, the highest safe dose according to sound medical judgment. It will be understood by those of ordinary skill in the art, however, that a subject may insist upon a lower dose or tolerable dose for medical reasons, psychological reasons or for virtually any other reasons. Empirical considerations, such as the half-life, generally will contribute to the determination of the dosage. For example, therapeutic agents that are compatible with the human immune system, such as polypeptides comprising regions from humanized antibodies or fully human antibodies, may be used to prolong half-life of the polypeptide and to prevent the polypeptide being attacked by the host's immune system. Upstream [0426] As used herein, the terms “upstream” and “downstream” are terms of relativity that define the linear position of at least two elements located in a nucleic acid molecule (whether single or double-stranded) that is orientated in a 5ʹ-to-3ʹ direction. In particular, a first element is upstream of a second element in a nucleic acid molecule where the first element is positioned somewhere that is 5’ to the second element. For example, a SNP is upstream of a Cas9-induced nick site if the SNP is on the 5’ side of the nick site. Conversely, a first element is downstream of a second element in a nucleic acid molecule where the first element is positioned somewhere that is 3’ to the second element. For example, a SNP is downstream of a Cas9-induced nick site if the SNP is on the 3’ side of the nick site. The nucleic acid molecule can be a DNA (double or single stranded). RNA (double or single stranded), or a hybrid of DNA and RNA. The analysis is the same for single strand nucleic acid molecule and a double strand molecule since the terms upstream and downstream are in reference to only a single strand of a nucleic acid molecule, except that one needs to select which strand of the double stranded molecule is being considered. Often, the strand of a double stranded DNA which can be used to determine the positional relativity of at least two elements is the “sense” or “coding” strand. In genetics, a “sense” strand is the segment within double-stranded DNA that runs from 5' to 3', and which is complementary to the antisense strand of DNA, or template strand, which runs from 3' to 5'. Thus, as an example, a SNP nucleobase is “downstream” of a promoter sequence in a genomic DNA (which is double-stranded) if the SNP nucleobase is on the 3' side of the promoter on the sense or coding strand. Variant [0427] As used herein the term “variant” should be taken to mean the exhibition of qualities that have a pattern that deviates from what occurs in nature, e.g., a variant Cas9 is a Cas9 comprising one or more changes in amino acid residues as compared to a wild type Cas9 amino acid sequence. The term “variant” encompasses homologous proteins having at least 75%, or at least 80%, or at least 85%, or at least 90%, or at least 95%, or at least 99% percent identity with a reference sequence and having the same or substantially the same functional activity or activities as the reference sequence. The term also encompasses mutants, truncations, or domains of a reference sequence, and which display the same or substantially the same functional activity or activities as the reference sequence. Vector [0428] The term “vector,” as used herein, refers to a nucleic acid that can be modified to encode a gene of interest and that is able to enter into a host cell, mutate and replicate within the host cell, and then transfer a replicated form of the vector into another host cell. Exemplary suitable vectors include viral vectors, such as retroviral vectors or bacteriophages and filamentous phage, and conjugative plasmids. Additional suitable vectors will be apparent to those of skill in the art based on the instant disclosure. Wild type [0429] As used herein the term “wild type” is a term of the art understood by skilled persons and means the typical form of an organism, strain, gene or characteristic as it occurs in nature as distinguished from mutant or variant forms. DETAILED DESCRIPTION [0430] Provided herein, are compositions (e.g.,vectors, recombinant viruses), cells, and kits comprising nucleic acids encoding a prime editor and/or rAAV particles comprising nucleic acids encoding a prime editor. In some embodiments, the prime editor comprises a nucleic acid programmable DNA binding protein (hereinafter “napDNAbp”). The prime editor may, in some cases, comprise a polymerase (e.g., DNA-dependent DNA polymerase or RNA-dependent DNA polymerase, such as, reverse transcriptase), or a variant thereof, which can be provided as a fusion protein with the napDNAbp or other programmable nuclease. The napDNAbp and polymerase may be fused using any technique known to those of skill in the art, for example, using a linker covalently conjugated to each protein. [0431] In some embodiments, a nucleic acid encoding the fusion protein is split (hereinafter “split prime editor”) into two or more components, for example, to enable its delivery to a cell (e.g., in vitro or in vivo). In some embodiments, the split prime editor is split at a site located within the napDNAbp domian (e.g., SpCas9). [0432] Without being bound by any particular theory, it is generally believed that napDNAbp domain (e.g., Cas9, SpCas9, etc.), has a N-terminal lobe and a C-terminal lobe linked by a disordered linker (e.g., as described in Nishimasu et al., Cell, Volume 156, Issue 5, pp.935–949, 2014, incorporated herein by reference). In some embodiments, the N- terminal portion of the split prime editor comprises the N-terminal lobe of a napDNAbp protein (e.g., SpCas9). In some embodiments, the C-terminal portion of the split prime editor comprises the C-terminal lobe of napDNAbp (e.g., SpCas9). In some embodiments, the N- terminal portion of the split prime editor comprises a portion of any one of SEQ ID NO: 14, 17, 19, 24-53, 55-65, 67-82, 84 that corresponds to amino acids 1-844 or 1-1024 in SEQ ID NO: 14. “1-844” means starting from amino acid 1 and ending at amino acid 844 and “1- 1024” means starting from amino acid 1 and ending at amino acid 1024. [0433] The C-terminal portion of the split prime editor can be joined with the N-terminal portion of the split prime editor, e.g., via intein-mediated protein splicing, to form a complete fusion protein (e.g., prime editor). In some embodiments, the C-terminal portion of the prime editor starts from where the N-terminal portion of the napDNAbp protein ends. As such, in some embodiments, the C-terminal portion of the split prime editor comprises a portion of any one of SEQ ID NOs: 14, 17, 19, 24-53, 55-65, 67-82, 84 that corresponds to amino acids 845-1368 or 1024-1368 of SEQ ID NO: 14. “845-1368” means starting at amino acid 845 and ending at amino acid 1368. [0434] napDNAbp variants may also be delivered to cells using the methods described herein. For example, a napDNAbp variant may also be “split” as described herein. A napDNAbp variant may comprise an amino acid sequence that is at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to any one of the napDNAbp sequences provided herein. In some embodiments, the napDNAbp variant comprises an amino acid sequence that is shorter or longer in length (e.g., by no more than 30%, no more than 25%, no more than 20%, no more than 15%, no more than 10%, no more than 5%, no more than 1% longer or shorter) than any of the Cas9 proteins provided herein. In some embodiments, fusion protein comprises a UGI domain. The UGI domain, according to some embodiments, may comprise an amino acid sequence that is shorter or longer in length (e.g., by no more than 200 amino acids, no more than 150 amino acids, no more than 100 amino acids, no more than 50 amino acids, no more than 10 amino acids, no more than 5 amino acids, or no more than 2 amino acids longer or shorter) than any of the Cas9 proteins provided herein. [0435] In some embodiments, the N-terminal portion of a split prime editor comprises an amino acid sequence that is at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to the corresponding portion of any one of the napDNAbp sequences provided herein. In some embodiments, the N-terminal portion of the split prime editor comprises an amino acid sequence that is shorter or longer in length (e.g., by no more than 30%, no more than 25%, no more than 20%, no more than 15%, no more than 10%, no more than 5%, no more than 1% longer or shorter) than the corresponding portion of any of the napDNAbp sequences provided herein. In some embodiments, the N-terminal portion of the split prime editor comprises an amino acid sequence that is shorter or longer in length (e.g., by no more than 200 amino acids, no more than 150 amino acids, no more than 100 amino acids, no more than 50 amino acids, no more than 10 amino acids, no more than 5 amino acids, or no more than 2 amino acids longer or shorter) than the corresponding portion of any of the napDNAbp domains provided herein. [0436] In some embodiments, the C-terminal portion of a split prime editor comprises an amino acid sequence that is at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to the corresponding portion of any one of the napDNAbp sequences provided herein. In some embodiments, the C-terminal portion of the split prime editor comprises an amino acid sequence that is shorter or longer in length (e.g., by no more than 30%, no more than 25%, no more than 20%, no more than 15%, no more than 10%, no more than 5%, no more than 1% longer or shorter) than the corresponding portion of any of the napDNAbp sequences provided herein. In some embodiments, the C-terminal portion of the split prime editor comprises an amino acid sequence that is shorter or longer in length (e.g., by no more than 200 amino acids, no more than 150 amino acids, no more than 100 amino acids, no more than 50 amino acids, no more than 10 amino acids, no more than 5 amino acids, or no more than 2 amino acids longer or shorter) than the corresponding portion of any of the napDNAbp sequences provided herein. [0437] In some embodiments, the napDNAbp variant is a SpCas9. In some embodiments, the N-terminal portion of the split prime editor comprises a mutation corresponding to a D10A mutation in SEQ ID NO: 14. In some embodiments, the N-terminal portion of the split prime editor comprises a mutation corresponding to a D10A mutation in SEQ ID NO: 14 and the C-terminal portion of the split prime editor comprises a mutation corresponding to a H840A mutation in SEQ ID NO: 14. In some embodiments, the N-terminal portion of the split prime editor comprises a mutation corresponding to a D10A mutation in SEQ ID NO: 14, and the C-terminal portion of the split prime editor comprises a histidine at the position corresponding to position 840 in SEQ ID NO:14. [0438] In some embodiments, to join the N-terminal portion of the napDNAbp and the C- terminal portion of the napDNAbp, an intein system may be used. In some embodiments, the N-terminal portion of the napDNAbp is fused to an intein-N. In some embodiments, the intein-N is fused to the C-terminus of the N-terminal portion of the napDNAbp to form a structure of NH ₂ -[N-terminal portion of napDNAbp]-[intein-N]-COOH. In some embodiments, the intein-N is encoded by the dnaE-n gene. In some embodiments, the intein- N comprises the amino acid sequence of SEQ ID NOs: 2-9 , 183-184, or 187-188. In some embodiments, the C-terminal portion of the napDNAbp is fused to an intein-C, and the intein- C is fused to the N-terminus of the C-terminal portion of the napDNAbp to form a structure of NH ₂ -[intein-C]-[C-terminal portion of napDNAbp]-COOH. In some embodiments, the intein-C is encoded by the dnaE-c gene. In some embodiments, the intein-C comprises the amino acid sequence of SEQ ID NO: 2-9, 185-186, or 189-190. Other split intein systems may also be used in the present disclosure and are known in the art. [0439] In some embodiments, the inteins are catatlytically active (e.g., N-intein and C- intein). As used herein, the phrase “catalytically active” refers to the ability of the inteins to undergo an autocatalytic protein splicing reaction. In other embodiments, inteins have been mutated to decrease the efficiency of the autocatalytic protein splicing reation. In some embodiments, compositions comprising mutated inteins exhibit a decrease in editing efficiency of about 40% compared to compositions comprising catalytically competent constructs. In other words, catalatyically compentent split-intein constructs recombine more efficiently than constructs comprising catalytically inactive inteins domains. Thus, in some embodiments, the spilt-intein constructs of the present disclosure comprise catalytically active inteins. [0440] In some embodiments, a complete split prime editor is formed when a N-terminal portion and the C-terminal portion of the napDNAbp are joined. In some embodiments, the split prime editor may comprise any one of the following structures: [0441] NH ₂ -[ polymerase]-[ napDNAbp]-COOH [0442] NH ₂ -[ napDNAbp]-[ polymerase]-COOH. [0443] Other architectures are also possible and are herein contemplated. [0444] In some embodiments, the first nucleotide sequence or the second nucleotide sequence (encoding either the split prime editor protein) is operably linked to a nucleotide sequence encoding at least one bipartite nuclear localization signal (NLS). For example, the first nucleotide sequence may be operably linked to a nucleotide sequence encoding one or more (e.g., 2, 3, 4, 5, or more) bipartite NLS. In some embodiments, the second nucleotide sequence may be operably linked to a nucleotide sequence encoding one or more (e.g., 2, 3, 4, 5, or more) bipartite NLSs. As such, the split prime editor formed by joining the N- terminal portion and the C-terminal portion may comprise one or more bipartite NLSs. For example, the split prime editor may comprise any one of the following structures (bNLS means one or more bipartite nuclear localization signals): [0445] NH ₂ -bNLS-[napDNAbp]-COOH [0446] NH ₂ -[napDNAbp]-bNLS-COOH [0447] NH2-[bNLS]-[napDNAbp]-[ polymerase]-COOH [0448] NH2-[napDNAbp]-[bNLS]-[ polymerase]-COOH [0449] NH2-[napDNAbp]-[ polymerase]-[bNLS]-COOH [0450] NH2-[bNLS]-[napDNAbp]-[bNLS]-[ polymerase]-COOH [0451] NH2-[napDNAbp]-[bNLS]-[ polymerase]-[bNLS]-COOH [0452] NH2-[bNLS]-[napDNAbp]-[polymerase]-[bNLS]-COOH [0453] NH2-[bNLS]-[napDNAbp]-[bNLS]-[polymerase]-[bNLS]-COOH [0454] NH2-[bNLS]-[ polymerase]-[ napDNAbp]-COOH [0455] NH2-[ polymerase]-[bNLS]-[ napDNAbp]-COOH [0456] NH2-[ polymerase]-[ napDNAbp]-[bNLS]-COOH [0457] NH2-[bNLS]-[ polymerase]-[bNLS]-[ napDNAbp]-COOH [0458] NH2-[ polymerase]-[bNLS]-[ napDNAbp]-[bNLS]-COOH [0459] NH2-[bNLS]-[polymerase]-[ napDNAbp]-[bNLS]-COOH [0460] NH2-[bNLS]-[ polymerase]-[bNLS]-[ napDNAbp]-[bNLS]-COOH [0461] Aspects of the present disclosure relate to compositions comprising split prime editors configured to optimize in vivo expression in a mammal. In some embodiments, the composition comprises a v1em split prime editor, a v2em split prime editor, and/or a v3em split prime editor. It should be understood by those of skill in the art, however, that the following descriptions are non-limiting and are intended only to provide the skilled artisan exemplary embodiments. Other embodiments (e.g., compositions and/or configurations) are also herein contemplated. [0462] In some embodiments, a composition comprising a v1em split prime editor comprises a first nucleotide sequence encoding a N-terminal portion with the structure NH2- EFS promoter-N-term PEmax (start codon-SV40NLS-SpCAS9)NpuN-SV40NLS-W3-bGH polyA-sgRNA (protospacer in bold)-human U6-COOH and a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion with the structure NH2- EFS promoter- SV40NLS- NpuC-C-term PEmax (SpCas9-RT-SV40NLS)-W3-bGH polyA- epegRNA (protospacer in bold)-human U6-COOH. [0463] In some embodiments, a composition comprising a v2em split prime editor has a first nucleotide sequence encoding a N-terminal portion of a prime editor fused at its C- terminus to an intein-N with the structure NH2-Cbh promoter-N-term PEmax (start codon- SV40NLS-SpCas9)-NpuN-SV40NLS-W3- bGH polyA-COOH, a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of the prime editor with the structure NH2-Cbh promoter-SV40NLS-NpuC-C-term PEmax (SpCas9-RT- SV40NLS)-W3-bGHpolyA-COOH, and a third nucleotide sequence encoding at least one pegRNA and at least one sgRNA with exemplary structure NH2-Cbh promoter-EGFP:KASH -sgRNA (protospacer in bold)-mouse U6-epegRNA (protospacer in bold)-human U6-COOH. [0464] In some embodiments, a composition comprising a v3em split prime editor has a first nucleotide sequence encoding a N-terminal portion with structure NH2-Cbh promoter-N- term PEmax (start codon-SV40NLS-SpCas9)-NpuN-SV40NLS-SV40 late polyA-COOH and a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion with the structure NH2-Cbh promoter-SV40NLS-NpuC-C-term PEmax (SpCas9-RT- SV40NLS)-SV40 late polyA-sgRNA (protospacer in bold)-mouse U6-epegRNA (protospacer in bold)-human U6-COOH [0465] In some embodiments, the disclosure relates to compositions comprising an rAAV encoding any one of the prime editors disclosed herein (e.g., v1em prime editors, a v2em prime editors, and/or a v3em prime editors). [0466] In some embodiments, a composition comprising a first rAAV particle comprising a first nucleotide sequence encoding a N-terminal portion of a v1em-PE (herein v1em-PE- rAAV) fused at its C-terminus to an intein-N with the structure ITR-EFS promoter-N-term PEmax (start codon-SV40NLS-SpCAS9)NpuN-SV40NLS-W3-bGH polyA-sgRNA (protospacer in bold)-human U6-ITR and a second recombinant rAAV particle comprising a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of v1em-PE with the structure ITR-EFS promoter- SV40NLS- NpuC-C-term PEmax (SpCas9-RT-SV40NLS)-W3-bGH polyA-epegRNA (protospacer in bold)-human U6-ITR. [0467] In some embodiments, a composition comprising a first rAAV particle comprising a first nucleotide sequence encoding a N-terminal portion of a v2em-PE (herein v2em-PE- rAAV) fused at its C-terminus to an intein-N with the structure ITR-Cbh promoter-N-term PEmax (start codon-SV40NLS-SpCas9)-NpuN-SV40NLS-W3- bGH polyA-ITR, a second recombinant rAAV particle comprising a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of v2em-PE with the structure ITR-Cbh promoter-SV40NLS-NpuC-C-term PEmax (SpCas9-RT-SV40NLS)-W3-bGHpolyA-ITR and a third nucleotide sequence encoding at least one pegRNA and at least one sgRNA with exemplary structure ITR-Cbh promoter-EGFP:KASH -sgRNA (protospacer in bold)-mouse U6-epegRNA (protospacer in bold)-human U6-ITR. [0468] In some embodiments, a composition comprising a first rAAV particle comprising a first nucleotide sequence encoding a N-terminal portion of a v3em-PE (herein v3em-PE- rAAV) fused at its C-terminus to an intein-N with the structure ITR-Cbh promoter-N-term PEmax (start codon-SV40NLS-SpCas9)-NpuN-SV40NLS-SV40 late polyA-ITR and a second recombinant rAAV particle comprising a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of v3em-PE with the structure ITR- Cbh promoter-SV40NLS-NpuC-C-term PEmax (SpCas9-RT-SV40NLS)-SV40 late polyA- sgRNA (protospacer in bold)-mouse U6-epegRNA (protospacer in bold)-human U6-ITR. [0469] In some embodiments, the prime editors disclosed herein require co-transduction of one or more rAAVs to deliver all necessary components for the expression and assembly of the split prime editors. For example, the v1em-PE-AAV and v3em-PE-AAV systems described herein require co-delivery of both a first rAAV particle comprising a first nucleotide sequence encoding a N-terminal portion of the prime editor fused at its C-terminus to an intein-N and a second rAAV particle comprising a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of the prime editor. [0470] The v2em-PE-AAV systems, on the other hand, requires co-delivery of three rAAV particles to enable expression and assembly of the v3em-PE system. Similar to the v1em-PE and v3em-PE systems, the v2em-PE system also requires a first rAAV particle and a second rAAV particle encoding the N-terminal and C-terminal portions of the prime editor, respectively. Contrary to the other described systems, the v2em-PE system is designed to deliver nucleotide constructs that are too large to fit within a typical rAAV. For example, in some embodiments, the v2em-PE system may comprises a Cbh promoter (e.g., 0.7kb), which is significantly larger than other promoters (e.g., compared to EFS promoter in v1em-PE systems), but is known to be a stronger and ubiquitous promoter capable of mediating efficient AAV-mediated based editing when injected systemically. Thus, in some embodiments, the pegRNA and sgRNA cassettes are moved to a third AAV vector. In some cases, the third AAV vector further comprises one or more promoters (e.g., human U6 promoter that drives pegRNA expression and/or a mouse U6 promoter that drives nicking sgRNA expression). [0471] Alternatively, or additionally, the inventors have discovered that the dual v3em- PE-AAV system may be used to deliver nucleotides with larger promoters by truncating the polymerase domain of the fusion protein. Without wishing to be bound by theory, it is believed that truncated MMLV reverse transcriptase variants that lack the RNAseH domain retain reverse transcriptase activity across of variety of edits (e.g., FIG.11). For instance, in some embodiments, the truncated MMLV RT retain greater than or equal to 50% RT activity, greater than or equal to 60% RT activity, greater than or equal to 70% RT activity, greater than or equal to 80% RT activity, greater than or equal to 90% RT activity, and greater than or equal to 95% RT activity, relative to the full length MMLV RT. In some embodiments, the truncated MMLV RT retains less than or equal to 95% RT activity, less than or equal to 90% RT activity, less than or equal to 80% RT activity, less than or equal to 70% RT activity, less than or equal to 60% RT activity, and less than or equal to 50% RT activity, relative to the full length MMLV RT. Combinations are also possible. Other ranges are also possible. [0472] In some embodiments, any one of the prime editor systems disclosed herein (e.g., v1em-PE editors, v2em-PE editors, and v3em-PE editors) comprise a split site within the napDNAbp domain of the fusion protein located at either position 844 or 1024. The N- terminal portion of the prime editor, in some embodiments, comprises a portion of any one of SEQ ID NO: 14, 17, 19, 24-53, 55-65, 67-82, 84 corresponding to amino acids 1-844 or 1- 1024 of SEQ ID NO: 14. [0473] In some embodiments, any one of the prime editor systems disclosed herein (e.g., v1em-PE editors, v2em-PE editors, and v3em-PE editors) comprise three N-terminal amino acid mutations at the C-terminal portion of the split prime editor. The mutations may comprise any amino acid known to those of skill in the art and in any combination thereof. In one set of embodiments, the mutation comprises changing the three N-terminal amino acids of the C-terminal extein from SEQ to SFQ, SFN, SEN, or CFN In some embodiments, the preferred composition comprises a napDNAbp split at amino acid 1024, wherein the N- terminal amino acid of the C-terminal portion comprises the CFN e.g., Cys-Phen-Asn) mutation. In other embodiments, the preferred composition comprises a napDNAbp split at amino acid 844, wherein the N-terminal amino acid of the C-terminal portion comprises the CFN e.g., Cys-Phen-Asn) mutation [0474] In some embodiments, any one of the rAAV compositions disclosed herein (e.g., v1em-PE-AAV, v2em-PE-AAV, and v3em-PE-AAV) comprise a split site within the napDNAbp domain of the fusion protein located at either position 844 or 1024. The N- terminal portion of the prime editor, in some embodiments, comprises a portion of any one of SEQ ID NO: 14, 17, 19, 24-53, 55-65, 67-82, 84 corresponding to amino acids 1-844 or 1- 1024 of SEQ ID NO: 14. [0475] In some embodiments, any one of the rAAV compositions disclosed here in (e.g., v1em-PE-AAV, v2em-PE-AAV, and v3em-PE-AAV) comprise three N-terminal amino acid mutations at the C-terminal portion of the split prime editor. The mutations may comprise any amino acid known to those of skill in the art and in any combination thereof. In one set of embodiments, the mutation comprises changing the three N-terminal amino acids from SEQ to SFQ, SFN, SEN, or CFN. In some embodiments, the preferred composition comprises a napDNAbp split at amino acid 1024, wherein the N-terminal amino acid of the C-terminal portion comprises the CFN e.g., Cys-Phen-Asn) mutation. In other embodiments, the preferred composition comprises a napDNAbp split at amino acid 844, wherein the N- terminal amino acid of the C-terminal portion comprises the CFN e.g., Cys-Phen-Asn) mutation. [0476] In some embodiments, any one of the prime editor systems disclosed herein (e.g., v1em-PE editors, v2em-PE editors, and v3em-PE editors) further comprise a nucleotide encoding a pegRNA. In some cases, the pegRNA is encoded within the first nucleotide sequence or the second nucleotide sequence, optionally, being operably linked to a promoter. Any pegRNA known to the skilled artisan may be used. A detailed description of pegRNAs may be found elsewhere herein. [0477] In some embodiments, the pegRNA guides the prime editor to an editing site. Without wishing to be bound by any particular theory, it is generally believed that the identity of the installed edit effects the susceptibility of the edit to repair by the DNA mismatch repair pathway (MMR). Thus, in some embodiments, the pegRNA is selected to encode edits that natively evade the MMR pathway. Any pegRNA sequence known in the art to instill edits that natively evade the MMR pathway are herein contemplated. For instance, in some embodiments, the pegRNA installs the following edits: (1) a +1 C-to-G edit, (2) a +1 C-to-G and +5 G-to-T edit, (3) a +2 G-to-C edit, (4) a +1 CTT insertion, (5) a +1 CCC insertion; and (6) a +1 GCA insertion at a target locus (e.g., Dnmt1 locus in mouse neuro 2a cells). In some embodiments, the pegRNA comprises a 3′ stabilizing motif. [0478] In some embodiments, the aforementioned pegRNA edits increase the average editing efficiency, from 7.6% to between 14% and 45%, relative to a previously validated +5 G-to-T edit (See FIG.7). In a preferred set of embodiments, the +2 G-to-C edit and +1 CCC insertion edit increase the average editing efficiency between 20% and 52%. Again, without wishing to be bound by theory, it is believed that the prime editing intermediates containing C-C mismatches and multiple contiguous insertions are poor substrates for MMR. [0479] The skilled artisan will understand that a prime editor comprising a pegRNA may be used to instill edits in a target locus that natively evade one or more repair pathways that decrease editing efficiency (e.g., MMR pathway). The edited site of interest, in some instances, may be the site of a mutation causing a disease; however, in other embodiments, the edited site may be any benign or silent bystander mutation known in the art to enhance in vitro and in vivo prime editing efficiency (e.g., the mammalian brain). [0480] In some embodiments, any one of the rAAV compositions disclosed herein (e.g., v1em-PE-AAV, v2em-PE-AAV, and v3em-PE-AAV) further comprises a nucleotide encoding a pegRNA. In some cases, the pegRNA is encoded within the first nucleotide sequence of the first rAAV particle or the second nucleotide sequence of the second rAAV particle, optionally, being operably linked to a promoter. [0481] In some embodiments, any one of the prime editors disclosed herein (e.g., v1em- PE editors, v2em-PE editors, and v3em-PE editors) further comprise a nucleotide encoding a polymerase. In some embodiments, the polymerase is a MMLV reverse transcriptase. In some embodiments, the MMLV reverse transcriptase is codon optimized for expression in a mammalian (e.g., human cell). [0482] In some embodiments, any one of the rAAV compositions disclosed herein (e.g., v1em-PE-AAV, v2em-PE-AAV, and v3em-PE-AAV) further comprise a nucleotide encoding a polymerase. In some embodiments, the polymerase is a MMLV reverse transcriptase. In some embodiments, the MMLV reverse transcriptase is codon optimized for expression in a mammalian (e.g., human cell). [0483] In some embodiments, any one of the prime editors disclosed herein (e.g., v1em- PE editors, v2em-PE editors, and v3em-PE editors) and/or any one of the rAAV compositions disclosed herein (e.g., v1em-PE-AAV, v2em-PE-AAV, and v3em-PE-AAV) further comprise a nucleotide encoding a nicking sgRNA. Without be bound by theory, it is believed that inclusion of a nicking sgRNA can increase prime editing efficiencies in cells by biasing cellular repair machinery to repair the non-edited strand. [0484] In some embodiments, in vivo editing using any of the systems, compositions, cells, and kits described herein may results in off-target effects. In some embodiments, off- target prime editing of off-target loci for pegRNA/sgRNA encoding a target edit using the v3em-PE3 prime editor or v3em-PE3-AAV systems is less than or equal to 0.1%, less than or equal to 0.05%, less than or equal to 0.01%, and less than or equal to 0.005% of the total sequencing reads with a specified target edit. In other embodiments, the percent indels for pegRNA/sgRNAs encoding a target edit using the v3em-PE3 prime editor or v3em-PE3- AAV systems is less than or equal to 1%, less than or equal to 0.5%, less than or equal to 0.1%, less than or equal to 0.05%, less than or equal to 0.01%, and less than 0.005% of the total sequencing reads with indels. [0485] In some embodiments, off-target prime editing of off-target loci for pegRNA/sgRNA encoding a target edit using the v1em-PE prime editor or v1em-PE-AAV systems described herein is less than or equal to 0.1%, less than or equal to 0.05%, less than or equal to 0.01%, and less than or equal to 0.005% of the total sequencing reads with a specified target edit. In other embodiments, the percent indels for pegRNA/sgRNAs encoding a target edit using the v1em-PE prime editor or v1em-PE-AAV systems is less than or equal to 1%, less than or equal to 0.5%, less than or equal to 0.1%, less than or equal to 0.05%, less than or equal to 0.01%, and less than 0.005% of the total sequencing reads with indels. [0486] In some embodiments, off-target prime editing of off-target loci for pegRNA/sgRNA encoding a target edit using the v2em-PE prime editor or v2em-PE-AAV systems described herein is less than or equal to 0.1%, less than or equal to 0.05%, less than or equal to 0.01%, and less than or equal to 0.005% of the total sequencing reads with a specified target edit. In other embodiments, the percent indels for pegRNA/sgRNAs encoding a target edit using the v2em-PE prime editor or v2em-PE-AAV systems is less than or equal to 1%, less than or equal to 0.5%, less than or equal to 0.1%, less than or equal to 0.05%, less than or equal to 0.01%, and less than 0.005% of the total sequencing reads with indels. [0487] Aspects of the present disclosure relate to a cell comprising any one of the prime editors (e.g., v1em-PE, v2em-PE, and v3em-PE) and/or rAAV particles (e.g., v1em-PE- AAV, v2em-PE-AAV, and v3em-PE-AAV) disclosed herein. In some cases, any one of the prime editors disclosed herein (e.g., v1em-PE, v2em-PE, and v3em-PE) may be complexed with a pharmaceutical excipient known in the art to enhance transfection of the nucleotide sequences into the cell. For example, in some embodiments, a first nucleotide sequence encoding a N-terminal portion of a prime editor fused at its C-terminus to an intein-N and a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of the prime editor may be encapsulated in a lipid nanoparticle or liposome, or complexed with PEI to form a nanoparticle, as described elsewhere herein (see Pharmaceutical Compositions Section). Thus, in some embodiments, the first nucleotide sequence, second nucleotide sequence, and third nucleotide sequence may be simultaneously encapsulated within a single nanoparticle or complex; or alternatively, each nucleotide sequence may be individually encapsulated and/or complexed to a carrier known to enhance transfection. Other combinations are also possible. [0488] Combinations of delivery methods are also possible. For example, in some cases, any one of the disclosed split prime editing systems disclosed herein may be delivered using any one of the AAV systems described herein. In some embodiments, a combination of AAV systems and other delivery systems may be used, for example, lipid nanoparticles, liposomes, lipid-polymer complexes and the like. [0489] Aspects of the present disclosure relate to methods of using any one of the compositions comprising the split prime editors described herein. [0490] In some embodiments, the method comprises systemically delivering any one of the prime editors disclosed herein to an organ of a subject in need thereof. Any method known to one of skill in the art resulting in systemic delivery may be used. Non-limiting examples, intravenous injection, retroorbital injection (RO), intravenous injection (IV), and intraosseous injection (IO). In other embodiments, the direct injection of the composition into an organ of interest is preferred (e.g., intracerebroventricular injection, ICV, into the brain). In some embodiments, the subject is a mammal (e.g., a human). In some cases, the mammal is a human. The subject may be of any age (e.g., neonatal, an infant, a child, a teenager, or an adult) or gender (e.g., male, female) [0491] In some embodiments, the method comprises delivery of compositions comprising any one of the rAAV systems described herein. In some cases, the rAAV construct may be configured to cross the blood-brain delivery, for example, to perform editing in the brain (e.g., to treat Alzheimer’s disease). [0492] In some embodiments, the methods described herein increase the in vivo editing efficiency in one or more organs. For example, in some embodiments, administering to a newborn mammal (e.g., a P0 mouse pup), via ICV injection, the prime editor comprising v1 PE3-AAV9 with W3 encoding +1 C-to-G, +1 CCC insertion, or +2 G-to-C edits results in approximately 6.1%, 25%, and 42% prime editing for +1 C-to-G, +1 CCC insertion and +2 G-to-C edits, respectively in the brain. [0493] In some embodiments, v3em-PE3-AAV9 systems result in higher editing efficiencies in adult bulk heart and skeletal muscle, relative to v2em-PE3-AAV9 systems. For instance, in some cases, prime editing is increase 2.1-fold and 4.9-fold, respectively for heart and skeletal muscle, for v3em compared to v2em-PE3-AAV9. [0494] In some embodiments, the v3em-PE3-AAV9 system results in higher editing efficiencies in adult bulk liver tissue, relative to v1em-PE3-AAV9 systems. For instance, in some cases, prime editing is increased between 14% and 46% (depending on the dose administered) for the v3em-PE3-AAV9 system, compared to between 0.1% and 5.7% prime editing for the v1em-PE3-AAV9 system. Other exemplary embodiments are described elsewhere herein (see Examples). [0495] In some embodiments, the method comprises preferentially editing a neuron or a plurality of neurons. In some cases, the method comprises editing a combination of neurons and astrocytes or a plurality of neurons and a plurality of astrocytes in a subject in need thereof. In some embodiments, the method comprises administering to the subject the v1em- PE-AAV system to preferentially edit a neuron or a plurality of neurons. In other embodiments, the method comprises administering to the subject the v3em-PE-AAV system to broadly edit multiple CNS cell types (e.g., neurons and astrocytes). [0496] In some embodiments, the disclosure relates to a method of contacting a cell with the composition of any one of the compositions described herein, wherein the contacting results in the delivery of the first nucleotide sequence and the second nucleotide sequence into the cell, and wherein the N-terminal portion of the prime editor and the C-terminal portion of the prime editor are joined to form a prime editor. In some embodiments, the method comprises delivery of a third nucleotide sequences into the cell. [0497] In some embodiments, the disclosure relates to methods for editing one or more target genes in an organ of interest. The method, according to some embodiments, comprises administering, to a subject in need, an N-terminal portion of a prime editor. In some embodiments, the method comprises administering, to a subject in need, a C-termial portion of the prime editor. The N-terminal portion and the C-terminal portion both comprise a nucleic acid, in some embodiments. [0498] In some embodiments, the ratio of the N-terminal portion to the C-terminal portion is 1:1. In other embodiments, the ratio of the N-terminal portion to the C-terminal portion is greater than or equal to 1:10, greater than or equal to 1:9, greater than or equal to 1:8, greater than or equal to 1:7, greater than or equal to 1:6, greater than or equal to 1:5, greater than or equal to 1:4, greater than or equal to 1:2, greater than or equal to 1:1. In some embodiments, the ratio of the N-terminal portion to the C-terminal portion is less than or equal to 1:1, less than or equal to 1:2; less than or equal to 1:3, less than or equal to 1:4, less than or equal to 1:5, less than or equal to 1:6, less than or equal to 1:7, less than or equal to 1:8, less than or equal to 1:9, or less than or equal to 1:10. [0499] In some embodiments, the ratio of the N-terminal portion to the C-terminal portion is greater than or equal to 1:1, greater than or equal to 2:1, greater than or equal to 3:1, greater than or equal to 4:1, greater than or equal to 5:1, greater than or equal to 6:1, greater than or equal to 7:1, greater than or equal to 8:1, greater than or equal to 9:1, or greater than or equal to 10:1. In other embodiments, the ratioof the N-terminal portion to the C-terminal portion is less than or equal to 10:1, less than or equal to 9:1, less than or equal to 8:1, less than or equal to 7:1, less than or equal to 6:1, less than or equal to 5:1, less than or equal to 4:1, less than or equal to 3:1, less than or equal to 2:1, or less than or equal to 1:1. [0500] In some embodiments, the disclosure relates to a method comprising administering to a subject in need thereof a therapeutically effective amount of any one of the compositions described and a pharmaceutically acceptable excipient. [0501] In some embodiments, the disclosure relates to a method of treating a disease (e.g., a neurological disease) in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of any one of the compositions described herein and a pharmaceutically acceptable excipient. For example, in some instances, the compositions described herein may be used to install the putatively protective APOE Christchurch (APOE3 R136S) coding variant, which is a G-to-T transversion mutation that cannot be installed via base editing and would be difficult to install in post-mitotic or slowly dividing cells via HDR. This mutation is of biological and therapeutic interest, as it has been observed in an individual who carried the risk-associated PSEN1 (presenilin 1) E280A mutation but who did not develop cognitive impairment until three decades after the expected age of clinical onset of Alzheimer’s Disease (AD) among PSEN1 E280A carriers. A subsequent study suggests the APOE Christchurch variant may be deleterious in other genetic contexts. The ability to precisely install the APOE Christchurch allele in relevant cells in vivo could help illuminate the mutation’s influence on AD pathology. [0502] Other exemplary therapeutic targets include, for example, the proprotein convertase subtilisin/kexin type 9 (e.g., Pcsk9), a therapeutically relevant gene involved in cholesterol homeostasis. Without wishing to be bound by theory, it is believed that installing a premature stop codon or splice site mutation in the Pcsk9 results in a reduction of Psck9 protein levels in the liver and a drop in circulating LDL cholesterol. Vectors [0503] Some aspects of the present disclosure relate to using recombinant virus vectors (e.g., adeno-associated virus vectors, adenovirus vectors, or herpes simplex virus vectors) for the delivery of the prime editors or components thereof described herein, e.g., the split prime editor, into a cell. In the case of a split-PE approach, the N-terminal portion of a PE fusion protein and the C-terminal portion of a PE fusion are delivered by separate recombinant virus vectors (e.g., adeno-associated virus vectors, adenovirus vectors, or herpes simplex virus vectors) into the same cell, since the full-length Cas9 protein or prime editors exceeds the packaging limit of various virus vectors, e.g., rAAV (~4.9 kb). [0504] Thus, in one embodiment, the disclosure contemplates vectors capable of delivering split prime editor fusion proteins, or split components thereof. In some embodiments, a composition for delivering the split prime editor protein or split prime editor into a cell (e.g., a mammalian cell, a human cell) is provided. In some embodiments, the composition of the present disclosure comprises: (i) a first recombinant adeno-associated virus (rAAV) particle comprising a first nucleotide sequence encoding a N-terminal portion of a napDNAbp or prime editor fused at its C-terminus to an intein-N; and (ii) a second recombinant adeno-associated virus (rAAV) particle comprising a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of the napDNAbp or prime editor. The rAAV particles of the present disclosure comprise a rAAV vector (i.e., a recombinant genome of the rAAV) encapsidated in the viral capsid proteins. [0505] In some embodiments, the rAAV vector comprises: (1) a heterologous nucleic acid region comprising the first or second nucleotide sequence encoding the N-terminal portion or C-terminal portion of a split prime editor protein or a split prime editor in any form as described herein, (2) one or more nucleotide sequences comprising a sequence that facilitates expression of the heterologous nucleic acid region (e.g., a promoter), and (3) one or more nucleic acid regions comprising a sequence that facilitate integration of the heterologous nucleic acid region (optionally with the one or more nucleic acid regions comprising a sequence that facilitates expression) into the genome of a cell. In some embodiments, viral sequences that facilitate integration comprise Inverted Terminal Repeat (ITR) sequences. In some embodiments, the first or second nucleotide sequence encoding the N-terminal portion or C-terminal portion of a split prime editor protein or a split prime editor is flanked on each side by an ITR sequence. In some embodiments, the nucleic acid vector further comprises a region encoding an AAV Rep protein as described herein, either contained within the region flanked by ITRs or outside the region. The ITR sequences can be derived from any AAV serotype (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) or can be derived from more than one serotype. In some embodiments, the ITR sequences are derived from AAV2 or AAV6. [0506] Thus, in some embodiments, the rAAV particles disclosed herein comprise at least one rAAV2 particle, rAAV6 particle, rAAV8 particle, rPHP.B particle, rPHP.eB particle, or rAAV9 particle, or a variant thereof. In particular embodiments, the disclosed rAAV particles are rPHP.B particles, rPHP.eB particles, rAAV9 particles. [0507] ITR sequences and plasmids containing ITR sequences are known in the art and commercially available (see, e.g., products and services available from Vector Biolabs, Philadelphia, PA; Cellbiolabs, San Diego, CA; Agilent Technologies, Santa Clara, Ca; and Addgene, Cambridge, MA; and Gene delivery to skeletal muscle results in sustained expression and systemic delivery of a therapeutic protein. Kessler PD, Podsakoff GM, Chen X, McQuiston SA, Colosi PC, Matelis LA, Kurtzman GJ, Byrne BJ. Proc Natl Acad Sci USA.1996 Nov 26;93(24):14082-7; and Curtis A. Machida. Methods in Molecular Medicine™. Viral Vectors for Gene Therapy Methods and Protocols.10.1385/1-59259-304- 6:201 © Humana Press Inc.2003. Chapter 10. Targeted Integration by Adeno-Associated Virus. Matthew D. Weitzman, Samuel M. Young Jr., Toni Cathomen and Richard Jude Samulski; U.S. Pat. Nos.5,139,941 and 5,962,313, all of which are incorporated herein by reference). [0508] In some embodiments, the rAAV vector of the present disclosure comprises one or more regulatory elements to control the expression of the heterologous nucleic acid region (e.g., promoters, transcriptional terminators, and/or other regulatory elements). In some embodiments, the first and/or second nucleotide sequence is operably linked to one or more (e.g., 1, 2, 3, 4, 5, or more) transcriptional terminators. Non-limiting examples of transcriptional terminators that may be used in accordance with the present disclosure include transcription terminators of the bovine growth hormone gene (bGH), human growth hormone gene (hGH), SV40, CW3, ϕ, or combinations thereof. The efficiencies of several transcriptional terminators have been tested to determine their respective effects in the expression level of the split prime editor protein or the split prime editor. In some embodiments, the transcriptional terminator used in the present disclosure is a bGH transcriptional terminator. In some embodiments, the rAAV vector further comprises a Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element (WPRE). In certain embodiments, the WPRE is a truncated WPRE sequence, such as “W3.” In some embodiments, the WPRE is inserted 5´ of the transcriptional terminator. Such sequences, when transcribed, create a tertiary structure which enhances expression, in particular, from viral vectors. [0509] In some embodiments, the vectors used herein may encode the PE fusion proteins, or any of the components thereof (e.g., napDNAbp, linkers, or polymerases). In addition, the vectors used herein may encode the PEgRNAs, and/or the accessory gRNA for second strand nicking. The vectors may be capable of driving expression of one or more coding sequences in a cell. In some embodiments, the cell may be a prokaryotic cell, such as, e.g., a bacterial cell. In some embodiments, the cell may be a eukaryotic cell, such as, e.g., a yeast, plant, insect, or mammalian cell. In some embodiments, the eukaryotic cell may be a mammalian cell. In some embodiments, the eukaryotic cell may be a rodent cell. In some embodiments, the eukaryotic cell may be a human cell. Suitable promoters to drive expression in different types of cells are known in the art. In some embodiments, the promoter may be wild-type. In other embodiments, the promoter may be modified for more efficient or efficacious expression. In yet other embodiments, the promoter may be truncated yet retain its function. For example, the promoter may have a normal size or a reduced size that is suitable for proper packaging of the vector into a virus. [0510] In some embodiments, the promoters that may be used in the prime editor vectors may be constitutive, inducible, or tissue-specific. In some embodiments, the promoters may be a constitutive promoters. Non-limiting exemplary constitutive promoters include cytomegalovirus immediate early promoter (CMV), simian virus (SV40) promoter, adenovirus major late (MLP) promoter, Rous sarcoma virus (RSV) promoter, mouse mammary tumor virus (MMTV) promoter, phosphoglycerate kinase (PGK) promoter, elongation factor-alpha (EFla) promoter, ubiquitin promoters, actin promoters, tubulin promoters, immunoglobulin promoters, a functional fragment thereof, or a combination of any of the foregoing. In some embodiments, the promoter may be a CMV promoter. In some embodiments, the promoter may be a truncated CMV promoter. In other embodiments, the promoter may be an EFla promoter. In some embodiments, the promoter may be an inducible promoter. Non-limiting exemplary inducible promoters include those inducible by heat shock, light, chemicals, peptides, metals, steroids, antibiotics, or alcohol. In some embodiments, the inducible promoter may be one that has a low basal (non-induced) expression level, such as, e.g., the Tet-On® promoter (Clontech). In some embodiments, the promoter may be a tissue-specific promoter. In some embodiments, the tissue-specific promoter is exclusively or predominantly expressed in liver tissue. Non-limiting exemplary tissue-specific promoters include B29 promoter, CD14 promoter, CD43 promoter, CD45 promoter, CD68 promoter, desmin promoter, elastase- 1 promoter, endoglin promoter, fibronectin promoter, Flt-1 promoter, GFAP promoter, GPIIb promoter, ICAM- 2 promoter, INF-β promoter, Mb promoter, Nphsl promoter, OG-2 promoter, SP-B promoter, SYN1 promoter, and WASP promoter. [0511] In some embodiments, the first nucleotide sequence, second nucleotide sequence, and optionally, a third nucleotide sequence are on the same nucleic acid vector. In some embodiments, the first nucleotide sequence, second nucleotide sequence, and optionally, the third nucleotide sequence are on different nucleic acid vectors. In some embodiments, the vector is a plasmid. In some embodiments, the nucleic acid vector is a recombinant genome of a rAAV. In some embodiments, the nucleic acid vector is the genome of an adeno- associated virus packaged in a rAAV particle. In some embodiments, the first and/or the second nucleotide sequence is operably linked to a promoter. In some embodiments, the nucleic acid vector further comprises a nucleotide sequence encoding one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) gRNAs operably linked to a promoter. In some embodiments, the promoter is a constitutive promoter. In some embodiments, the promoter is an inducible promoter. [0512] An inducible promoter of the present disclosure may be induced by (or repressed by) one or more physiological condition(s), such as changes in light, pH, temperature, radiation, osmotic pressure, saline gradients, cell surface binding, and the concentration of one or more extrinsic or intrinsic inducing agent(s). An extrinsic inducer signal or inducing agent may comprise, without limitation, amino acids and amino acid analogs, saccharides and polysaccharides, nucleic acids, protein transcriptional activators and repressors, cytokines, toxins, petroleum-based compounds, metal containing compounds, salts, ions, enzyme substrate analogs, hormones, or combinations thereof. [0513] Inducible promoters of the present disclosure include any inducible promoter described herein or known to one of ordinary skill in the art. Examples of inducible promoters include, without limitation, chemically/biochemically-regulated and physically- regulated promoters such as alcohol-regulated promoters, tetracycline-regulated promoters (e.g., anhydrotetracycline (aTc)-responsive promoters and other tetracycline-responsive promoter systems, which include a tetracycline repressor protein (tetR), a tetracycline operator sequence (tetO) and a tetracycline transactivator fusion protein (tTA)), steroid- regulated promoters (e.g., promoters based on the rat glucocorticoid receptor, human estrogen receptor, moth ecdysone receptors, and promoters from the steroid/retinoid/thyroid receptor superfamily), metal-regulated promoters (e.g., promoters derived from metallothionein (proteins that bind and sequester metal ions) genes from yeast, mouse and human), pathogenesis-regulated promoters (e.g., induced by salicylic acid, ethylene or benzothiadiazole (BTH)), temperature/heat-inducible promoters (e.g., heat shock promoters), and light-regulated promoters (e.g., light responsive promoters from plant cells). Other inducible promoter systems are known in the art and may be used in accordance with the present disclosure. [0514] In some embodiments, inducible promoters of the present disclosure function in prokaryotic cells (e.g., bacterial cells). Examples of inducible promoters for use prokaryotic cells include, without limitation, bacteriophage promoters (e.g. Pls1con, T3, T7, SP6, PL) and bacterial promoters (e.g., Pbad, PmgrB, Ptrc2, Plac/ara, Ptac, Pm), or hybrids thereof (e.g. PLlacO, PLtetO). Examples of bacterial promoters for use in accordance with the present disclosure include, without limitation, positively regulated E. coli promoters, such as positively regulated σ70 promoters (e.g., inducible pBad/araC promoter, Lux cassette right promoter, modified lamdba Prm promote, plac Or2-62 (positive), pBad/AraC with extra REN sites, pBad, P(Las) TetO, P(Las) CIO, P(Rhl), Pu, FecA, pRE, cadC, hns, pLas, pLux), σS promoters (e.g., Pdps), σ32 promoters (e.g., heat shock), and σ54 promoters (e.g., glnAp2); negatively regulated E. coli promoters such as negatively regulated σ70 promoters (e.g., Promoter (PRM+), modified lamdba Prm promoter, TetR - TetR-4C P(Las) TetO, P(Las) CIO, P(Lac) IQ, RecA_DlexO_DLacO1, dapAp, FecA, Pspac-hy, pcI, plux-cI, plux-lac, CinR, CinL, glucose controlled, modified Pr, modified Prm+, FecA, Pcya, rec A (SOS), Rec A (SOS), EmrR_regulated, BetI_regulated, pLac_lux, pTet_Lac, pLac/Mnt, pTet/Mnt, LsrA/cI, pLux/cI, LacI, LacIQ, pLacIQ1, pLas/cI, pLas/Lux, pLux/Las, pRecA with LexA binding site, reverse BBa_R0011, pLacI/ara-1, pLacIq, rrnB P1, cadC, hns, PfhuA, pBad/araC, nhaA, OmpF, RcnR), σS promoters (e.g., Lutz-Bujard LacO with alternative sigma factor σ38), σ32 promoters (e.g., Lutz-Bujard LacO with alternative sigma factor σ32), and σ54 promoters (e.g., glnAp2); negatively regulated B. subtilis promoters such as repressible B. subtilis σA promoters (e.g., Gram-positive IPTG-inducible, Xyl, hyper-spank) and σB promoters. Other inducible microbial promoters may be used in accordance with the present disclosure. [0515] In some embodiments, inducible promoters of the present disclosure function in eukaryotic cells (e.g., mammalian cells). Examples of inducible promoters for use eukaryotic cells include, without limitation, chemically-regulated promoters (e.g., alcohol-regulated promoters, tetracycline-regulated promoters, steroid-regulated promoters, metal-regulated promoters, and pathogenesis-related (PR) promoters) and physically-regulated promoters (e.g., temperature-regulated promoters and light-regulated promoters). [0516] In some embodiments, the prime editor vectors (e.g., including any vectors encoding the prime editor fusion protein and/or the PEgRNAs, and/or the accessory second strand nicking gRNAs) may comprise inducible promoters to start expression only after it is delivered to a target cell. Non-limiting exemplary inducible promoters include those inducible by heat shock, light, chemicals, peptides, metals, steroids, antibiotics, or alcohol. In some embodiments, the inducible promoter may be one that has a low basal (non-induced) expression level, such as, e.g., the Tet-On® promoter (Clontech). [0517] In additional embodiments, the prime editor vectors (e.g., including any vectors encoding the prime editor fusion protein and/or the PEgRNAs, and/or the accessory second strand nicking gRNAs) may comprise tissue- specific promoters to start expression only after it is delivered into a specific tissue. Non-limiting exemplary tissue-specific promoters include B29 promoter, CD14 promoter, CD43 promoter, CD45 promoter, CD68 promoter, desmin promoter, elastase- 1 promoter, endoglin promoter, fibronectin promoter, Flt-1 promoter, GFAP promoter, GPIIb promoter, ICAM- 2 promoter, INF-β promoter, Mb promoter, Nphsl promoter, OG-2 promoter, SP-B promoter, SYN1 promoter, and WASP promoter. [0518] In some embodiments, the nucleotide sequence encoding the PEgRNA (or any guide RNAs used in connection with prime editing) may be operably linked to at least one transcriptional or translational control sequence. In some embodiments, the nucleotide sequence encoding the guide RNA may be operably linked to at least one promoter. In some embodiments, the promoter may be recognized by RNA polymerase III (Pol III). Non- limiting examples of Pol III promoters include U6, HI and tRNA promoters. In some embodiments, the nucleotide sequence encoding the guide RNA may be operably linked to a mouse or human U6 promoter. In other embodiments, the nucleotide sequence encoding the guide RNA may be operably linked to a mouse or human HI promoter. In some embodiments, the nucleotide sequence encoding the guide RNA may be operably linked to a mouse or human tRNA promoter. In embodiments with more than one guide RNA, the promoters used to drive expression may be the same or different. In some embodiments, the nucleotide encoding the crRNA of the guide RNA and the nucleotide encoding the tracr RNA of the guide RNA may be provided on the same vector. In some embodiments, the nucleotide encoding the crRNA and the nucleotide encoding the tracr RNA may be driven by the same promoter. In some embodiments, the crRNA and tracr RNA may be transcribed into a single transcript. For example, the crRNA and tracr RNA may be processed from the single transcript to form a double-molecule guide RNA. Alternatively, the crRNA and tracr RNA may be transcribed into a single-molecule guide RNA. [0519] In some embodiments, the nucleotide sequence encoding the guide RNA may be located on the same vector comprising the nucleotide sequence encoding the PE fusion protein. In some embodiments, expression of the guide RNA and of the PE fusion protein may be driven by their corresponding promoters. In some embodiments, expression of the guide RNA may be driven by the same promoter that drives expression of the PE fusion protein. In some embodiments, the guide RNA and the PE fusion protein transcript may be contained within a single transcript. For example, the guide RNA may be within an untranslated region (UTR) of the Cas9 protein transcript. In some embodiments, the guide RNA may be within the 5' UTR of the PE fusion protein transcript. In other embodiments, the guide RNA may be within the 3' UTR of the PE fusion protein transcript. In some embodiments, the intracellular half-life of the PE fusion protein transcript may be reduced by containing the guide RNA within its 3' UTR and thereby shortening the length of its 3' UTR. In additional embodiments, the guide RNA may be within an intron of the PE fusion protein transcript. In some embodiments, suitable splice sites may be added at the intron within which the guide RNA is located such that the guide RNA is properly spliced out of the transcript. In some embodiments, expression of the Cas9 protein and the guide RNA in close proximity on the same vector may facilitate more efficient formation of the CRISPR complex. [0520] The prime editor vector system may comprise one vector, or two vectors, or three vectors, or four vectors, or five vector, or more. In some embodiments, the vector system may comprise one single vector, which encodes both the PE fusion protein and PEgRNA. In other embodiments, the vector system may comprise two vectors, wherein one vector encodes the PE fusion protein and the other encodes the PEgRNA. In additional embodiments, the vector system may comprise three vectors, wherein the third vector encodes the second strand nicking gRNA used in the herein methods. [0521] In some embodiments, the composition comprising the rAAV particle (in any form contemplated herein) further comprises a pharmaceutically acceptable carrier. In some embodiments, the composition is formulated in appropriate pharmaceutical vehicles for administration to human or animal subjects. [0522] Some examples of materials which can serve as pharmaceutically-acceptable carriers include: (1) sugars, such as lactose, glucose and sucrose; (2) starches, such as corn starch and potato starch; (3) cellulose, and its derivatives, such as sodium carboxymethyl cellulose, methylcellulose, ethyl cellulose, microcrystalline cellulose and cellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) lubricating agents, such as magnesium stearate, sodium lauryl sulfate and talc; (8) excipients, such as cocoa butter and suppository waxes; (9) oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols, such as propylene glycol; (11) polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol (PEG); (12) esters, such as ethyl oleate and ethyl laurate; (13) agar; (14) buffering agents, such as magnesium hydroxide and aluminum hydroxide; (15) alginic acid; (16) pyrogen-free water; (17) isotonic saline; (18) Ringer’s solution; (19) ethyl alcohol; (20) pH buffered solutions; (21) polyesters, polycarbonates and/or polyanhydrides; (22) bulking agents, such as polypeptides and amino acids (23) serum component, such as serum albumin, HDL and LDL; (22) C2-C12 alcohols, such as ethanol; and (23) other non-toxic compatible substances employed in pharmaceutical formulations. Wetting agents, coloring agents, release agents, coating agents, sweetening agents, flavoring agents, perfuming agents, preservative and antioxidants can also be present in the formulation. The terms such as “excipient”, “carrier”, “pharmaceutically acceptable carrier” or the like are used interchangeably herein. Recombinant Adeno-associated Virus (rAAV) [0523] Some aspects of the present disclosure relate to using recombinant adeno- associated virus vectors for the delivery of a split prime editor into a cell. The N-terminal portion of the prime editor and the C-terminal portion of the prime editor are delivered by separate rAAV vectors or particles into the same cell, since the full-length prime editor exceeds the packaging limit of rAAV (~4.9 kb). [0524] As such, in some embodiments, a composition for delivering the split prime editor protein into a cell (e.g., a mammalian cell, a human cell) is provided. In some embodiments, the composition of the present disclosure comprises: (i) a first recombinant adeno-associated virus (rAAV) particle comprising a first nucleotide sequence encoding a N-terminal portion of split prime editor fused at its C-terminus to an intein-N; and (ii) a second recombinant adeno-associated virus (rAAV) particle comprising a second nucleotide sequence encoding an intein-C fused to the N-terminus of a C-terminal portion of the prime editor. The rAAV particles of the present disclosure comprise a rAAV vector (i.e., a recombinant genome of the rAAV) encapsidated in the viral capsid proteins. [0525] In some embodiments, the rAAV vector comprises: (1) a heterologous nucleic acid region comprising the first or second nucleotide sequence encoding the N-terminal portion or C-terminal portion of a split prime editor in any form as described herein, (2) one or more nucleotide sequences comprising a sequence that facilitates expression of the heterologous nucleic acid region (e.g., a promoter), and (3) one or more nucleic acid regions comprising a sequence that facilitate integration of the heterologous nucleic acid region (optionally with the one or more nucleic acid regions comprising a sequence that facilitates expression) into the genome of a cell. In some embodiments, viral sequences that facilitate integration comprise Inverted Terminal Repeat (ITR) sequences. In some embodiments, the first or second nucleotide sequence encoding the N-terminal portion or C-terminal portion of a split prime editor is flanked on each side by an ITR sequence. In some embodiments, the nucleic acid vector further comprises a region encoding an AAV Rep protein as described herein, either contained within the region flanked by ITRs or outside the region. The ITR sequences can be derived from any AAV serotype (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) or can be derived from more than one serotype. In some embodiments, the ITR sequences are derived from AAV2 or AAV6. [0526] ITR sequences and plasmids containing ITR sequences are known in the art and commercially available (see, e.g., products and services available from Vector Biolabs, Philadelphia, PA; Cellbiolabs, San Diego, CA; Agilent Technologies, Santa Clara, Ca; and Addgene, Cambridge, MA; and Gene delivery to skeletal muscle results in sustained expression and systemic delivery of a therapeutic protein. Kessler PD, Podsakoff GM, Chen X, McQuiston SA, Colosi PC, Matelis LA, Kurtzman GJ, Byrne BJ. Proc Natl Acad Sci USA.1996 Nov 26;93(24):14082-7; and Curtis A. Machida. Methods in Molecular Medicine™. Viral Vectors for Gene Therapy Methods and Protocols. 10.1385/1-59259-304- 6:201 © Humana Press Inc.2003. Chapter 10. Targeted Integration by Adeno-Associated Virus. Matthew D. Weitzman, Samuel M. Young Jr., Toni Cathomen and Richard Jude Samulski; U.S. Pat. Nos.5,139,941 and 5,962,313, all of which are incorporated herein by reference). Exemplary ITR sequences are provided in the Description of the Sequences Section (SEQ ID NOs: 10-13). [0527] In some embodiments, the rAAV vector of the present disclosure comprises one or more regulatory elements to control the expression of the heterologous nucleic acid region (e.g., promoters, transcriptional terminators, and/or other regulatory elements). In some embodiments, the first and/or second nucleotide sequence is operably linked to one or more (e.g., 1, 2, 3, 4, 5, or more) transcriptional terminators. Non-limiting examples of transcriptional terminators that may be used in accordance with the present disclosure include transcription terminators of the bovine growth hormone gene (bGH), human growth hormone gene (hGH), SV40, CW3, ϕ, or combinations thereof. The efficiencies of several transcriptional terminators have been tested to determine their respective effects in the expression level of the split prime editor protein. In some embodiments, the transcriptional terminator used in the present disclosure is a bGH transcriptional terminator. In some embodiments, the rAAV vector further comprises a Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element (WPRE). In some embodiments, the WPRE is inserted 5´ of the transcriptional terminator. napDNAbp [0528] The prime editors and trans prime editors described herein may comprise a nucleic acid programmable DNA binding protein (napDNAbp). [0529] In one aspect, a napDNAbp can be associated with or complexed with at least one guide nucleic acid (e.g., guide RNA or a PEgRNA), which localizes the napDNAbp to a DNA sequence that comprises a DNA strand (i.e., a target strand) that is complementary to the guide nucleic acid, or a portion thereof (e.g., the spacer of a guide RNA which anneals to the protospacer of the DNA target). In other words, the guide nucleic-acid “programs” the napDNAbp (e.g., Cas9 or equivalent) to localize and bind to complementary sequence of the protospacer in the DNA. [0530] Any suitable napDNAbp may be used in the prime editors described herein. In various embodiments, the napDNAbp may be any Class 2 CRISPR-Cas system, including any type II, type V, or type VI CRISPR-Cas enzyme. Given the rapid development of CRISPR-Cas as a tool for genome editing, there have been constant developments in the nomenclature used to describe and/or identify CRISPR-Cas enzymes, such as Cas9 and Cas9 orthologs. This application references CRISPR-Cas enzymes with nomenclature that may be old and/or new. The skilled person will be able to identify the specific CRISPR-Cas enzyme being referenced in this Application based on the nomenclature that is used, whether it is old (i.e., “legacy”) or new nomenclature. CRISPR-Cas nomenclature is extensively discussed in Makarova et al., “Classification and Nomenclature of CRISPR-Cas Systems: Where from Here?,” The CRISPR Journal, Vol.1. No.5, 2018, the entire contents of which are incorporated herein by reference. The particular CRISPR-Cas nomenclature used in any given instance in this Application is not limiting in any way and the skilled person will be able to identify which CRISPR-Cas enzyme is being referenced. [0531] For example, the following type II, type V, and type VI Class 2 CRISPR-Cas enzymes have the following art-recognized old (i.e., legacy) and new names. Each of these enzymes, and/or variants thereof, may be used with the prime editors described herein:

[0569] * See Makarova et al., The CRISPR Journal, Vol.1, No.5, 2018 [0570] Without being bound by theory, the mechanism of action of certain napDNAbp contemplated herein includes the step of forming an R-loop whereby the napDNAbp induces the unwinding of a double-strand DNA target, thereby separating the strands in the region bound by the napDNAbp. The guide RNA spacer then hybridizes to the “target strand” at the protospacer sequence. This displaces a “non-target strand” that is complementary to the target strand, which forms the single strand region of the R-loop. In some embodiments, the napDNAbp includes one or more nuclease activities, which then cut the DNA leaving various types of lesions. For example, the napDNAbp may comprises a nuclease activity that cuts the non-target strand at a first location, and/ or cuts the target strand at a second location. Depending on the nuclease activity, the target DNA can be cut to form a “double-stranded break” whereby both strands are cut. In other embodiments, the target DNA can be cut at only a single site, i.e., the DNA is “nicked” on one strand. Exemplary napDNAbp with different nuclease activities include “Cas9 nickase” (“nCas9”) and a deactivated Cas9 having no nuclease activities (“dead Cas9” or “dCas9”). [0571] The below description of various napDNAbps which can be used in connection with the presently disclose prime editors is not meant to be limiting in any way. The prime editors may comprise the canonical SpCas9, or any ortholog Cas9 protein, or any variant Cas9 protein—including any naturally occurring variant, mutant, or otherwise engineered version of Cas9—that is known or which can be made or evolved through a directed evolutionary or otherwise mutagenic process. In various embodiments, the Cas9 or Cas9 variants have a nickase activity, i.e., only cleave of strand of the target DNA sequence. In other embodiments, the Cas9 or Cas9 variants have inactive nucleases, i.e., are “dead” Cas9 proteins. Other variant Cas9 proteins that may be used are those having a smaller molecular weight than the canonical SpCas9 (e.g., for easier delivery) or having modified or rearranged primary amino acid structure (e.g., the circular permutant formats). [0572] The prime editors described herein may also comprise Cas9 equivalents, including Cas12a (Cpf1) and Cas12b1 proteins which are the result of convergent evolution. The napDNAbps used herein (e.g., SpCas9, Cas9 variant, or Cas9 equivalents) may also may also contain various modifications that alter/enhance their PAM specifities. Lastly, the application contemplates any Cas9, Cas9 variant, or Cas9 equivalent which has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.9% sequence identity to a reference Cas9 sequence, such as a references SpCas9 canonical sequence or a reference Cas9 equivalent (e.g., Cas12a (Cpf1)). [0573] The napDNAbp can be a CRISPR (clustered regularly interspaced short palindromic repeat)-associated nuclease. As outlined above, CRISPR is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and a Cas9 protein. The tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA. Subsequently, Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer. The target strand not complementary to crRNA is first cut endonucleolytically, then trimmed 3´-5′ exonucleolytically. In nature, DNA-binding and cleavage typically requires protein and both RNAs. However, single guide RNAs (“sgRNA”, or simply “gRNA”) can be engineered so as to incorporate aspects of both the crRNA and tracrRNA into a single RNA species. See, e.g., Jinek M. et al., Science 337:816-821(2012), the entire contents of which is hereby incorporated by reference. [0574] In some embodiments, the napDNAbp directs cleavage of one or both strands at the location of a target sequence, such as within the target sequence and/or within the complement of the target sequence. In some embodiments, the napDNAbp directs cleavage of one or both strands within about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 50, 100, 200, 500, or more base pairs from the first or last nucleotide of a target sequence. In some embodiments, a vector encodes a napDNAbp that is mutated to with respect to a corresponding wild-type enzyme such that the mutated napDNAbp lacks the ability to cleave one or both strands of a target polynucleotide containing a target sequence. For example, an aspartate-to-alanine substitution (D10A) in the RuvC I catalytic domain of Cas9 from S. pyogenes converts Cas9 from a nuclease that cleaves both strands to a nickase (cleaves a single strand). Other examples of mutations that render Cas9 a nickase include, without limitation, H840A, N854A, and N863A in reference to the canonical SpCas9 sequence, or to equivalent amino acid positions in other Cas9 variants or Cas9 equivalents. [0575] As used herein, the term “Cas protein” refers to a full-length Cas protein obtained from nature, a recombinant Cas protein having a sequences that differs from a naturally occurring Cas protein, or any fragment of a Cas protein that nevertheless retains all or a significant amount of the requisite basic functions needed for the disclosed methods, i.e., (i) possession of nucleic-acid programmable binding of the Cas protein to a target DNA, and (ii) ability to nick the target DNA sequence on one strand. The Cas proteins contemplated herein embrace CRISPR Cas 9 proteins, as well as Cas9 equivalents, variants (e.g., Cas9 nickase (nCas9) or nuclease inactive Cas9 (dCas9)) homologs, orthologs, or paralogs, whether naturally occurring or non-naturally occurring (e.g., engineered or recombinant), and may include a Cas9 equivalent from anyClass 2 CRISPR system (e.g., type II, V, VI), including Cas12a (Cpf1), Cas12e (CasX), Cas12b1 (C2c1), Cas12b2, Cas12c (C2c3), C2c4, C2c8, C2c5, C2c10, C2c9 Cas13a (C2c2), Cas13d, Cas13c (C2c7), Cas13b (C2c6), and Cas13b. Further Cas-equivalents are described in Makarova et al., “C2c2 is a single- component programmable RNA-guided RNA-targeting CRISPR effector,” Science 2016; 353(6299) and Makarova et al., “Classification and Nomenclature of CRISPR-Cas Systems: Where from Here?,” The CRISPR Journal, Vol.1. No.5, 2018, the contents of which are incorporated herein by reference. [0576] The terms “Cas9” or “Cas9 nuclease” or “Cas9 moiety” or “Cas9 domain” embrace any naturally occurring Cas9 from any organism, any naturally-occurring Cas9 equivalent or functional fragment thereof, any Cas9 homolog, ortholog, or paralog from any organism, and any mutant or variant of a Cas9, naturally-occurring or engineered. The term Cas9 is not meant to be particularly limiting and may be referred to as a “Cas9 or equivalent.” Exemplary Cas9 proteins are further described herein and/or are described in the art and are incorporated herein by reference. The present disclosure is unlimited with regard to the particular Cas9 that is employed in the prime editor (PE) of the invention. [0577] As noted herein, Cas9 nuclease sequences and structures are well known to those of skill in the art (see, e.g., “Complete genome sequence of an M1 strain of Streptococcus pyogenes.” Ferretti et al., J.J., McShan W.M., Ajdic D.J., Savic D.J., Savic G., Lyon K., primeaux C., Sezate S., Suvorov A.N., Kenton S., Lai H.S., Lin S.P., Qian Y., Jia H.G., Najar F.Z., Ren Q., Zhu H., Song L., White J., Yuan X., Clifton S.W., Roe B.A., McLaughlin R.E., Proc. Natl. Acad. Sci. U.S.A.98:4658-4663(2001); “CRISPR RNA maturation by trans- encoded small RNA and host factor RNase III.” Deltcheva E., Chylinski K., Sharma C.M., Gonzales K., Chao Y., Pirzada Z.A., Eckert M.R., Vogel J., Charpentier E., Nature 471:602- 607(2011); and “A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.” Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J.A., Charpentier E. Science 337:816-821(2012), the entire contents of each of which are incorporated herein by reference). [0578] Examples of Cas9 and Cas9 equivalents are provided as follows; however, these specific examples are not meant to be limiting. The primer editor of the present disclosure may use any suitable napDNAbp, including any suitable Cas9 or Cas9 equivalent. Wild type canonical SpCas9 [0579] In one embodiment, the primer editor constructs described herein may comprise the “canonical SpCas9” nuclease from S. pyogenes, which has been widely used as a tool for genome engineering and is categorized as the type II subgroup of enzymes of the Class 2 CRISPR-Cas systems. This Cas9 protein is a large, multi-domain protein containing two distinct nuclease domains. Point mutations can be introduced into Cas9 to abolish one or both nuclease activities, resulting in a nickase Cas9 (nCas9) or dead Cas9 (dCas9), respectively, that still retains its ability to bind DNA in a sgRNA-programmed manner. In principle, when fused to another protein or domain, Cas9 or variant thereof (e.g., nCas9) can target that protein to virtually any DNA sequence simply by co-expression with an appropriate sgRNA. As used herein, the canonical SpCas9 protein refers to the wild type protein from Streptococcus pyogenes having SEQ ID NOs: 14-20 (See Description of the Sequences Section). [0580] The prime editors described herein may include canonical SpCas9, or any variant thereof having at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity with a wild type Cas9 sequence provided above. These variants may include SpCas9 variants containing one or more mutations, including any known mutation reported with the SwissProt Accession No. Q99ZW2 (SEQ ID NO: 14) entry, which include:

[0619] Other wild type SpCas9 sequences that may be used in the present disclosure include any of those with amino acid sequences in SEQ ID NOs: 22-35 (See Description of the Sequences) [0620] The prime editors described herein may include any SpCas9 with amino acid sequences in SEQ ID NOs 14, 17, 19, or any variant thereof having at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity thereto. [0621] Wild type Cas9 orthologs [0622] In other embodiments, the Cas9 protein can be a wild type Cas9 ortholog from another bacterial species different from the canonical Cas9 from S. pyogenes. For example, Cas9 orthologs with amino acid sequences of any SEQ ID NOs: 22-35 (see Description of the SEQUENCES) can be used in connection with the prime editor constructs described in this specification. In addition, any variant Cas9 orthologs having at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity to any one of SEQ ID NOs: 22-35 may also be used with the present prime editors. [0623] The prime editors described herein may include any Cas9 ortholog with amino acid sequences in SEQ ID NOs: 22-35, or any variants thereof having at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity thereto. [0624] The napDNAbp may include any suitable homologs and/or orthologs or naturally occurring enzymes, such as, Cas9. Cas9 homologs and/or orthologs have been described in various species, including, but not limited to, S. pyogenes and S. thermophilus. Preferably, the Cas moiety is configured (e.g, mutagenized, recombinantly engineered, or otherwise obtained from nature) as a nickase, i.e., capable of cleaving only a single strand of the target doubpdditional suitable Cas9 nucleases and sequences will be apparent to those of skill in the art based on this disclosure, and such Cas9 nucleases and sequences include Cas9 sequences from the organisms and loci disclosed in Chylinski, Rhun, and Charpentier, “The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems” (2013) RNA Biology 10:5, 726-737; the entire contents of which are incorporated herein by reference. In some embodiments, a Cas9 nuclease has an inactive (e.g., an inactivated) DNA cleavage domain, that is, the Cas9 is a nickase. In some embodiments, the Cas9 protein comprises an amino acid sequence that is at least 80% identical to the amino acid sequence of a Cas9 protein as provided by any one of the variants of Table 3. In some embodiments, the Cas9 protein comprises an amino acid sequence that is at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to the amino acid sequence of a Cas9 protein as provided by any one of the Cas9 orthologs listed in the Description of the Sequences (SEQ ID NOs: 22-35). Dead Cas9 variant [0625] In certain embodiments, the prime editors described herein may include a dead Cas9, e.g., dead SpCas9, which has no nuclease activity due to one or more mutations that inactive both nuclease domains of Cas9, namely the RuvC domain (which cleaves the non- protospacer DNA strand) and HNH domain (which cleaves the protospacer DNA strand). The nuclease inactivation may be due to one or mutations that result in one or more substitutions and/or deletions in the amino acid sequence of the encoded protein, or any variants thereof having at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity thereto. [0626] As used herein, the term “dCas9” refers to a nuclease-inactive Cas9 or nuclease- dead Cas9, or a functional fragment thereof, and embraces any naturally occurring dCas9 from any organism, any naturally-occurring dCas9 equivalent or functional fragment thereof, any dCas9 homolog, ortholog, or paralog from any organism, and any mutant or variant of a dCas9, naturally-occurring or engineered. The term dCas9 is not meant to be particularly limiting and may be referred to as a “dCas9 or equivalent.” Exemplary dCas9 proteins and method for making dCas9 proteins are further described herein and/or are described in the art and are incorporated herein by reference. [0627] In other embodiments, dCas9 corresponds to, or comprises in part or in whole, a Cas9 amino acid sequence having one or more mutations that inactivate the Cas9 nuclease activity. In other embodiments, Cas9 variants having mutations other than D10A and H840A are provided which may result in the full or partial inactivate of the endogneous Cas9 nuclease acivity (e.g., nCas9 or dCas9, respectively). Such mutations, by way of example, include other amino acid substitutions at D10 and H820, or other substitutions within the nuclease domains of Cas9 (e.g., substitutions in the HNH nuclease subdomain and/or the RuvC1 subdomain) with reference to a wild type sequence such as Cas9 from Streptococcus pyogenes (NCBI Reference Sequence: NC_017053.1). In some embodiments, variants or homologues of Cas9 (e.g., variants of Cas9 from Streptococcus pyogenes (NCBI Reference Sequence: NC_017053.1 (SEQ ID NO: 16 or 17))) are provided which are at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to NCBI Reference Sequence: NC_017053.1. In some embodiments, variants of dCas9 (e.g., variants of NCBI Reference Sequence: NC_017053.1 (SEQ ID NO: 17)) are provided having amino acid sequences which are shorter, or longer than NC_017053.1 (SEQ ID NO: 17) by about 5 amino acids, by about 10 amino acids, by about 15 amino acids, by about 20 amino acids, by about 25 amino acids, by about 30 amino acids, by about 40 amino acids, by about 50 amino acids, by about 75 amino acids, by about 100 amino acids or more. [0628] In one embodiment, the dead Cas9 may be based on the canonical SpCas9 sequence of Q99ZW2 and may have the a sequence comprising an amino acid sequence of SEQ ID NO: 36, which comprises a D10X and an H810X, wherein X may be any amino acid, substitutions (underlined and bolded), or a variant of SEQ ID NO: 36 having at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity thereto. [0629] In one embodiment, the dead Cas9 may be based on the canonical SpCas9 sequence of Q99ZW2 and may have any one of SEQ ID NOs: 36-37, which comprises a D10A and an H810A substitutions (underlined and bolded), or be a variant of SEQ ID NOs: 36-37 having at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity thereto. [0630] Cas9 nickase variant [0631] In one embodment, the prime editors described herein comprise a Cas9 nickase. The term “Cas9 nickase” of “nCas9” refers to a variant of Cas9 which is capable of introducing a single-strand break in a double strand DNA molecule target. In some embodiments, the Cas9 nickase comprises only a single functioning nuclease domain. The wild type Cas9 (e.g., the canonical SpCas9) comprises two separate nuclease domains, namely, the RuvC domain (which cleaves the non-protospacer DNA strand) and HNH domain (which cleaves the protospacer DNA strand). In one embodiment, the Cas9 nickase comprises a mutation in the RuvC domain which inactivates the RuvC nuclease activity. For example, mutations in aspartate (D) 10, histidine (H) 983, aspartate (D) 986, or glutamate (E) 762, have been reported as loss-of-function mutations of the RuvC nuclease domain and the creation of a functional Cas9 nickase (e.g., Nishimasu et al., “Crystal structure of Cas9 in complex with guide RNA and target DNA,” Cell 156(5), 935–949, which is incorporated herein by reference). Thus, nickase mutations in the RuvC domain could include D10X, H983X, D986X, or E762X, wherein X is any amino acid other than the wild type amino acid. In certain embodiments, the nickase could be D10A, of H983A, or D986A, or E762A, or a combination thereof. [0632] In various embodiments, the Cas9 nickase can have a mutation in the RuvC nuclease domain and have any one of amino acid sequences of SEQ ID NOs: 38-53 (See Description of the Sequences, Cas9 nickase sequences), or a variant thereof having an amino acid sequence that has at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity thereto. [0633] In another embodiment, the Cas9 nickase comprises a mutation in the HNH domain which inactivates the HNH nuclease activity. For example, mutations in histidine (H) 840 or asparagine (R) 863 have been reported as loss-of-function mutations of the HNH nuclease domain and the creation of a functional Cas9 nickase (e.g., Nishimasu et al., “Crystal structure of Cas9 in complex with guide RNA and target DNA,” Cell 156(5), 935– 949, which is incorporated herein by reference). Thus, nickase mutations in the HNH domain could include H840X and R863X, wherein X is any amino acid other than the wild type amino acid. In certain embodiments, the nickase could be H840A or R863A or a combination thereof. [0634] In various embodiments, the Cas9 nickase can have a mutation in the HNH nuclease domain and have any one of amino acid sequences in SEQ ID NOs: 38-53, or a variant thereof having an amino acid sequence that has at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity thereto. [0635] In some embodiments, the N-terminal methionine is removed from a Cas9 nickase, or from any Cas9 variant, ortholog, or equivalent disclosed or contemplated herein. For example, in some embodiments, the methionine-minus Cas9 nickase comprises an amino acid sequence of any one of SEQ ID NOs: 50-53, or a variant thereof having an amino acid sequence that has at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity thereto. In some embodiments, the methionine-minus Cas9 nickase comprises an amino acid sequence of any one of SEQ ID NOs: 38-49, or a variant thereof having an amino acid sequence that has at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity thereto. Other Cas9 variants [0636] Besides dead Cas9 and Cas9 nickase variants, the Cas9 proteins used herein may also include other “Cas9 variants” having at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to any reference Cas9 protein, including any wild type Cas9, or mutant Cas9 (e.g., a dead Cas9 or Cas9 nickase), or fragment Cas9, or circular permutant Cas9, or other variant of Cas9 disclosed herein or known in the art. In some embodiments, a Cas9 variant may have 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or more amino acid changes compared to a reference Cas9. In some embodiments, the Cas9 variant comprises a fragment of a reference Cas9 (e.g., a gRNA binding domain or a DNA-cleavage domain), such that the fragment is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to the corresponding fragment of wild type Cas9. In some embodiments, the fragment is is at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% identical, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% of the amino acid length of a corresponding wild type Cas9 (e.g., SEQ ID NOs: 14, 17, 19, 24-53, 55-65, 67-82, 84). [0637] In some embodiments, the disclosure also may utilize Cas9 fragments which retain their functionality and which are fragments of any herein disclosed Cas9 protein. In some embodiments, the Cas9 fragment is at least 100 amino acids in length. In some embodiments, the fragment is at least 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, or at least 1300 amino acids in length. [0638] In various embodiments, the prime editors disclosed herein may comprise one of the Cas9 variants described as follows, or a Cas9 variant thereof having at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to any reference Cas9 variants. Small-sized Cas9 variants [0639] In some embodiments, the prime editors contemplated herein can include a Cas9 protein that is of smaller molecular weight than the canonical SpCas9 sequence. In some embodiments, the smaller-sized Cas9 variants may facilitate delivery to cells, e.g., by an expression vector, nanoparticle, or other means of delivery. In certain embodiments, the smaller-sized Cas9 variants can include enzymes categorized as type II enzymes of the Class 2 CRISPR-Cas systems. In some embodiments, the smaller-sized Cas9 variants can include enzymes categorized as type V enzymes of the Class 2 CRISPR-Cas systems. In other embodiments, the smaller-sized Cas9 variants can include enzymes categorized as type VI enzymes of the Class 2 CRISPR-Cas systems. [0640] The canonical SpCas9 protein is 1368 amino acids in length and has a predicted molecular weight of 158 kilodaltons. The term “small-sized Cas9 variant”, as used herein, refers to any Cas9 variant—naturally occurring, engineered, or otherwise—that is less than at least 1300 amino acids, or at least less than 1290 amino acids, or than less than 1280 amino acids, or less than 1270 amino acid, or less than 1260 amino acid, or less than 1250 amino acids, or less than 1240 amino acids, or less than 1230 amino acids, or less than 1220 amino acids, or less than 1210 amino acids, or less than 1200 amino acids, or less than 1190 amino acids, or less than 1180 amino acids, or less than 1170 amino acids, or less than 1160 amino acids, or less than 1150 amino acids, or less than 1140 amino acids, or less than 1130 amino acids, or less than 1120 amino acids, or less than 1110 amino acids, or less than 1100 amino acids, or less than 1050 amino acids, or less than 1000 amino acids, or less than 950 amino acids, or less than 900 amino acids, or less than 850 amino acids, or less than 800 amino acids, or less than 750 amino acids, or less than 700 amino acids, or less than 650 amino acids, or less than 600 amino acids, or less than 550 amino acids, or less than 500 amino acids, but at least larger than about 400 amino acids and retaining the required functions of the Cas9 protein. The Cas9 variants can include those categorized as type II, type V, or type VI enzymes of the Class 2 CRISPR-Cas system. [0641] In various embodiments, the prime editors disclosed herein may comprise any one of the small-sized Cas9 variants comprising an amino acid sequence of any one of SEQ ID NOs: 54-59 (see Description of the Sequences, small sized Cas9 variants), or a Cas9 variant thereof having at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to any reference small-sized Cas9 protein. Cas9 equivalents [0642] In some embodiments, the prime editors described herein can include any Cas9 equivalent. As used herein, the term “Cas9 equivalent” is a broad term that encompasses any napDNAbp protein that serves the same function as Cas9 in the present prime editors despite that its amino acid primary sequence and/or its three-dimensional structure may be different and/or unrelated from an evolutionary standpoint. Thus, while Cas9 equivalents include any Cas9 ortholog, homolog, mutant, or variant described or embraced herein that are evolutionarily related, the Cas9 equivalents also embrace proteins that may have evolved through convergent evolution processes to have the same or similar function as Cas9, but which do not necessarily have any similarity with regard to amino acid sequence and/or three dimensional structure. The prime editors described here embrace any Cas9 equivalent that would provide the same or similar function as Cas9 despite that the Cas9 equivalent may be based on a protein that arose through convergent evolution. For instance, if Cas9 refers to a type II enzyme of the CRISPR-Cas system, a Cas9 equivalent can refer to a type V or type VI enzyme of the CRISPR-Cas system. [0643] For example, Cas12e (CasX) is a Cas9 equivalent that reportedly has the same function as Cas9 but which evolved through convergent evolution. Thus, the Cas12e (CasX) protein described in Liu et al., “CasX enzymes comprises a distinct family of RNA-guided genome editors,” Nature, 2019, Vol.566: 218-223, is contemplated to be used with the prime editors described herein. In addition, any variant or modification of Cas12e (CasX) is conceivable and within the scope of the present disclosure. [0644] Cas9 is a bacterial enzyme that evolved in a wide variety of species. However, the Cas9 equivalents contemplated herein may also be obtained from archaea, which constitute a domain and kingdom of single-celled prokaryotic microbes different from bacteria. [0645] In some embodiments, Cas9 equivalents may refer to Cas12e (CasX) or Cas12d (CasY), which have been described in, for example, Burstein et al., “New CRISPR–Cas systems from uncultivated microbes.” Cell Res.2017 Feb 21. doi: 10.1038/cr.2017.21, the entire contents of which is hereby incorporated by reference. Using genome-resolved metagenomics, a number of CRISPR–Cas systems were identified, including the first reported Cas9 in the archaeal domain of life. This divergent Cas9 protein was found in little- studied nanoarchaea as part of an active CRISPR–Cas system. In bacteria, two previously unknown systems were discovered, CRISPR– Cas12e and CRISPR– Cas12d, which are among the most compact systems yet discovered. In some embodiments, Cas9 refers to Cas12e, or a variant of Cas12e. In some embodiments, Cas9 refers to a Cas12d, or a variant of Cas12d. It should be appreciated that other RNA-guided DNA binding proteins may be used as a nucleic acid programmable DNA binding protein (napDNAbp), and are within the scope of this disclosure. Also see Liu et al., “CasX enzymes comprises a distinct family of RNA-guided genome editors,” Nature, 2019, Vol.566: 218-223. Any of these Cas9 equivalents are contemplated. [0646] In some embodiments, the Cas9 equivalent comprises an amino acid sequence that is at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to a naturally-occurring Cas12e (CasX) or Cas12d (CasY) protein. In some embodiments, the napDNAbp is a naturally-occurring Cas12e (CasX) or Cas12d (CasY) protein. In some embodiments, the napDNAbp comprises an amino acid sequence that is at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to a wild-type Cas moiety or any Cas moiety provided herein. [0647] In various embodiments, the nucleic acid programmable DNA binding proteins include, without limitation, Cas9 (e.g., dCas9 and nCas9), Cas12e (CasX), Cas12d (CasY), Cas12a (Cpf1), Cas12b1 (C2c1), Cas13a (C2c2), Cas12c (C2c3), Argonaute, , and Cas12b1. One example of a nucleic acid programmable DNA-binding protein that has different PAM specificity than Cas9 is Clustered Regularly Interspaced Short Palindromic Repeats from Prevotella and Francisella 1 (i.e, Cas12a (Cpf1)). Similar to Cas9, Cas12a (Cpf1) is also a Class 2 CRISPR effector, but it is a member of type V subgroup of enzymes, rather than the type II subgroup. It has been shown that Cas12a (Cpf1) mediates robust DNA interference with features distinct from Cas9. Cas12a (Cpf1) is a single RNA-guided endonuclease lacking tracrRNA, and it utilizes a T-rich protospacer-adjacent motif (TTN, TTTN, or YTN). Moreover, Cpf1 cleaves DNA via a staggered DNA double-stranded break. Out of 16 Cpf1- family proteins, two enzymes from Acidaminococcus and Lachnospiraceae are shown to have efficient genome-editing activity in human cells. Cpf1 proteins are known in the art and have been described previously, for example Yamano et al., “Crystal structure of Cpf1 in complex with guide RNA and target DNA.” Cell (165) 2016, p.949-962; the entire contents of which is hereby incorporated by reference. [0648] In still other embodiments, the Cas protein may include any CRISPR associated protein, including but not limited to, Cas12a, Cas12b1, Cas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csn1 and Csx12), Cas10, Csy1, Csy2, Csy3, Cse1, Cse2, Csc1, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3, Csx1, Csx15, Csf1, Csf2, Csf3, Csf4, homologs thereof, or modified versions thereof, and preferably comprising a nickase mutation (e.g., a mutation corresponding to the D10A mutation of the wild type Cas9 polypeptide of SEQ ID NO: 14). [0649] In various other embodiments, the napDNAbp can be any of the following proteins: a Cas9, a Cas12a (Cpf1), a Cas12e (CasX), a Cas12d (CasY), a Cas12b1 (C2c1), a Cas13a (C2c2), a Cas12c (C2c3), a GeoCas9, a CjCas9, a Cas12g, a Cas12h, a Cas12i, a Cas13b, a Cas13c, a Cas13d, a Cas14, a Csn2, an xCas9, an SpCas9-NG, a circularly permuted Cas9, or an Argonaute (Ago) domain, or a variant thereof. [0650] Exemplary Cas9 equivalent protein sequences can be found in the Description of Sequences (SEQ ID NOs: 60-69). [0651] The prime editors described herein may also comprise Cas12a (Cpf1) (dCpf1) variants that may be used as a guide nucleotide sequence-programmable DNA-binding protein domain. The Cas12a (Cpf1) protein has a RuvC-like endonuclease domain that is similar to the RuvC domain of Cas9 but does not have a HNH endonuclease domain, and the N-terminal of Cas12a (Cpf1) does not have the alfa-helical recognition lobe of Cas9. It was shown in Zetsche et al., Cell, 163, 759–771, 2015 (which is incorporated herein by reference) that, the RuvC-like domain of Cas12a (Cpf1) is responsible for cleaving both DNA strands and inactivation of the RuvC-like domain inactivates Cas12a (Cpf1) nuclease activity. [0652] In some embodiments, the napDNAbp is a single effector of a microbial CRISPR- Cas system. Single effectors of microbial CRISPR-Cas systems include, without limitation, Cas9, Cas12a (Cpf1), Cas12b1 (C2c1), Cas13a (C2c2), and Cas12c (C2c3). Typically, microbial CRISPR-Cas systems are divided into Class 1 and Class 2 systems. Class 1 systems have multisubunit effector complexes, while Class 2 systems have a single protein effector. For example, Cas9 and Cas12a (Cpf1) are Class 2 effectors. In addition to Cas9 and Cas12a (Cpf1), three distinct Class 2 CRISPR-Cas systems (Cas12b1, Cas13a, and Cas12c) have been described by Shmakov et al., “Discovery and Functional Characterization of Diverse Class 2 CRISPR Cas Systems”, Mol. Cell, 2015 Nov 5; 60(3): 385–397, the entire contents of which are hereby incorporated by reference. [0653] Effectors of two of the systems, Cas12b1 and Cas12c, contain RuvC-like endonuclease domains related to Cas12a. A third system, Cas13a contains an effector with two predicated HEPN RNase domains. Production of mature CRISPR RNA is tracrRNA- independent, unlike production of CRISPR RNA by Cas12b1. Cas12b1 depends on both CRISPR RNA and tracrRNA for DNA cleavage. Bacterial Cas13a has been shown to possess a unique RNase activity for CRISPR RNA maturation distinct from its RNA-activated single- stranded RNA degradation activity. These RNase functions are different from each other and from the CRISPR RNA-processing behavior of Cas12a. See, e.g., East-Seletsky, et al., “Two distinct RNase activities of CRISPR-Cas13a enable guide-RNA processing and RNA detection”, Nature, 2016 Oct 13;538(7624):270-273, the entire contents of which are hereby incorporated by reference. In vitro biochemical analysis of Cas13a in Leptotrichia shahii has shown that Cas13a is guided by a single CRISPR RNA and can be programed to cleave ssRNA targets carrying complementary protospacers. Catalytic residues in the two conserved HEPN domains mediate cleavage. Mutations in the catalytic residues generate catalytically inactive RNA-binding proteins. See e.g., Abudayyeh et al., “C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector”, Science, 2016 Aug 5; 353(6299), the entire contents of which are hereby incorporated by reference. [0654] The crystal structure of Alicyclobaccillus acidoterrastris Cas12b1 (AacC2c1) has been reported in complex with a chimeric single-molecule guide RNA (sgRNA). See e.g., Liu et al., “C2c1-sgRNA Complex Structure Reveals RNA-Guided DNA Cleavage Mechanism”, Mol. Cell, 2017 Jan 19;65(2):310-322, the entire contents of which are hereby incorporated by reference. The crystal structure has also been reported in Alicyclobacillus acidoterrestris C2c1 bound to target DNAs as ternary complexes. See e.g., Yang et al., “PAM-dependent Target DNA Recognition and Cleavage by C2C1 CRISPR-Cas endonuclease”, Cell, 2016 Dec 15;167(7):1814-1828, the entire contents of which are hereby incorporated by reference. Catalytically competent conformations of AacC2c1, both with target and non-target DNA strands, have been captured independently positioned within a single RuvC catalytic pocket, with C2c1-mediated cleavage resulting in a staggered seven- nucleotide break of target DNA. Structural comparisons between C2c1 ternary complexes and previously identified Cas9 and Cpf1 counterparts demonstrate the diversity of mechanisms used by CRISPR-Cas9 systems. [0655] In some embodiments, the napDNAbp may be a C2c1, a C2c2, or a C2c3 protein. In some embodiments, the napDNAbp is a C2c1 protein. In some embodiments, the napDNAbp is a Cas13a protein. In some embodiments, the napDNAbp is a Cas12c protein. In some embodiments, the napDNAbp comprises an amino acid sequence that is at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to a naturally-occurring Cas12b1 (C2c1), Cas13a (C2c2), or Cas12c (C2c3) protein. In some embodiments, the napDNAbp is a naturally-occurring Cas12b1 (C2c1), Cas13a (C2c2), or Cas12c (C2c3) protein. Cas9 circular permutants [0656] In various embodiments, the prime editors disclosed herein may comprise a circular permutant of Cas9. [0657] The term “circularly permuted Cas9” or “circular permutant” of Cas9 or “CP- Cas9”) refers to any Cas9 protein, or variant thereof, that occurs or has been modify to engineered as a circular permutant variant, which means the N-terminus and the C-terminus of a Cas9 protein (e.g., a wild type Cas9 protein) have been topically rearranged. Such circularly permuted Cas9 proteins, or variants thereof, retain the ability to bind DNA when complexed with a guide RNA (gRNA). See, Oakes et al., “Protein Engineering of Cas9 for enhanced function,” Methods Enzymol, 2014, 546: 491–511 and Oakes et al., “CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification,” Cell, January 10, 2019, 176: 254-267, each of are incorporated herein by reference. The instant disclosure contemplates any previously known CP-Cas9 or use a new CP-Cas9 so long as the resulting circularly permuted protein retains the ability to bind DNA when complexed with a guide RNA (gRNA). [0658] Any of the Cas9 proteins described herein, including any variant, ortholog, or naturally occurring Cas9 or equivalent thereof, may be reconfigured as a circular permutant variant. [0659] In various embodiments, the circular permutants of Cas9 may have the following structure: [0660] N-terminus-[original C-terminus] – [optional linker] – [original N-terminus]-C- terminus. [0661] As an example, the present disclosure contemplates the following circular permutants of canonical S. pyogenes Cas9 (1368 amino acids of UniProtKB - Q99ZW2 (CAS9_STRP1) (numbering is based on the amino acid position in SEQ ID NO: 14)): [0662] N-terminus-[1268-1368]-[optional linker]-[1-1267]-C-terminus; [0663] N-terminus-[1168-1368]-[optional linker]-[1-1167]-C-terminus; [0664] N-terminus-[1068-1368]-[optional linker]-[1-1067]-C-terminus; [0665] N-terminus-[968-1368]-[optional linker]-[1-967]-C-terminus; [0666] N-terminus-[868-1368]-[optional linker]-[1-867]-C-terminus; [0667] N-terminus-[768-1368]-[optional linker]-[1-767]-C-terminus; [0668] N-terminus-[668-1368]-[optional linker]-[1-667]-C-terminus; [0669] N-terminus-[568-1368]-[optional linker]-[1-567]-C-terminus; [0670] N-terminus-[468-1368]-[optional linker]-[1-467]-C-terminus; [0671] N-terminus-[368-1368]-[optional linker]-[1-367]-C-terminus; [0672] N-terminus-[268-1368]-[optional linker]-[1-267]-C-terminus; [0673] N-terminus-[168-1368]-[optional linker]-[1-167]-C-terminus; [0674] N-terminus-[68-1368]-[optional linker]-[1-67]-C-terminus; or [0675] N-terminus-[10-1368]-[optional linker]-[1-9]-C-terminus, or the corresponding circular permutants of other Cas9 proteins (including other Cas9 orthologs, variants, etc). [0676] In particular embodiments, the circular permuant Cas9 has the following structure (based on S. pyogenes Cas9 (1368 amino acids of UniProtKB - Q99ZW2 (CAS9_STRP1) (numbering is based on the amino acid position in SEQ ID NO: 14): [0677] N-terminus-[102-1368]-[optional linker]-[1-101]-C-terminus; [0678] N-terminus-[1028-1368]-[optional linker]-[1-1027]-C-terminus; [0679] N-terminus-[1041-1368]-[optional linker]-[1-1043]-C-terminus; [0680] N-terminus-[1249-1368]-[optional linker]-[1-1248]-C-terminus; or [0681] N-terminus-[1300-1368]-[optional linker]-[1-1299]-C-terminus, or the corresponding circular permutants of other Cas9 proteins (including other Cas9 orthologs, variants, etc). [0682] In still other embodiments, the circular permuant Cas9 has the following structure (based on S. pyogenes Cas9 (1368 amino acids of UniProtKB - Q99ZW2 (CAS9_STRP1) (numbering is based on the amino acid position in SEQ ID NO: 14): [0683] N-terminus-[103-1368]-[optional linker]-[1-102]-C-terminus; [0684] N-terminus-[1029-1368]-[optional linker]-[1-1028]-C-terminus; [0685] N-terminus-[1042-1368]-[optional linker]-[1-1041]-C-terminus; [0686] N-terminus-[1250-1368]-[optional linker]-[1-1249]-C-terminus; or [0687] N-terminus-[1301-1368]-[optional linker]-[1-1300]-C-terminus, or the corresponding circular permutants of other Cas9 proteins (including other Cas9 orthologs, variants, etc). [0688] In some embodiments, the circular permutant can be formed by linking a C- terminal fragment of a Cas9 to an N-terminal fragment of a Cas9, either directly or by using a linker, such as an amino acid linker. In some embodiments, The C-terminal fragment may correspond to the C-terminal 95% or more of the amino acids of a Cas9 (e.g., amino acids about 1300-1368), or the C-terminal 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, or 5% or more of a Cas9 (e.g., any one of SEQ ID NOs:70-79). The N-terminal portion may correspond to the N-terminal 95% or more of the amino acids of a Cas9 (e.g., amino acids about 1-1300), or the N-terminal 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, or 5% or more of a Cas9 (e.g., of SEQ ID NOs: 14). [0689] In some embodiments, the circular permutant can be formed by linking a C- terminal fragment of a Cas9 to an N-terminal fragment of a Cas9, either directly or by using a linker, such as an amino acid linker. In some embodiments, the C-terminal fragment that is rearranged to the N-terminus, includes or corresponds to the C-terminal 30% or less of the amino acids of a Cas9 (e.g., amino acids 1012-1368 of SEQ ID NO: 14). In some embodiments, the C-terminal fragment that is rearranged to the N-terminus, includes or corresponds to the C-terminal 30%, 29%, 28%, 27%, 26%, 25%, 24%, 23%, 22%, 21%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or 1% of the amino acids of a Cas9 (e.g., the Cas9 of SEQ ID NO: 14). In some embodiments, the C-terminal fragment that is rearranged to the N-terminus, includes or corresponds to the C-terminal 410 residues or less of a Cas9 (e.g., the Cas9 of SEQ ID NO: 14). In some embodiments, the C-terminal portion that is rearranged to the N-terminus, includes or corresponds to the C-terminal 410, 400, 390, 380, 370, 360, 350, 340, 330, 320, 310, 300, 290, 280, 270, 260, 250, 240, 230, 220, 210, 200, 190, 180, 170, 160, 150, 140, 130, 120, 110, 100, 90, 80, 70, 60, 50, 40, 30, 20, or 10 residues of a Cas9 (e.g., the Cas9 of SEQ ID NO: 14). In some embodiments, the C-terminal portion that is rearranged to the N- terminus, includes or corresponds to the C-terminal 357, 341, 328, 120, or 69 residues of a Cas9 (e.g., the Cas9 of SEQ ID NO: 14). [0690] In other embodiments, circular permutant Cas9 variants may be defined as a topological rearrangement of a Cas9 primary structure based on the following method, which is based on S. pyogenes Cas9 of SEQ ID NO: 14: (a) selecting a circular permutant (CP) site corresponding to an internal amino acid residue of the Cas9 primary structure, which dissects the original protein into two halves: an N-terminal region and a C-terminal region; (b) modifying the Cas9 protein sequence (e.g., by genetic engineering techniques) by moving the original C-terminal region (comprising the CP site amino acid) to preceed the original N- terminal region, thereby forming a new N-terminus of the Cas9 protein that now begins with the CP site amino acid residue. The CP site can be located in any domain of the Cas9 protein, including, for example, the helical-II domain, the RuvCIII domain, or the CTD domain. For example, the CP site may be located (relative the S. pyogenes Cas9 of SEQ ID NO: 14) at original amino acid residue 181, 199, 230, 270, 310, 1010, 1016, 1023, 1029, 1041, 1247, 1249, or 1282. Thus, once relocated to the N-terminus, original amino acid 181, 199, 230, 270, 310, 1010, 1016, 1023, 1029, 1041, 1247, 1249, or 1282 would become the new N-terminal amino acid. Nomenclature of these CP-Cas9 proteins may be referred to as Cas9-CP181, Cas9-CP199, Cas9-CP230, Cas9-CP270, Cas9-CP310, Cas9-CP1010, Cas9- CP1016, Cas9-CP1023, Cas9-CP1029, Cas9-CP1041, Cas9-CP1247, Cas9-CP1249, and Cas9-CP1282, respectively. This description is not meant to be limited to making CP variants from SEQ ID NO: 14, but may be implemented to make CP variants in any Cas9 sequence (e.g., SEQ ID NOs: 14), either at CP sites that correspond to these positions, or at other CP sites entirely. This description is not meant to limit the specific CP sites in any way. Virtually any CP site may be used to form a CP-Cas9 variant. [0691] Exemplary CP-Cas9 amino acid sequences, based on the Cas9 of SEQ ID NO: 14, are shown in SEQ ID NOs: 70-74 (see Description of Sequences, Circular permutants) in which linker sequences are indicated by underlining and optional methionine (M) residues are indicated in bold. It should be appreciated that the disclosure provides CP-Cas9 sequences that do not include a linker sequence or that include different linker sequences. It should be appreciated that CP-Cas9 sequences may be based on Cas9 sequences other than that of SEQ ID NO: 14 and any examples provided herein are not meant to be limiting. Exempalry CP- Cas9 sequences may be found in the Description of Sequences (SEQ ID NOs: 70-74, Cas9 Circular Permutants). [0692] The Cas9 circular permutants that may be useful in the prime editing constructs described herein. Exemplary C-terminal fragments of Cas9, based on the Cas9 of SEQ ID NO: 14, which may be rearranged to an N-terminus of Cas9, are provided in the Description of Sequences (SEQ ID NOs: 75-79, Cas9 circular permutants). It should be appreciated that such C-terminal fragments of Cas9 are exemplary and are not meant to be limiting. These exemplary CP-Cas9 fragments may have an amino acid sequences of any one of SEQ ID NOs: 70-79. Cas9 variants with modified PAM specificities [0693] The prime editors of the present disclosure may also comprise Cas9 variants with modified PAM specificities. Some aspects of this disclosure provide Cas9 proteins that exhibit activity on a target sequence that does not comprise the canonical PAM (5′-NGG-3′, where N is A, C, G, or T) at its 3′-end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5′-NGG-3′ PAM sequence at its 3′-end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5´-NNG- 3´ PAM sequence at its 3′-end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5′-NNA-3′ PAM sequence at its 3ʹ-end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5′-NNC-3′ PAM sequence at its 3ʹ-end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5´-NNT-3´ PAM sequence at its 3ʹ-end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5´-NGT-3´ PAM sequence at its 3ʹ-end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5´-NGA-3´ PAM sequence at its 3ʹ-end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5´-NGC-3´ PAM sequence at its 3ʹ-end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5´- NAA-3´ PAM sequence at its 3´-end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5´-NAC-3´ PAM sequence at its 3′-end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5´-NAT-3´ PAM sequence at its 3´-end. In still other embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5´-NAG-3´ PAM sequence at its 3´-end. [0694] It should be appreciated that any of the amino acid mutations described herein, (e.g., A262T) from a first amino acid residue (e.g., A) to a second amino acid residue (e.g., T) may also include mutations from the first amino acid residue to an amino acid residue that is similar to (e.g., conserved) the second amino acid residue. For example, mutation of an amino acid with a hydrophobic side chain (e.g., alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, or tryptophan) may be a mutation to a second amino acid with a different hydrophobic side chain (e.g., alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, or tryptophan). For example, a mutation of an alanine to a threonine (e.g., a A262T mutation) may also be a mutation from an alanine to an amino acid that is similar in size and chemical properties to a threonine, for example, serine. As another example, mutation of an amino acid with a positively charged side chain (e.g., arginine, histidine, or lysine) may be a mutation to a second amino acid with a different positively charged side chain (e.g., arginine, histidine, or lysine). As another example, mutation of an amino acid with a polar side chain (e.g., serine, threonine, asparagine, or glutamine) may be a mutation to a second amino acid with a different polar side chain (e.g., serine, threonine, asparagine, or glutamine). Additional similar amino acid pairs include, but are not limited to, the following: phenylalanine and tyrosine; asparagine and glutamine; methionine and cysteine; aspartic acid and glutamic acid; and arginine and lysine. The skilled artisan would recognize that such conservative amino acid substitutions will likely have minor effects on protein structure and are likely to be well tolerated without compromising function. In some embodiments, any amino of the amino acid mutations provided herein from one amino acid to a threonine may be an amino acid mutation to a serine. In some embodiments, any amino of the amino acid mutations provided herein from one amino acid to an arginine may be an amino acid mutation to a lysine. In some embodiments, any amino of the amino acid mutations provided herein from one amino acid to an isoleucine, may be an amino acid mutation to an alanine, valine, methionine, or leucine. In some embodiments, any amino of the amino acid mutations provided herein from one amino acid to a lysine may be an amino acid mutation to an arginine. In some embodiments, any amino of the amino acid mutations provided herein from one amino acid to an aspartic acid may be an amino acid mutation to a glutamic acid or asparagine. In some embodiments, any amino of the amino acid mutations provided herein from one amino acid to a valine may be an amino acid mutation to an alanine, isoleucine, methionine, or leucine. In some embodiments, any amino of the amino acid mutations provided herein from one amino acid to a glycine may be an amino acid mutation to an alanine. It should be appreciated, however, that additional conserved amino acid residues would be recognized by the skilled artisan and any of the amino acid mutations to other conserved amino acid residues are also within the scope of this disclosure. [0695] In some embodiments, the Cas9 protein comprises a combination of mutations that exhibit activity on a target sequence comprising a 5´-NAA-3´ PAM sequence at its 3´- end. In some embodiments, the combination of mutations are present in any one of the clones listed in Table 1. In some embodiments, the combination of mutations are conservative mutations of the clones listed in Table 1. In some embodiments, the Cas9 protein comprises the combination of mutations of any one of the Cas9 clones listed in Table 1. [0696] Table 1: NAA PAM Clones [0697] In some embodiments, the Cas9 protein comprises an amino acid sequence that is at least 80% identical to the amino acid sequence of a Cas9 protein as provided by any one of the variants of Table 1. In some embodiments, the Cas9 protein comprises an amino acid sequence that is at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to the amino acid sequence of a Cas9 protein as provided by any one of the variants of Table 1. [0698] In some embodiments, the Cas9 protein exhibits an increased activity on a target sequence that does not comprise the canonical PAM (5´-NGG-3´) at its 3´ end as compared to Streptococcus pyogenes Cas9 as provided by SEQ ID NO: 14. In some embodiments, the Cas9 protein exhibits an activity on a target sequence having a 3ʹ end that is not directly adjacent to the canonical PAM sequence (5´-NGG-3´) that is at least 5-fold increased as compared to the activity of Streptococcus pyogenes Cas9 as provided by SEQ ID NO: 14 on the same target sequence. In some embodiments, the Cas9 protein exhibits an activity on a target sequence that is not directly adjacent to the canonical PAM sequence (5´-NGG-3´) that is at least 10-fold, at least 50-fold, at least 100-fold, at least 500-fold, at least 1,000-fold, at least 5,000-fold, at least 10,000-fold, at least 50,000-fold, at least 100,000-fold, at least 500,000-fold, or at least 1,000,000-fold increased as compared to the activity of Streptococcus pyogenes as provided by SEQ ID NO: 14 on the same target sequence. In some embodiments, the 3ʹ end of the target sequence is directly adjacent to an AAA, GAA, CAA, or TAA sequence. In some embodiments, the Cas9 protein comprises a combination of mutations that exhibit activity on a target sequence comprising a 5´-NAC-3´ PAM sequence at its 3ʹ-end. In some embodiments, the combination of mutations are present in any one of the clones listed in Table 2. In some embodiments, the combination of mutations are conservative mutations of the clones listed in Table 2. In some embodiments, the Cas9 protein comprises the combination of mutations of any one of the Cas9 clones listed in Table 2. [0699] Table 2: NAC PAM Clones

[0700] In some embodiments, the Cas9 protein comprises an amino acid sequence that is at least 80% identical to the amino acid sequence of a Cas9 protein as provided by any one of the variants of Table 2. In some embodiments, the Cas9 protein comprises an amino acid sequence that is at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to the amino acid sequence of a Cas9 protein as provided by any one of the variants of Table 2. [0701] In some embodiments, the Cas9 protein exhibits an increased activity on a target sequence that does not comprise the canonical PAM (5´-NGG-3´) at its 3ʹ end as compared to Streptococcus pyogenes Cas9 as provided by SEQ ID NO: 14. In some embodiments, the Cas9 protein exhibits an activity on a target sequence having a 3ʹ end that is not directly adjacent to the canonical PAM sequence (5´-NGG-3´) that is at least 5-fold increased as compared to the activity of Streptococcus pyogenes Cas9 as provided by SEQ ID NO: 14 on the same target sequence. In some embodiments, the Cas9 protein exhibits an activity on a target sequence that is not directly adjacent to the canonical PAM sequence (5´-NGG-3´) that is at least 10-fold, at least 50-fold, at least 100-fold, at least 500-fold, at least 1,000-fold, at least 5,000-fold, at least 10,000-fold, at least 50,000-fold, at least 100,000-fold, at least 500,000-fold, or at least 1,000,000-fold increased as compared to the activity of Streptococcus pyogenes as provided by SEQ ID NO: 14 on the same target sequence. In some embodiments, the 3ʹ end of the target sequence is directly adjacent to an AAC, GAC, CAC, or TAC sequence. [0702] In some embodiments, the Cas9 protein comprises a combination of mutations that exhibit activity on a target sequence comprising a 5´-NAT-3´ PAM sequence at its 3ʹ- end. In some embodiments, the combination of mutations are present in any one of the clones listed in Table 3. In some embodiments, the combination of mutations are conservative mutations of the clones listed in Table 3. In some embodiments, the Cas9 protein comprises the combination of mutations of any one of the Cas9 clones listed in Table 3. [0703] Table 3: NAT PAM Clones

[0704] The above description of various napDNAbps which can be used in connection with the presently disclose prime editors is not meant to be limiting in any way. The prime editors may comprise the canonical SpCas9, or any ortholog Cas9 protein, or any variant Cas9 protein—including any naturally occurring variant, mutant, or otherwise engineered version of Cas9—that is known or which can be made or evolved through a directed evolutionary or otherwise mutagenic process. In various embodiments, the Cas9 or Cas9 varants have a nickase activity, i.e., only cleave of strand of the target DNA sequence. In other embodiments, the Cas9 or Cas9 variants have inactive nucleases, i.e., are “dead” Cas9 proteins. Other variant Cas9 proteins that may be used are those having a smaller molecular weight than the canonical SpCas9 (e.g., for easier delivery) or having modified or rearranged primary amino acid structure (e.g., the circular permutant formats). The prime editors described herein may also comprise Cas9 equivalents, including Cas12a/Cpf1 and Cas12b proteins which are the result of convergent evolution. The napDNAbps used herein (e.g., SpCas9, Cas9 variant, or Cas9 equivalents) may also may also contain various modifications that alter/enhance their PAM specifities. Lastly, the application contemplates any Cas9, Cas9 variant, or Cas9 equivalent which has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.9% sequence identity to a reference Cas9 sequence, such as a references SpCas9 canonical sequences or a reference Cas9 equivalent (e.g., Cas12a/Cpf1). [0705] In a particular embodiment, the Cas9 variant having expanded PAM capabilities is SpCas9 (H840A) VRQR which comprises an amino acid sequence of SEQ ID NO: 80 (with the V, R, Q, R substitutions relative to the SpCas9 (H840A) of SEQ ID NO: 47). In addition, the methionine residue in SpCas9 (H840) was removed for SpCas9 (H840A) VRQR. [0706] In another particular embodiment, the Cas9 variant having expanded PAM capabilities is SpCas9 (H840A) VRER which comprises an amino acid sequence of SEQ ID NO: 81 (with the V, R, E, R substitutions relative to the SpCas9 (H840A) of SEQ ID NO: 47). In addition, the methionine residue in SpCas9 (H840) was removed for SpCas9 (H840A) VRER. [0707] In some embodiments, the napDNAbp that functions with a non-canonical PAM sequence is an Argonaute protein. One example of such a nucleic acid programmable DNA binding protein is an Argonaute protein from Natronobacterium gregoryi (NgAgo). NgAgo is a ssDNA-guided endonuclease. NgAgo binds 5′ phosphorylated ssDNA of ~24 nucleotides (gDNA) to guide it to its target site and will make DNA double-strand breaks at the gDNA site. In contrast to Cas9, the NgAgo–gDNA system does not require a protospacer-adjacent motif (PAM). Using a nuclease inactive NgAgo (dNgAgo) can greatly expand the bases that may be targeted. The characterization and use of NgAgo have been described in Gao et al., Nat Biotechnol., 2016 Jul;34(7):768-73. PubMed PMID: 27136078; Swarts et al., Nature. 507(7491) (2014):258-61; and Swarts et al., Nucleic Acids Res. 43(10) (2015):5120-9, each of which is incorporated herein by reference. [0708] In some embodiments, the napDNAbp is a prokaryotic homolog of an Argonaute protein. Prokaryotic homologs of Argonaute proteins are known and have been described, for example, in Makarova K., et al., “Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements”, Biol Direct.2009 Aug 25;4:29. doi: 10.1186/1745-6150-4-29, the entire contents of which is hereby incorporated by reference. In some embodiments, the napDNAbp is a Marinitoga piezophila Argunaute (MpAgo) protein. The CRISPR-associated Marinitoga piezophila Argunaute (MpAgo) protein cleaves single-stranded target sequences using 5ʹ- phosphorylated guides. The 5ʹ guides are used by all known Argonautes. The crystal structure of an MpAgo-RNA complex shows a guide strand binding site comprising residues that block 5ʹ phosphate interactions. This data suggests the evolution of an Argonaute subclass with noncanonical specificity for a 5ʹ-hydroxylated guide. See, e.g., Kaya et al., “A bacterial Argonaute with noncanonical guide RNA specificity”, Proc Natl Acad Sci U S A.2016 Apr 12;113(15):4057-62, the entire contents of which are hereby incorporated by reference). It should be appreciated that other argonaute proteins may be used, and are within the scope of this disclosure. [0709] Some aspects of the disclosure provide Cas9 domains that have different PAM specificities. Typically, Cas9 proteins, such as Cas9 from S. pyogenes (spCas9), require a canonical NGG PAM sequence to bind a particular nucleic acid region. This may limit the ability to edit desired bases within a genome. In some embodiments, the base editing fusion proteins provided herein may need to be placed at a precise location, for example where a target base is placed within a 4 base region (e.g., a “editing window”), which is approximately 15 bases upstream of the PAM. See Komor, A.C., et al., “Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage” Nature 533, 420-424 (2016), the entire contents of which are hereby incorporated by reference. Accordingly, in some embodiments, any of the fusion proteins provided herein may contain a Cas9 domain that is capable of binding a nucleotide sequence that does not contain a canonical (e.g., NGG) PAM sequence. Cas9 domains that bind to non-canonical PAM sequences have been described in the art and would be apparent to the skilled artisan. For example, Cas9 domains that bind non-canonical PAM sequences have been described in Kleinstiver, B. P., et al., “Engineered CRISPR-Cas9 nucleases with altered PAM specificities” Nature 523, 481-485 (2015); and Kleinstiver, B. P., et al., “Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition” Nature Biotechnology 33, 1293-1298 (2015); the entire contents of each are hereby incorporated by reference. [0710] In some embodiments, the nucleic acid programmable DNA binding protein (napDNAbp) is a nucleic acid programmable DNA binding protein that does not require a canonical (NGG) PAM sequence. In some embodiments, the napDNAbp is an argonaute protein. One example of such a nucleic acid programmable DNA binding protein is an Argonaute protein from Natronobacterium gregoryi (NgAgo). NgAgo is a ssDNA-guided endonuclease. NgAgo binds 5′ phosphorylated ssDNA of ~24 nucleotides (gDNA) to guide it to its target site and will make DNA double-strand breaks at the gDNA site. In contrast to Cas9, the NgAgo–gDNA system does not require a protospacer-adjacent motif (PAM). Using a nuclease inactive NgAgo (dNgAgo) can greatly expand the bases that may be targeted. The characterization and use of NgAgo have been described in Gao et al., Nat Biotechnol., 34(7): 768-73 (2016), PubMed PMID: 27136078; Swarts et al., Nature, 507(7491): 258-61 (2014); and Swarts et al., Nucleic Acids Res. 43(10) (2015): 5120-9, each of which is incorporated herein by reference. The sequence of Natronobacterium gregoryi Argonaute is provided in SEQ ID NO:84. [0711] In addition, any available methods may be utilized to obtain or construct a variant or mutant Cas9 protein. The term “mutation,” as used herein, refers to a substitution of a residue within a sequence, e.g., a nucleic acid or amino acid sequence, with another residue, or a deletion or insertion of one or more residues within a sequence. Mutations are typically described herein by identifying the original residue followed by the position of the residue within the sequence and by the identity of the newly substituted residue. Various methods for making the amino acid substitutions (mutations) provided herein are well known in the art, and are provided by, for example, Green and Sambrook, Molecular Cloning: A Laboratory Manual (4th ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2012)). Mutations can include a variety of categories, such as single base polymorphisms, microduplication regions, indel, and inversions, and is not meant to be limiting in any way. Mutations can include “loss-of-function” mutations which is the normal result of a mutation that reduces or abolishes a protein activity. Most loss-of-function mutations are recessive, because in a heterozygote the second chromosome copy carries an unmutated version of the gene coding for a fully functional protein whose presence compensates for the effect of the mutation. Mutations also embrace “gain-of-function” mutations, which is one which confers an abnormal activity on a protein or cell that is otherwise not present in a normal condition. Many gain-of-function mutations are in regulatory sequences rather than in coding regions, and can therefore have a number of consequences. For example, a mutation might lead to one or more genes being expressed in the wrong tissues, these tissues gaining functions that they normally lack. Because of their nature, gain-of-function mutations are usually dominant. [0712] Mutations can be introduced into a reference Cas9 protein using site-directed mutagenesis. Older methods of site-directed mutagenesis known in the art rely on sub- cloning of the sequence to be mutated into a vector, such as an M13 bacteriophage vector, that allows the isolation of single-stranded DNA template. In these methods, one anneals a mutagenic primer (i.e., a primer capable of annealing to the site to be mutated but bearing one or more mismatched nucleotides at the site to be mutated) to the single-stranded template and then polymerizes the complement of the template starting from the 3ʹ end of the mutagenic primer. The resulting duplexes are then transformed into host bacteria and plaques are screened for the desired mutation. More recently, site-directed mutagenesis has employed PCR methodologies, which have the advantage of not requiring a single-stranded template. In addition, methods have been developed that do not require sub-cloning. Several issues must be considered when PCR-based site-directed mutagenesis is performed. First, in these methods it is desirable to reduce the number of PCR cycles to prevent expansion of undesired mutations introduced by the polymerase. Second, a selection must be employed in order to reduce the number of non-mutated parental molecules persisting in the reaction. Third, an extended-length PCR method is preferred in order to allow the use of a single PCR primer set. And fourth, because of the non-template-dependent terminal extension activity of some thermostable polymerases it is often necessary to incorporate an end-polishing step into the procedure prior to blunt-end ligation of the PCR-generated mutant product. [0713] Mutations may also be introduced by directed evolution processes, such as phage- assisted continuous evolution (PACE) or phage-assisted noncontinuous evolution (PANCE). The term “phage-assisted continuous evolution (PACE),” as used herein, refers to continuous evolution that employs phage as viral vectors. The general concept of PACE technology has been described, for example, in International PCT Application, PCT/US2009/056194, filed September 8, 2009, published as WO 2010/028347 on March 11, 2010; International PCT Application, PCT/US2011/066747, filed December 22, 2011, published as WO 2012/088381 on June 28, 2012; U.S. Application, U.S. Patent No.9,023,594, issued May 5, 2015, International PCT Application, PCT/US2015/012022, filed January 20, 2015, published as WO 2015/134121 on September 11, 2015, and International PCT Application, PCT/US2016/027795, filed April 15, 2016, published as WO 2016/168631 on October 20, 2016, the entire contents of each of which are incorporated herein by reference. Variant Cas9s may also be obtain by phage-assisted non-continuous evolution (PANCE),” which as used herein, refers to non-continuous evolution that employs phage as viral vectors. PANCE is a simplified technique for rapid in vivo directed evolution using serial flask transfers of evolving ‘selection phage’ (SP), which contain a gene of interest to be evolved, across fresh E. coli host cells, thereby allowing genes inside the host E. coli to be held constant while genes contained in the SP continuously evolve. Serial flask transfers have long served as a widely-accessible approach for laboratory evolution of microbes, and, more recently, analogous approaches have been developed for bacteriophage evolution. The PANCE system features lower stringency than the PACE system. [0714] Any of the references noted above which relate to Cas9 or Cas9 equivalents are hereby incorporated by reference in their entireties, if not already stated so. Divided napDNAbp domains for split PE delivery [0715] In various embodiments, the prime editors described herein may be delivered to cells as two or more fragments which become assembled inside the cell (either by passive assembly, or by active assembly, such as using split intein sequences) into a reconstituted prime editor. In some cases, the self assembly may be passive whereby the two or more prime editor fragments associate inside the cell covalently or non-covalently to reconstitute the prime editor. In other cases, the self-assembly may be catalzyed by dimerization domains installed on each of the fragments. Examples of dimerization domains are described herein. In still other cases, the self-assembly may be catalyzed by split intein sequences installed on each of the prime editor fragments. [0716] Split PE delivery may be advantageous to address various size constraints of different delivery approaches. For example, delivery approaches may include virus-based delivery methods, messenger RNA-based delivery methods, or RNP-based delivery (ribonucleoprotein-based delivery). And, each of these methods of delivery may be more efficient and/or effective by dividing up the prime editor into smaller pieces. Once inside the cell, the smaller pieces can assemble into a functional prime editor. Depending on the means of splitting, the divided prime editor fragments can be reassembled in a non-covalent manner or a covalent manner to reform the prime editor. In one embodiment, the prime editor can be split at one or more split sites into two or more fragments. The fragments can be unmodified (other than being split). Once the fragments are delivered to the cell (e.g., by direct delivery of a ribonucleoprotein complex or by nucleic delivery – e.g., mRNA delivery or virus vector based delivery), the fragments can reassociate covalently or non-covalently to reconstitute the prime editor. In another embodiment, the prime editor can be split at one or more split sites into two or more fragments. Each of the fragments can be modified to comprise a dimerization domain, whereby each fragment that is formed is coupled to a dimerization domain. Once delivered or expressed within a cell, the dimerization domains of the different fragments associate and bind to one another, bringing the different prime editor fragments together to reform a functional prime editor. In yet another embodiment, the prime editor fragment may be modified to comprise a split intein. Once delivered or expressed within a cell, the split intein domains of the different fragments associate and bind to one another, and then undergo trans-splicing, which results in the excision of the split-intein domains from each of the fragments, and a concomitant formation of a peptide bond between the fragments, thereby restoring the prime editor. [0717] In one embodiment, the prime editor can be delivered using a split-intein approach. [0718] The location of the split site can be positioned between any one or more pair of residues in the prime editor and in any domains therein, including within the napDNAbp domain, the polymerase domain (e.g., RT domain), linker domain that joins the napDNAbp domain and the polymerase domain. [0719] In one embodiment, the prime editor (PE) is divided at a split site within the napDNAbp. [0720] In certain embodiments, the napDNAbp is a canonical SpCas9 polypeptide of SEQ ID NO: 14. [0721] In certain embodiments, the SpCas9 is split into two fragments at a split site located between residues 1 and 2, or 2 and 3, or 3 and 4, or 4 and 5, or 5 and 6, or 6 and 7, or 7 and 8, or 8 and 9, or 9 and 10, or between any two pair of residues located anywhere between residues 1-10, 10-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100- 200, 200-300, 300-400, 400-500, 500-600, 600-700, 700-800, 800-900, 1000-1100, 1100- 1200, 1200-1300, or 1300-1368 of canonical SpCas9 of SEQ ID NO: 14. [0722] In certain embodiments, a napDNAbp is split into two fragments at a split site that is located at a pair of residue that corresponds to any two pair of residues located anywhere between positions 1-10, 10-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100- 200, 200-300, 300-400, 400-500, 500-600, 600-700, 700-800, 800-900, 1000-1100, 1100- 1200, 1200-1300, or 1300-1368 of canonical SpCas9 of SEQ ID NO: 14. [0723] In certain embodiments, the SpCas9 is split into two fragments at a split site located between residues 1 and 2, or 2 and 3, or 3 and 4, or 4 and 5, or 5 and 6, or 6 and 7, or 7 and 8, or 8 and 9, or 9 and 10, or between any two pair of residues located anywhere between residues 1-10, 10-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100- 200, 200-300, 300-400, 400-500, 500-600, 600-700, 700-800, 800-900, 1000-1100, 1100- 1200, 1200-1300, or 1300-1368 of canonical SpCas9 of SEQ ID NO: 14. In certain embodiments, the split site is located one or more polypeptide bond sites (i.e., a “split site or split-intein split site”), fused to a split intein, and then delivered to cells as separately- encoded fusion proteins. Once the split-intein fusion proteins (i.e., protein halves) are expressed within a cell, the proteins undergo trans-splicing to form a complete or whole PE with the concomitant removal of the joined split-intein sequences. [0724] In some embodiments, the N-terminal extein can be fused to a first split-intein (e.g., N intein) and the C-terminal extein can be fused to a second split-intein (e.g., C intein). The N-terminal extein becomes fused to the C-terminal extein to reform a whole prime editor fusion protein comprising an napDNAbp domain and a polymerase domain (e.g., RT domain) upon the self-association of the N intein and the C intein inside the cell, followed by their self-excision, and the concomitant formation of a peptide bond between the N-terminal extein and C-terminal extein portions of a whole prime editor (PE). [0725] To take advantage of a split-PE delivery strategy using split-inteins, the prime editor needs to be divided at one or more split sites to create at least two separate halves of a prime editor, each of which may be rejoined inside a cell if each half is fused to a split-intein sequence. [0726] In certain embodiments, the prime editor is split at a single split site. In certain other embodiments, the prime editor is split at two split sites, or three split sites, or four split sites, or more. [0727] In a preferred embodiment, the prime editor is split at a single split site to create two separate halves of a prime editor, each of which can be fused to a split intein sequence [0728] An exemplary split intein is the Ssp DnaE intein, which comprises two subunits, namely, DnaE-N and DnaE-C. The two different subunits are encoded by separate genes, namely dnaE-n and dnaE-c, which encode the DnaE-N and DnaE-C subunits, respectively. DnaE is a naturally occurring split intein in Synechocytis sp. PCC6803 and is capable of directing trans-splicing of two separate proteins, each comprising a fusion with either DnaE- N or DnaE-C. [0729] Additional naturally occurring or engineered split-intein sequences are known in the or can be made from whole-intein sequences described herein or those available in the art. Examples of split-intein sequences can be found in Stevens et al., “A promiscuous split intein with expanded protein engineering applications,” PNAS, 2017, Vol.114: 8538-8543; Iwai et al., “Highly efficient protein trans-splicing by a naturally split DnaE intein from Nostc punctiforme, FEBS Lett, 580: 1853-1858, each of which are incorporated herein by reference. Additional split intein sequences can be found, for example, in WO 2013/045632, WO 2014/055782, WO 2016/069774, and EP2877490, the contents each of which are incorporated herein by reference. [0730] In addition, protein splicing in trans has been described in vivo and in vitro (Shingledecker, et al., [0076] Gene 207:187 (1998), Southworth, et al., EMBO J.17:918 (1998); Mills, et al., Proc. Natl. Acad. Sci. USA, 95:3543-3548 (1998); Lew, et al., J. Biol. Chem., 273:15887-15890 (1998); Wu, et al., Biochim. Biophys. Acta 35732:1 (1998b), Yamazaki, et al., J. Am. Chem. Soc.120:5591 (1998), Evans, et al., J. Biol. Chem.275:9091 (2000); Otomo, et al., Biochemistry 38:16040-16044 (1999); Otomo, et al., J. Biolmol. NMR 14:105-114 (1999); Scott, et al., Proc. Natl. Acad. Sci. USA 96:13638-13643 (1999)) and provides the opportunity to express a protein as to two inactive fragments that subsequently undergo ligation to form a functional product. [0731] In various embodiments described herein, the continuous evolution methods (e.g., PACE) may be used to evolve a first portion of a base editor. A first portion could include a single component or domain, e.g., a Cas9 domain, a deaminase domain, or a UGI domain. The separately evolved component or domain can be then fused to the remaining portions of the base editor within a cell by separately express both the evolved portion and the remaining non-evolved portions with split-intein polypeptide domains. The first portion could more broadly include any first amino acid portion of a base editor that is desired to be evolved using a continuous evolution method described herein. The second portion would in this embodiment refer to the remaining amino acid portion of the base editor that is not evolved using the herein methods. The evolved first portion and the second portion of the base editor could each be expressed with split-intein polypeptide domains in a cell. The natural protein splicing mechanisms of the cell would reassemble the evolved first portion and the non- evolved second portion to form a single fusion protein evolved base editor. The evolved first portion may comprise either the N- or C-terminal part of the single fusion protein. In an analogous manner, use of a second orthogonal trans-splicing intein pair could allow the evolved first portion to comprise an internal part of the single fusion protein. [0732] Thus, any of the evolved and non-evolved components of the base editors herein described may be expressed with split-intein tags in order to facilitate the formation of a complete base editor comprising the evolved and non-evolved component within a cell. [0733] The mechanism of the protein splicing process has been studied in great detail (Chong, et al., J. Biol. Chem.1996, 271, 22159-22168; Xu, M-Q & Perler, F. B. EMBO Journal, 1996, 15, 5146-5153) and conserved amino acids have been found at the intein and extein splicing points (Xu, et al., EMBO Journal, 1994, 135517-522). The constructs described herein contain an intein sequence fused to the 5′-terminus of the first gene (e.g., the evolved portion of the base editor). Suitable intein sequences can be selected from any of the proteins known to contain protein splicing elements. A database containing all known inteins can be found on the World Wide Web (Perler, F. B. Nucleic Acids Research, 1999, 27, 346- 347). The intein sequence is fused at the 3′ end to the 5′ end of a second gene. For targeting of this gene to a certain organelle, a peptide signal can be fused to the coding sequence of the gene. After the second gene, the intein-gene sequence can be repeated as often as desired for expression of multiple proteins in the same cell. For multi-intein containing constructs, it may be useful to use intein elements from different sources. After the sequence of the last gene to be expressed, a transcription termination sequence must be inserted.In one embodiment, a modified intein splicing unit is designed so that it can both catalyze excision of the exteins from the inteins as well as prevent ligation of the exteins. Mutagenesis of the C-terminal extein junction in the Pyrococcus species GB-D DNA polymerase was found to produce an altered splicing element that induces cleavage of exteins and inteins but prevents subsequent ligation of the exteins (Xu, M-Q & Perler, F. B. EMBO Journal, 1996, 15, 5146-5153). Mutation of serine 538 to either an alanine or glycine induced cleavage but prevented ligation. Mutation of equivalent residues in other intein splicing units should also prevent extein ligation due to the conservation of amino acids at the C-terminal extein junction to the intein. A preferred intein not containing an endonuclease domain is the Mycobacterium xenopi GyrA protein (Telenti, et al. J. Bacteriol.1997, 179, 6378-6382). Others have been found in nature or have been created artificially by removing the endonuclease domains from endonuclease containing inteins (Chong, et al. J. Biol. Chem.1997, 272, 15587-15590). In a preferred embodiment, the intein is selected so that it consists of the minimal number of amino acids needed to perform the splicing function, such as the intein from the Mycobacterium xenopi GyrA protein (Telenti, A., et al., J. Bacteriol.1997, 179, 6378-6382). In an alternative embodiment, an intein without endonuclease activity is selected, such as the intein from the Mycobacterium xenopi GyrA protein or the Saccharaomyces cerevisiae VMA intein that has been modified to remove endonuclease domains (Chong, 1997).Further modification of the intein splicing unit may allow the reaction rate of the cleavage reaction to be altered allowing protein dosage to be controlled by simply modifying the gene sequence of the splicing unit. [0734] Inteins can also exist as two fragments encoded by two separately transcribed and translated genes. These so-called split inteins self-associate and catalyze protein- splicing activity in trans. Split inteins have been identified in diverse cyanobacteria and archaea (Caspi et al, Mol Microbiol.50: 1569-1577 (2003); Choi J. et al, J Mol Biol.556: 1093-1106 (2006.); Dassa B. et al, Biochemistry.46:322-330 (2007.); Liu X. and Yang J., J Biol Chem. 275:26315-26318 (2003); Wu H. et al. [0735] Proc Natl Acad Sci USA. £5:9226-9231 (1998.); and Zettler J. et al, FEBS Letters.553:909-914 (2009)), but have not been found in eukaryotes thus far. Recently, a bioinformatic analysis of environmental metagenomic data revealed 26 different loci with a novel genomic arrangement. At each locus, a conserved enzyme coding region is interrupted by a split intein, with a freestanding endonuclease gene inserted between the sections coding for intein subdomains. Among them, five loci were completely assembled: DNA helicases (gp41-l, gp41-8); Inosine-5 '-monophosphate dehydrogenase (IMPDH-1); and Ribonucleotide reductase catalytic subunits (NrdA-2 and NrdJ-1). This fractured gene organization appears to be present mainly in phages (Dassa et al, Nucleic Acids Research.57:2560-2573 (2009)). [0736] The split intein Npu DnaE was characterized as having the highest rate reported for the protein trans-splicing reaction. In addition, the Npu DnaE protein splicing reaction is considered robust and high-yielding with respect to different extein sequences, temperatures from 6 to 37°C, and the presence of up to 6M Urea (Zettler J. et al, FEBS Letters.553:909- 914 (2009); Iwai I. et al, FEBS Letters 550: 1853-1858 (2006)). As expected, when the Cysl Ala mutation at the N-domain of these inteins was introduced, the initial N to S- acyl shift and therefore protein splicing was blocked. Unfortunately, the C- terminal cleavage reaction was also almost completely inhibited. The dependence of the asparagine cyclization at the C- terminal splice junction on the acyl shift at the N-terminal scissile peptide bond seems to be a unique property common to the naturally split DnaE intein alleles (Zettler J. et al. FEBS Letters.555:909-914 (2009)). [0737] The mechanism of protein splicing typically has four steps [29-30]: 1) an N-S or N-O acyl shift at the intein N-terminus, which breaks the upstream peptide bond and forms an ester bond between the N- extein and the side chain of the intein's first amino acid (Cys or Ser); 2) a transesterification relocating the N-extein to the intein C-terminus, forming a new ester bond linking the N-extein to the side chain of the C-extein's first amino acid (Cys, Ser, or Thr); 3) Asn cyclization breaking the peptide bond between the intein and the C-extein; and 4) a S-N or O-N acyl shift that replaces the ester bond with a peptide bond between the N-extein and C-extein. [0738] Protein trans-splicing, catalyzed by split inteins, provides an entirely enzymatic method for protein ligation [31]. A split-intein is essentially a contiguous intein (e.g. a mini- intein) split into two pieces named N-intein and C-intein, respectively. The N-intein and C- intein of a split intein can associate non-covalently to form an active intein and catalyze the splicing reaction essentially in same way as a contiguous intein does. Split inteins have been found in nature and also engineered in laboratories [31-35]. As used herein, the term "split intein" refers to any intein in which one or more peptide bond breaks exists between the N- terminal and C-terminal amino acid sequences such that the N-terminal and C-terminal sequences become separate molecules that can non-covalently reassociate, or reconstitute, into an intein that is functional for trans-splicing reactions. Any catalytically active intein, or fragment thereof, may be used to derive a split intein for use in the methods of the invention. For example, in one aspect the split intein may be derived from a eukaryotic intein. In another aspect, the split intein may be derived from a bacterial intein. In another aspect, the split intein may be derived from an archaeal intein. Preferably, the split intein so-derived will possess only the amino acid sequences essential for catalyzing trans-splicing reactions. [0739] As used herein, the "N-terminal split intein (In)" refers to any intein sequence that comprises an N- terminal amino acid sequence that is functional for trans-splicing reactions. An In thus also comprises a sequence that is spliced out when trans-splicing occurs. An In can comprise a sequence that is a modification of the N-terminal portion of a naturally occurring intein sequence. For example, an In can comprise additional amino acid residues and/or mutated residues so long as the inclusion of such additional and/or mutated residues does not render the In non-functional in trans-splicing. Preferably, the inclusion of the additional and/or mutated residues improves or enhances the trans-splicing activity of the In. [0740] As used herein, the "C-terminal split intein (Ic)" refers to any intein sequence that comprises a C- terminal amino acid sequence that is functional for trans-splicing reactions. In one aspect, the Ic comprises 4 to 7 contiguous amino acid residues, at least 4 amino acids of which are from the last β-strand of the intein from which it was derived. An Ic thus also comprises a sequence that is spliced out when trans-splicing occurs. An Ic can comprise a sequence that is a modification of the C-terminal portion of a naturally occurring intein sequence. For example, an Ic can comprise additional amino acid residues and/or mutated residues so long as the inclusion of such additional and/or mutated residues does not render the In non-functional in trans-splicing. Preferably, the inclusion of the additional and/or mutated residues improves or enhances the trans-splicing activity of the Ic. [0741] In some embodiments of the invention, a peptide linked to an Ic or an In can comprise an additional chemical moiety including, among others, fluorescence groups, biotin, polyethylene glycol (PEG), amino acid analogs, unnatural amino acids, phosphate groups, glycosyl groups, radioisotope labels, and pharmaceutical molecules. In other embodiments, a peptide linked to an Ic can comprise one or more chemically reactive groups including, among others, ketone, aldehyde, Cys residues and Lys residues. The N-intein and C-intein of a split intein can associate non-covalently to form an active intein and catalyze the splicing reaction when an "intein-splicing polypeptide (ISP)" is present. As used herein, "intein- splicing polypeptide (ISP)" refers to the portion of the amino acid sequence of a split intein that remains when the Ic, In, or both, are removed from the split intein. In certain embodiments, the In comprises the ISP. In another embodiment, the Ic comprises the ISP. In yet another embodiment, the ISP is a separate peptide that is not covalently linked to In nor to Ic. [0742] Split inteins may be created from contiguous inteins by engineering one or more split sites in the unstructured loop or intervening amino acid sequence between the -12 conserved beta-strands found in the structure of mini-inteins [25-28]. Some flexibility in the position of the split site within regions between the beta-strands may exist, provided that creation of the split will not disrupt the structure of the intein, the structured beta-strands in particular, to a sufficient degree that protein splicing activity is lost. [0743] In protein trans-splicing, one precursor protein consists of an N-extein part followed by the N-intein, another precursor protein consists of the C-intein followed by a C- extein part, and a trans-splicing reaction (catalyzed by the N- and C-inteins together) excises the two intein sequences and links the two extein sequences with a peptide bond. Protein trans-splicing, being an enzymatic reaction, can work with very low (e.g. micromolar) concentrations of proteins and can be carried out under physiological conditions. Other programmable nucleases [0744] In various embodiments described herein, the prime editors comprise a napDNAbp, such as a Cas9 protein. These proteins are “programmable” by way of their becoming complexed with a guide RNA (or a PEgRNA, as the case may be), which guides the Cas9 protein to a target site on the DNA which possess a sequence that is complementary to the spacer portion of the gRNA (or PEgRNA) and also which possesses the required PAM sequence. However, in certain embodiment envisioned here, the napDNAbp may be substituted with a different type of programmable protein, such as a zinc finger nuclease or a transcription activator-like effector nuclease (TALEN). [0745] In some embodiments, the prime editors contemplated herein may replace the napDNAbp (e.g., SpCas9 nickase) with any programmable nuclease domain, such as zinc finger nucleases (ZFN) or transcription activator-like effector nucleases (TALEN). As such, it is contemplated that suitable nucleases do not necessarily need to be “programmed” by a nucleic acid targeting molecule (such as a guide RNA), but rather, may be programmed by defining the specificity of a DNA-binding domain, such as and in particular, a nuclease. Just as in prime editing with napDNAbp moities, it is preferable that such alternative programmable nucleases be modified such that only one strand of a target DNA is cut. In other words, the programmable nucleases should function as nickases, preferably. Once a programmable nuclease is selected (e.g., a ZFN or a TALEN), then additional functionalities may be engineered into the system to allow it to operate in accordance with a prime editing- like mechanism. For example, the programmable nucleases may be modified by coupling (e.g., via a chemical linker) an RNA or DNA extension arm thereto, wherein the extension arm comprises a primer binding site (PBS) and a DNA synthesis template. The programmable nuclease may also be coupled (e.g., via a chemical or amino acid linker) to a polymerase, the nature of which will depend upon whether the extension arm is DNA or RNA. In the case of an RNA extension arm, the polymerase can be an RNA-dependent DNA polymerase (e.g., reverse transcriptase). In the case of a DNA extension arm, the polymerase can be a DNA-dependent DNA polymerase (e.g., a prokaryotic polymerase, including Pol I, Pol II, or Pol III, or a eukaryotic polymerase, including Pol a, Pol b, Pol g, Pol d, Pol e, or Pol z). The system may also include other functionalities added as fusions to the programmable nucleases, or added in trans to facilitate the reaction as a whole (e.g., (a) a helicase to unwind the DNA at the cut site to make the cut strand with the 3’ end available as a primer, (b) a FEN1 to help remove the endogenous strand on the cut strand to drive the reaction towards replacement of the endogenous strand with the synthesized strand, or (c) a nCas9:gRNA complex to create a second site nick on the opposite strand, which may help drive the integration of the synthesize repair through favored cellular repair of the non-edited strand). In an analogous manner to prime editing with a napDNAbp, such a complex with an otherwise programmable nuclease could be used to synthesize and then install a newly synthesized replacement strand of DNA carrying an edit of interest permanently into a target site of DNA. [0746] Suitable alternative programmable nucleases are well known in the art which may be used in place of a napDNAbp:gRNA complex to construct an alternative prime editor system that can be programmed to selectively bind a target site of DNA, and which can be further modified in the manner described above to co-localize a polymerase and an RNA or DNA extension arm comprising a primer binding site and a DNA synthesis template to specific nick site. In some embodiments, the Transcription Activator-Like Effector Nucleases (TALENs) may be used as the programmable nuclease in the prime editing methods and compositions of matter described herein. TALENS are artificial restriction enzymes generated by fusing the TAL effector DNA binding domain to a DNA cleavage domain. These reagents enable efficient, programmable, and specific DNA cleavage and represent powerful tools for genome editing in situ. Transcription activator-like effectors (TALEs) can be quickly engineered to bind practically any DNA sequence. The term TALEN, as used herein, is broad and includes a monomeric TALEN that can cleave double stranded DNA without assistance from another TALEN. The term TALEN is also used to refer to one or both members of a pair of TALENs that are engineered to work together to cleave DNA at the same site. TALENs that work together may be referred to as a left-TALEN and a right- TALEN, which references the handedness of DNA. See U.S. Ser. No.12/965,590; U.S. Ser. No.13/426,991 (U.S. Pat. No.8,450,471); U.S. Ser. No.13/427,040 (U.S. Pat. No. 8,440,431); U.S. Ser. No.13/427,137 (U.S. Pat. No.8,440,432); and U.S. Ser. No. 13/738,381, all of which are incorporated by reference herein in their entirety. In addition, TALENS are described in WO 2015/027134, US 9,181,535, Boch et al., "Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors", Science, vol.326, pp.1509-1512 (2009), Bogdanove et al., TAL Effectors: Customizable Proteins for DNA Targeting, Science, vol.333, pp.1843-1846 (2011), Cade et al., "Highly efficient generation of heritable zebrafish gene mutations using homo- and heterodimeric TALENs", Nucleic Acids Research, vol.40, pp.8001-8010 (2012), and Cermak et al., "Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting", Nucleic Acids Research, vol.39, No.17, e82 (2011), each of which are incorporated herein by reference. [0747] In some embodiments, zinc finger nucleases may also be used as alternative programmable nucleases for use in prime editing in place of napDNAbps, such as Cas9 nickases. Like with TALENS, the ZFN proteins may be modified such that they function as nickases, i.e., engineering the ZFN such that it cleaves only one strand of the target DNA in a manner similar to the napDNAbp used with the prime editors described herein. ZFN proteins have been extensively described in the art, for example, in Carroll et al., “Genome Engineering with Zinc-Finger Nucleases,” Genetics, Aug 2011, Vol.188: 773-782; Durai et al., “Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells,” Nucleic Acids Res, 2005, Vol.33: 5978-90; and Gaj et al., “ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering,” Trends Biotechnol.2013, Vol.31: 397-405, each of which are incorporated herein by reference in their entireties. Polymerases (e.g., reverse transcriptase) [0748] In various embodiments, the prime editor (PE) system disclosed herein includes a polymerase (e.g., DNA-dependent DNA polymerase or RNA-dependent DNA polymerase, such as, reverse transcriptase), or a variant thereof, which can be provided as a fusion protein with a napDNAbp or other programmable nuclease, or provide in trans. [0749] Any polymerase may be used in the prime editors disclosed herein. The polymerases may be wild type polymerases, functional fragments, mutants, variants, or truncated variants, and the like. The polymerases may include wild type polymerases from eukaryotic, prokaryotic, archael, or viral organisms, and/or the polymerases may be modified by genetic engineering, mutagenesis, directed evolution-based processes. The polymerases may include T7 DNA polymerase, T5 DNA polymerase, T4 DNA polymerase, Klenow fragment DNA polymerase, DNA polymerase III and the like. The polymerases may also be thermostable, and may include Taq, Tne, Tma, Pfu, Tfl, Tth, Stoffel fragment, VENT® and DEEPVENT® DNA polymerases, KOD, Tgo, JDF3, and mutants, variants and derivatives thereof (see U.S. Pat. No.5,436,149; U.S. Pat. No.4,889,818; U.S. Pat. No.4,965,185; U.S. Pat. No.5,079,352; U.S. Pat. No.5,614,365; U.S. Pat. No.5,374,553; U.S. Pat. No. 5,270,179; U.S. Pat. No.5,047,342; U.S. Pat. No.5,512,462; WO 92/06188; WO 92/06200; WO 96/10640; Barnes, W. M., Gene 112:29-35 (1992); Lawyer, F. C., et al., PCR Meth. Appl.2:275-287 (1993); Flaman, J.-M, et al., Nuc. Acids Res.22(15):3259-3260 (1994), each of which are incorporated by reference). For synthesis of longer nucleic acid molecules (e.g, nucleic acid molecules longer than about 3-5 Kb in length), at least two DNA polymerases can be employed. In certain embodiments, one of the polymerases can be substantially lacking a 3' exonuclease activity and the other may have a 3' exonuclease activity. Such pairings may include polymerases that are the same or different. Examples of DNA polymerases substantially lacking in 3' exonuclease activity include, but are not limited to, Taq, Tne(exo-), Tma(exo-), Pfu(exo-), Pwo(exo-), exo-KOD and Tth DNA polymerases, and mutants, variants and derivatives thereof. [0750] Preferably, the polymerase usable in the prime editors disclosed herein are “template-dependent” polymerase (since the polymerases are intended to rely on the DNA synthesis template to specify the sequence of the DNA strand under synthesis during prime editing. As used herein, the term “template DNA molecule” refers to that strand of a nucleic acid from which a complementary nucleic acid strand is synthesized by a DNA polymerase, for example, in a primer extension reaction of the DNA synthesis template of a PEgRNA. [0751] As used herein, the term “template dependent manner” is intended to refer to a process that involves the template dependent extension of a primer molecule (e.g., DNA synthesis by DNA polymerase). The term “template dependent manner” refers to polynucleotide synthesis of RNA or DNA wherein the sequence of the newly synthesized strand of polynucleotide is dictated by the well-known rules of complementary base pairing (see, for example, Watson, J. D. et al., In: Molecular Biology of the Gene, 4th Ed., W. A. Benjamin, Inc., Menlo Park, Calif. (1987)). The term “complementary” refers to the broad concept of sequence complementarity between regions of two polynucleotide strands or between two nucleotides through base-pairing. It is known that an adenine nucleotide is capable of forming specific hydrogen bonds (“base pairing”) with a nucleotide which is thymine or uracil. Similarly, it is known that a cytosine nucleotide is capable of base pairing with a guanine nucleotide. As such, in the case of prime editing, it can be said that the single strand of DNA synthesized by the polymerase of the prime editor against the DNA synthesis template is said to be “complementary” to the sequence of the DNA synthesis template. Exemplary polymerases [0752] In various embodiments, the prime editors described herein comprise a polymerase. The disclosure contemplates any wild type polymerase obtained from any naturally-occurring organim or virus, or obtained from a commercial or non-commercial source. In addition, the polymerases usable in the prime editors of the disclosure can include any naturally-occuring mutant polymerase, engineered mutant polymerase, or other variant polymerase, including truncated variants that retain function. The polymerases usable herein may also be engineered to contain specific amino acid substitutions, such as those specifically disclosed herein. In certain preferred embodiments, the polymerases usable in the prime editors of the disclosure are template-based polymerases, i.e., they synthesize nucleotide sequences in a template-dependent manner. [0753] A polymerase is an enzyme that synthesizes a nucleotide strand and which may be used in connection with the prime editor systems described herein. The polymerases are preferrably “template-dependent” polymerases (i.e., a polymerase which synthesizes a nucleotide strand based on the order of nucleotide bases of a template strand). In certain configurations, the polymerases can also be a “template-independent” (i.e., a polymerase which synthesizes a nucleotide strand without the requirement of a template strand). A polymerase may also be further categorized as a “DNA polymerase” or an “RNA polymerase.” In various embodiments, the prime editor system comprises a DNA polymerase. In various embodiments, the DNA polymerase can be a “DNA-dependent DNA polymerase” (i.e., whereby the template molecule is a strand of DNA). In such cases, the DNA template molecule can be a PEgRNA, wherein the extension arm comprises a strand of DNA. In such cases, the PEgRNA may be referred to as a chimeric or hybrid PEgRNA which comprises an RNA portion (i.e., the guide RNA components, including the spacer and the gRNA core) and a DNA portion (i.e., the extension arm). In various other embodiments, the DNA polymerase can be an “RNA-dependent DNA polymerase” (i.e., whereby the template molecule is a strand of RNA). In such cases, the PEgRNA is RNA, i.e., including an RNA extension. The term “polymerase” may also refer to an enzyme that catalyzes the polymerization of nucleotide (i.e., the polymerase activity). Generally, the enzyme will initiate synthesis at the 3'-end of a primer annealed to a polynucleotide template sequence (e.g., such as a primer sequence annealed to the primer binding site of a PEgRNA), and will proceed toward the 5' end of the template strand. A “DNA polymerase” catalyzes the polymerization of deoxynucleotides. As used herein in reference to a DNA polymerase, the term DNA polymerase includes a “functional fragment thereof”. A “functional fragment thereof” refers to any portion of a wild-type or mutant DNA polymerase that encompasses less than the entire amino acid sequence of the polymerase and which retains the ability, under at least one set of conditions, to catalyze the polymerization of a polynucleotide. Such a functional fragment may exist as a separate entity, or it may be a constituent of a larger polypeptide, such as a fusion protein. [0754] In some embodiments, the polymerases can be from bacteriophage. Bacteriophage DNA polymerases are generally devoid of 5' to 3' exonuclease activity, as this activity is encoded by a separate polypeptide. Examples of suitable DNA polymerases are T4, T7, and phi29 DNA polymerase. The enzymes available commercially are: T4 (available from many sources e.g., Epicentre) and T7 (available from many sources, e.g. Epicentre for unmodified and USB for 3' to 5' exo T7 "Sequenase" DNA polymerase). [0755] The other embodiments, the polymerases are archaeal polymerases. There are 2 different classes of DNA polymerases which have been identified in archaea: 1. Family B/pol I type (homologs of Pfu from Pyrococcus furiosus) and 2. pol II type (homologs of P. furiosus DP1/DP22-subunit polymerase). DNA polymerases from both classes have been shown to naturally lack an associated 5' to 3' exonuclease activity and to possess 3' to 5' exonuclease (proofreading) activity. Suitable DNA polymerases (pol I or pol II) can be derived from archaea with optimal growth temperatures that are similar to the desired assay temperatures. [0756] Thermostable archaeal DNA polymerases are isolated from Pyrococcus species (furiosus, species GB-D, woesii, abysii, horikoshii), Thermococcus species (kodakaraensis KOD1, litoralis, species 9 degrees North-7, species JDF-3, gorgonarius), Pyrodictium occultum, and Archaeoglobus fulgidus. [0757] Polymerases may also be from eubacterial species. There are 3 classes of eubacterial DNA polymerases, pol I, II, and III. Enzymes in the Pol I DNA polymerase family possess 5' to 3' exonuclease activity, and certain members also exhibit 3' to 5' exonuclease activity. Pol II DNA polymerases naturally lack 5' to 3' exonuclease activity, but do exhibit 3' to 5' exonuclease activity. Pol III DNA polymerases represent the major replicative DNA polymerase of the cell and are composed of multiple subunits. The pol III catalytic subunit lacks 5' to 3' exonuclease activity, but in some cases 3' to 5' exonuclease activity is located in the same polypeptide. [0758] There are a variety of commercially available Pol I DNA polymerases, some of which have been modified to reduce or abolish 5' to 3' exonuclease activity. [0759] Suitable thermostable pol I DNA polymerases can be isolated from a variety of thermophilic eubacteria, including Thermus species and Thermotoga maritima such as Thermus aquaticus (Taq), Thermus thermophilus (Tth) and Thermotoga maritima (Tma UlTma). [0760] Additional eubacteria related to those listed above are described in Thermophilic Bacteria (Kristjansson, J. K., ed.) CRC Press, Inc., Boca Raton, Fla., 1992. [0761] The invention further provides for chimeric or non-chimeric DNA polymerases that are chemically modified according to methods disclosed in U.S. Pat. Nos.5,677,152, 6,479,264 and 6,183,998, the contents of which are hereby incorporated by reference in their entirety. [0762] Additional archaea DNA polymerases related to those listed above are described in the following references: Archaea: A Laboratory Manual (Robb, F. T. and Place, A. R., eds.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1995 and Thermophilic Bacteria (Kristjansson, J. K., ed.) CRC Press, Inc., Boca Raton, Fla., 1992. Exemplary reverse transcriptase [0763] In various embodiments, the prime editors described herein comprise a reverse transcriptase as the polymerase. The disclosure contemplates any wild type reverse transcriptase obtained from any naturally-occurring organim or virus, or obtained from a commercial or non-commercial source. In addition, the reverse transcriptases usable in the prime editors of the disclosure can include any naturally-occuring mutant RT, engineered mutant RT, or other variant RT, including truncated variants that retain function. The RTs may also be engineered to contain specific amino acid substitutions, such as those specifically disclosed herein. [0764] Reverse transcriptases are multi-functional enzymes typically with three enzymatic activities including RNA- and DNA-dependent DNA polymerization activity, and an RNaseH activity that catalyzes the cleavage of RNA in RNA-DNA hybrids. Some mutants of reverse transcriptases have disabled the RNaseH moiety to prevent unintended damage to the mRNA. These enzymes that synthesize complementary DNA (cDNA) using mRNA as a template were first identified in RNA viruses. Subsequently, reverse transcriptases were isolated and purified directly from virus particles, cells or tissues. (e.g., see Kacian et al., 1971, Biochim. Biophys. Acta 46: 365-83; Yang et al., 1972, Biochem. Biophys. Res. Comm.47: 505-11; Gerard et al., 1975, J. Virol.15: 785-97; Liu et al., 1977, Arch. Virol.55 187-200; Kato et al., 1984, J. Virol. Methods 9: 325-39; Luke et al., 1990, Biochem.29: 1764-69 and Le Grice et al., 1991, J. Virol.65: 7004-07, each of which are incorporated by reference). More recently, mutants and fusion proteins have been created in the quest for improved properties such as thermostability, fidelity and activity. Any of the wild type, variant, and/or mutant forms of reverse transcriptase which are known in the art or which can be made using methods known in the art are contemplated herein. [0765] The reverse transcriptase (RT) gene (or the genetic information contained therein) can be obtained from a number of different sources. For instance, the gene may be obtained from eukaryotic cells which are infected with retrovirus, or from a number of plasmids which contain either a portion of or the entire retrovirus genome. In addition, messenger RNA-like RNA which contains the RT gene can be obtained from retroviruses. Examples of sources for RT include, but are not limited to, Moloney murine leukemia virus (M-MLV or MLVRT); human T-cell leukemia virus type 1 (HTLV-1); bovine leukemia virus (BLV); Rous Sarcoma Virus (RSV); human immunodeficiency virus (HIV); yeast, including Saccharomyces, Neurospora, Drosophila; primates; and rodents. See, for example, Weiss, et al., U.S. Pat. No. 4,663,290 (1987); Gerard, G. R., DNA:271-79 (1986); Kotewicz, M. L., et al., Gene 35:249- 58 (1985); Tanese, N., et al., Proc. Natl. Acad. Sci. (USA):4944-48 (1985); Roth, M. J., at al., J. Biol. Chem.260:9326-35 (1985); Michel, F., et al., Nature 316:641-43 (1985); Akins, R. A., et al., Cell 47:505-16 (1986), EMBO J.4:1267-75 (1985); and Fawcett, D. F., Cell 47:1007-15 (1986) (each of which are incorporated herein by reference in their entireties). Wild type RTs [0766] Exemplary enzymes for use with the herein disclosed prime editors can include, but are not limited to, M-MLV reverse transcriptase and RSV reverse transcriptase. Enzymes having reverse transcriptase activity are commercially available. In certain embodiments, the reverse transcriptase provided in trans to the other components of the prime editor (PE) system. That is, the reverse transcriptase is expressed or otherwise provided as an individual component, i.e., not as a fusion protein with a napDNAbp. [0767] A person of ordinary skill in the art will recognize that wild type reverse transcriptases, including but not limited to, Moloney Murine Leukemia Virus (M-MLV); Human Immunodeficiency Virus (HIV) reverse transcriptase and avian Sarcoma-Leukosis Virus (ASLV) reverse transcriptase, which includes but is not limited to Rous Sarcoma Virus (RSV) reverse transcriptase, Avian Myeloblastosis Virus (AMV) reverse transcriptase, Avian Erythroblastosis Virus (AEV) Helper Virus MCAV reverse transcriptase, Avian Myelocytomatosis Virus MC29 Helper Virus MCAV reverse transcriptase, Avian Reticuloendotheliosis Virus (REV-T) Helper Virus REV-A reverse transcriptase, Avian Sarcoma Virus UR2 Helper Virus UR2AV reverse transcriptase, Avian Sarcoma Virus Y73 Helper Virus YAV reverse transcriptase, Rous Associated Virus (RAV) reverse transcriptase, and Myeloblastosis Associated Virus (MAV) reverse transcriptase may be suitably used in the subject methods and composition described herein. [0768] Exemplary wild type RT enzymes are provided in the Description of Sequences, Wild Type Polymerases (see SEQ ID NOs: 86-97): Variant and error-prone RTs [0769] Reverse transcriptases are essential for synthesizing complementary DNA (cDNA) strands from RNA templates. Reverse transcriptases are enzymes composed of distinct domains that exhibit different biochemical activities. The enzymes catalyze the synthesis of DNA from an RNA template, as follows: In the presence of an annealed primer, reverse transcriptase binds to an RNA template and initiates the polymerization reaction. RNA-dependent DNA polymerase activity synthesizes the complementary DNA (cDNA) strand, incorporating dNTPs. RNase H activity degrades the RNA template of the DNA:RNA complex. Thus, reverse transcriptases comprise (a) a binding activity that recognizes and binds to a RNA/DNA hybrid, (b) an RNA-dependent DNA polymerase activity, and (c) an RNase H activity. In addition, reverse transcriptases generally are regarded as having various attributes, including their thermostability, processivity (rate of dNTP incorporation), and fidelity (or error-rate). The reverse transcriptase variants contemplated herein may include any mutations to reverse transcriptase that impacts or changes any one or more of these enzymatic activities (e.g., RNA-dependent DNA polymerase activity, RNase H activity, or DNA/RNA hybrid-binding activity) or enzyme properties (e.g., thermostability, processivity, or fidelity). Such variants may be available in the art in the public domain, available commercially, or may be made using known methods of mutagenesis, including directed evolutionary processes (e.g., PACE or PANCE). [0770] In various embodiments, the reverse transcriptase may be a variant reverse transcriptase. As used herein, a “variant reverse transcriptase” includes any naturally occurring or genetically engineered variant comprising one or more mutations (including singular mutations, inversions, deletions, insertions, and rearrangements) relative to a reference sequences (e.g., a reference wild type sequence). RT naturally have several activities, including an RNA-dependent DNA polymerase activity, ribonuclease H activity, and DNA-dependent DNA polymerase activity. Collectively, these activities enable the enzyme to convert single-stranded RNA into double-stranded cDNA. In retroviruses and retrotransposons, this cDNA can then integrate into the host genome, from which new RNA copies can be made via host-cell transcription. Variant RT’s may comprise a mutation which impacts one or more of these activities (either which reduces or increases these activities, or which eliminates these activities all together). In addition, variant RTs may comprise one or more mutations which render the RT more or less stable, less prone to aggregration, and facilitates purification and/or detection, and/or other the modification of properties or characteristics. [0771] A person of ordinary skill in the art will recognize that variant reverse transcriptases derived from other reverse transcriptases, including but not limited to Moloney Murine Leukemia Virus (M-MLV); Human Immunodeficiency Virus (HIV) reverse transcriptase and avian Sarcoma-Leukosis Virus (ASLV) reverse transcriptase, which includes but is not limited to Rous Sarcoma Virus (RSV) reverse transcriptase, Avian Myeloblastosis Virus (AMV) reverse transcriptase, Avian Erythroblastosis Virus (AEV) Helper Virus MCAV reverse transcriptase, Avian Myelocytomatosis Virus MC29 Helper Virus MCAV reverse transcriptase, Avian Reticuloendotheliosis Virus (REV-T) Helper Virus REV-A reverse transcriptase, Avian Sarcoma Virus UR2 Helper Virus UR2AV reverse transcriptase, Avian Sarcoma Virus Y73 Helper Virus YAV reverse transcriptase, Rous Associated Virus (RAV) reverse transcriptase, and Myeloblastosis Associated Virus (MAV) reverse transcriptase may be suitably used in the subject methods and composition described herein. [0772] One method of preparing variant RTs is by genetic modification (e.g., by modifying the DNA sequence of a wild-type reverse transcriptase). A number of methods are known in the art that permit the random as well as targeted mutation of DNA sequences (see for example, Ausubel et. al. Short Protocols in Molecular Biology (1995) 3.sup.rd Ed. John Wiley & Sons, Inc.). In addition, there are a number of commercially available kits for site- directed mutagenesis, including both conventional and PCR-based methods. Examples include the QuikChange Site-Directed Mutagenesis Kits (AGILENT®), the Q5® Site- Directed Mutagenesis Kit (NEW ENGLAND BIOLABS®), and GeneArt™ Site-Directed Mutagenesis System (THERMOFISHER SCIENTIFIC®). [0773] In addition, mutant reverse transcriptases may be generated by insertional mutation or truncation (N-terminal, internal, or C-terminal insertions or truncations) according to methodologies known to one skilled in the art. The term “mutation,” as used herein, refers to a substitution of a residue within a sequence, e.g., a nucleic acid or amino acid sequence, with another residue, or a deletion or insertion of one or more residues within a sequence. Mutations are typically described herein by identifying the original residue followed by the position of the residue within the sequence and by the identity of the newly substituted residue. Various methods for making the amino acid substitutions (mutations) provided herein are well known in the art, and are provided by, for example, Green and Sambrook, Molecular Cloning: A Laboratory Manual (4th ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2012)). Mutations can include a variety of categories, such as single base polymorphisms, microduplication regions, indel, and inversions, and is not meant to be limiting in any way. Mutations can include “loss-of- function” mutations which is the normal result of a mutation that reduces or abolishes a protein activity. Most loss-of-function mutations are recessive, because in a heterozygote the second chromosome copy carries an unmutated version of the gene coding for a fully functional protein whose presence compensates for the effect of the mutation. Mutations also embrace “gain-of-function” mutations, which is one which confers an abnormal activity on a protein or cell that is otherwise not present in a normal condition. Many gain-of-function mutations are in regulatory sequences rather than in coding regions, and can therefore have a number of consequences. For example, a mutation might lead to one or more genes being expressed in the wrong tissues, these tissues gaining functions that they normally lack. Because of their nature, gain-of-function mutations are usually dominant. [0774] Older methods of site-directed mutagenesis known in the art rely on sub-cloning of the sequence to be mutated into a vector, such as an M13 bacteriophage vector, that allows the isolation of single-stranded DNA template. In these methods, one anneals a mutagenic primer (i.e., a primer capable of annealing to the site to be mutated but bearing one or more mismatched nucleotides at the site to be mutated) to the single-stranded template and then polymerizes the complement of the template starting from the 3ʹ end of the mutagenic primer. The resulting duplexes are then transformed into host bacteria and plaques are screened for the desired mutation. [0775] More recently, site-directed mutagenesis has employed PCR methodologies, which have the advantage of not requiring a single-stranded template. In addition, methods have been developed that do not require sub-cloning. Several issues must be considered when PCR-based site-directed mutagenesis is performed. First, in these methods it is desirable to reduce the number of PCR cycles to prevent expansion of undesired mutations introduced by the polymerase. Second, a selection must be employed in order to reduce the number of non- mutated parental molecules persisting in the reaction. Third, an extended-length PCR method is preferred in order to allow the use of a single PCR primer set. And fourth, because of the non-template-dependent terminal extension activity of some thermostable polymerases it is often necessary to incorporate an end-polishing step into the procedure prior to blunt-end ligation of the PCR-generated mutant product. [0776] Methods of random mutagenesis, which will result in a panel of mutants bearing one or more randomly situated mutations, exist in the art. Such a panel of mutants may then be screened for those exhibiting the desired properties, for example, increased stability, relative to a wild-type reverse transcriptase. [0777] An example of a method for random mutagenesis is the so-called “error-prone PCR method.” As the name implies, the method amplifies a given sequence under conditions in which the DNA polymerase does not support high fidelity incorporation. Although the conditions encouraging error-prone incorporation for different DNA polymerases vary, one skilled in the art may determine such conditions for a given enzyme. A key variable for many DNA polymerases in the fidelity of amplification is, for example, the type and concentration of divalent metal ion in the buffer. The use of manganese ion and/or variation of the magnesium or manganese ion concentration may therefore be applied to influence the error rate of the polymerase. [0778] In various aspects, the RT of the prime editors may be an “error-prone” reverse transcriptase variant. Error-prone reverse transcriptases that are known and/or available in the art may be used. It will be appreciated that reverse transcriptases naturally do not have any proofreading function; thus the error rate of reverse transcriptase is generally higher than DNA polymerases comprising a proofreading activity. The error-rate of any particular reverse transcriptase is a property of the enzyme’s “fidelity,” which represents the accuracy of template-directed polymerization of DNA against its RNA template. An RT with high fidelity has a low-error rate. Conversely, an RT with low fidelity has a high-error rate. The fidelity of M-MLV-based reverse transcriptases are reported to have an error rate in the range of one error in 15,000 to 27,000 nucleotides synthesized. See Boutabout et al., “DNA synthesis fidelity by the reverse transcriptase of the yeast retrotransposon Ty1,” Nucleic Acids Res, 2001, 29: 2217-2222, which is incorporated by reference. Thus, for purposes of this application, those reverse transcriptases considered to be “error-prone” or which are considered to have an “error-prone fidelity” are those having an error rate that is less than one error in 15,000 nucleotides synthesized. [0779] Error-prone reverse transcriptase also may be created through mutagenesis of a starting RT enzyme (e.g., a wild type M-MLV RT). The method of mutagenesis is not limited and may include directed evolution processes, such as phage-assisted continuous evolution (PACE) or phage-assisted noncontinuous evolution (PANCE). The term “phage- assisted continuous evolution (PACE),” as used herein, refers to continuous evolution that employs phage as viral vectors. The general concept of PACE technology has been described, for example, in International PCT Application, PCT/US2009/056194, filed September 8, 2009, published as WO 2010/028347 on March 11, 2010; International PCT Application, PCT/US2011/066747, filed December 22, 2011, published as WO 2012/088381 on June 28, 2012; U.S. Application, U.S. Patent No.9,023,594, issued May 5, 2015, International PCT Application, PCT/US2015/012022, filed January 20, 2015, published as WO 2015/134121 on September 11, 2015, and International PCT Application, PCT/US2016/027795, filed April 15, 2016, published as WO 2016/168631 on October 20, 2016, the entire contents of each of which are incorporated herein by reference. [0780] Error-prone reverse transcriptases may also be obtain by phage-assisted non- continuous evolution (PANCE),” which as used herein, refers to non-continuous evolution that employs phage as viral vectors. PANCE is a simplified technique for rapid in vivo directed evolution using serial flask transfers of evolving ‘selection phage’ (SP), which contain a gene of interest to be evolved, across fresh E. coli host cells, thereby allowing genes inside the host E. coli to be held constant while genes contained in the SP continuously evolve. Serial flask transfers have long served as a widely-accessible approach for laboratory evolution of microbes, and, more recently, analogous approaches have been developed for bacteriophage evolution. The PANCE system features lower stringency than the PACE system. [0781] Other error-prone reverse transcriptases have been described in the literature, each of which are contemplated for use in the herein methods and compositions. For example, error-prone reverse transcriptases have been described in Bebenek et al., “Error-prone Polymerization by HIV-1 Reverse Transcriptase,” J Biol Chem, 1993, Vol.268: 10324- 10334 and Sebastian-Martin et al., “Transcriptional inaccuracy threshold attenuates differences in RNA-dependent DNA synthesis fidelity between retroviral reverse transcriptases,” Scientific Reports, 2018, Vol.8: 627, each of which are incorporated by reference. Still further, reverse transcriptases, including error-prone reverse transcriptases can be obtained from a commercial supplier, including ProtoScript® (II) Reverse Transcriptase, AMV Reverse Transcriptase, WarmStart® Reverse Transcriptase, and M- MuLV Reverse Transcriptase, all from NEW ENGLAND BIOLABS®, or AMV Reverse Transcriptase XL, SMARTScribe Reverse Transcriptase, GPR ultra-pure MMLV Reverse Transcriptase, all from TAKARA BIO USA, INC. (formerly CLONTECH). [0782] The herein disclosure also contemplates reverse transcriptases having mutations in RNaseH domain. As mentioned above, one of the intrinsic properties of reverse transcriptases is the RNase H activity, which cleaves the RNA template of the RNA:cDNA hybrid concurrently with polymerization. The RNase H activity can be undesirable for synthesis of long cDNAs because the RNA template may be degraded before completion of full-length reverse transcription. The RNase H activity may also lower reverse transcription efficiency, presumably due to its competition with the polymerase activity of the enzyme. Thus, the present disclosure contemplates any reverse transcriptase variants that comprise a modified RNaseH activity. [0783] The herein disclosure also contemplates reverse transcriptases having mutations in the RNA-dependent DNA polymerase domain. As mentioned above, one of the intrinsic properties of reverse transcriptases is the RNA-dependent DNA polymerase activity, which incorporates the nucleobases into the nascent cDNA strand as coded by the template RNA strand of the RNA:cDNA hybrid. The RNA-dependent DNA polymerase activity can be increased or decreased (i.e., in terms of its rate of incorporation) to either increase or decrease the processivity of the enzyme. Thus, the present disclosure contemplates any reverse transcriptase variants that comprise a modified RNA-dependent DNA polymerase activity such that the processivity of the enzyme of either increased or decreased relative to an unmodified version. [0784] Also contemplated herein are reverse transcriptase variants that have altered thermostability characteristics. The ability of a reverse transcriptase to withstand high temperatures is an important aspect of cDNA synthesis. Elevated reaction temperatures help denature RNA with strong secondary structures and/or high GC content, allowing reverse transcriptases to read through the sequence. As a result, reverse transcription at higher temperatures enables full-length cDNA synthesis and higher yields, which can lead to an improved generation of the 3ʹ flap ssDNA as a result of the prime editing process. Wild type M-MLV reverse transcriptase typically has an optimal temperature in the range of 37-48ºC; however, mutations may be introduced that allow for the reverse transcription activity at higher temperatures of over 48ºC, including 49ºC, 50ºC, 51ºC, 52ºC, 53ºC, 54ºC, 55ºC, 56ºC, 57ºC, 58ºC, 59ºC, 60ºC, 61ºC, 62ºC, 63ºC¸64ºC¸65ºC¸66ºC, and higher. [0785] The variant reverse transcriptases contemplated herein, including error-prone RTs, thermostable RTs, increase-processivity RTs, can be engineered by various routine strategies, including mutagenesis or evolutionary processes. In some cases, the variants can be produced by introducing a single mutation. In other cases, the variants may require more than one mutation. For those mutants comprising more than one mutation, the effect of a given mutation may be evaluated by introduction of the identified mutation to the wild-type gene by site-directed mutagenesis in isolation from the other mutations borne by the particular mutant. Screening assays of the single mutant thus produced will then allow the determination of the effect of that mutation alone. [0786] Variant RT enzymes used herein may also include other “RT variants” having at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to any reference RT protein, including any wild type RT, or mutant RT, or fragment RT, or other variant of RT disclosed or contemplated herein or known in the art. [0787] In some embodiments, an RT variant may have 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, or up to 100, or up to 200, or up to 300, or up to 400, or up to 500 or more amino acid changes compared to a reference RT. In some embodiments, the RT variant comprises a fragment of a reference RT, such that the fragment is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to the corresponding fragment of the reference RT. In some embodiments, the fragment is is at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% identical, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% of the amino acid length of a corresponding wild type RT (M-MLV reverse transcriptase) (e.g., SEQ ID NO: 86) or to any of the reverse transcriptases of SEQ ID NOs: 87-97. [0788] In some embodiments, the disclosure also may utilize RT fragments which retain their functionality and which are fragments of any herein disclosed RT proteins. In some embodiments, the RT fragment is at least 100 amino acids in length. In some embodiments, the fragment is at least 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, or up to 600 or more amino acids in length. [0789] In still other embodiments, the disclosure also may utilize RT variants which are truncated at the N-terminus or the C-terminus, or both, by a certain number of amino acids which results in a truncated variant which still retains sufficient polymerase function. In some embodiments, the RT truncated variant has a truncation of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, or 250 amino acids at the N-terminal end of the protein. In other embodiments, the RT truncated variant has a truncation of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, or 250 amino acids at the C-terminal end of the protein. In still other embodiments, the RT truncated variant has a trunction at the N-terminal and the C- terminal end which are the same or different lengths. [0790] For example, the prime editors disclosed herein may include a truncated version of M-MLV reverse transcriptase. In this embodiment, the reverse transcriptase contains 4 mutations (D200N, T306K, W313F, T330P; noting that the L603W mutation present in PE2 is no longer present due to the truncation). The DNA sequence encoding this truncated editor is 522 bp smaller than PE2, and therefore makes its potentially useful for applications where delivery of the DNA sequence is challenging due to its size (i.e., adeno-associated virus and lentivirus delivery). This embodiment is referred to as MMLV-RT(trunc) and has the following amino acid sequence of SEQ ID NO:98 (see Description of Sequences, Variant and error prone RTs) [0791] In various embodiments, the prime editors disclosed herein may comprise one of the RT variants described herein, or a RT variant thereof having at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to any reference Cas9 variants. [0792] In still other embodiments, the present methods and compositions may utilize a DNA polymerase that has been evolved into a reverse transcriptase, as described in Effefson et al., “Synthetic evolutionary origin of a proofreading reverse transcriptase,” Science, June 24, 2016, Vol.352: 1590-1593, the contents of which are incorporated herein by reference. [0793] In certain other embodiments, the reverse transcriptase is provided as a component of a fusion protein also comprising a napDNAbp. In other words, in some embodiments, the reverse transcriptase is fused to a napDNAbp as a fusion protein. [0794] In various embodiments, variant reverse transcriptases can be engineered from wild type M-MLV reverse transcriptase as represented by SEQ ID NO: 86. [0795] In various embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising one or more of the following mutations: P51L, S67K, E69K, L139P, T197A, D200N, H204R, F209N, E302K, E302R, T306K, F309N, W313F, T330P, L345G, L435G, N454K, D524G, E562Q, D583N, H594Q, L603W, E607K, or D653N in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence. [0796] Some exemplary reverse transcriptases that can be fused to napDNAbp proteins or provided as individual proteins according to various embodiments of this disclosure are provided in the Description of Sequences (Variant and error prone RTs, SEQ ID NOs: 86- 97). Exemplary reverse transcriptases include variants with at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity to wild-type enzymes or partial enzymes comprising SEQ ID NOs: 86-97: [0797] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising one or more of the following mutations: P51X, S67X, E69X, L139X, T197X, D200X, H204X, F209X, E302X, T306X, F309X, W313X, T330X, L345X, L435X, N454X, D524X, E562X, D583X, H594X, L603X, E607X, or D653X in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. [0798] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a P51X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is L. [0799] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a S67X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is K. [0800] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a E69X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is K. [0801] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a L139X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is P. [0802] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a T197X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is A. [0803] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a D200X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is N. [0804] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a H204X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is R. [0805] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a F209X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is N. [0806] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a E302X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is K. [0807] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a E302X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is R. [0808] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a T306X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is K. [0809] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a F309X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is N. [0810] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a W313X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is F. [0811] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a T330X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is P. [0812] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a L345X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is G. [0813] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a L435X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is G. [0814] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a N454X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is K. [0815] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a D524X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is G. [0816] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a E562X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is Q. [0817] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a D583X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is N. [0818] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a H594X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is Q. [0819] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a L603X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is W. [0820] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a E607X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is K. [0821] In various other embodiments, the prime editors described herein (with RT provided as either a fusion partner or in trans) can include a variant RT comprising a D653X mutation in the wild type M-MLV RT of SEQ ID NO: 86 or at a corresponding amino acid position in another wild type RT polypeptide sequence, wherein “X” can be any amino acid. In certain embodiments, X is N. [0822] Some exemplary reverse transcriptases that can be fused to napDNAbp proteins or provided as individual proteins according to various embodiments of this disclosure are provided in the Description of Sequences (Variant and error prone RTs, see SEQ ID NOs: 86, 98, or 100-116). Exemplary reverse transcriptases include variants with at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to wild-type enzymes or partial enzymes with SEQ ID NOs: 86, 98, or 100-116. [0823] The prime editor (PE) system described here contemplates any publicly-available reverse transcriptase described or disclosed in any of the following U.S. patents (each of which are incorporated by reference in their entireties): U.S. Patent Nos: 10,202,658; 10,189,831; 10,150,955; 9,932,567; 9,783,791; 9,580,698; 9,534,201; and 9,458,484, and any variant thereof that can be made using known methods for installing mutations, or known methods for evolving proteins. The following references describe reverse transcriptases in art. Each of their disclosures are incorporated herein by reference in their entireties. [0824] Herzig, E., Voronin, N., Kucherenko, N. & Hizi, A. A Novel Leu92 Mutant of HIV-1 Reverse Transcriptase with a Selective Deficiency in Strand Transfer Causes a Loss of Viral Replication. J. Virol.89, 8119–8129 (2015). [0825] Mohr, G. et al. A Reverse Transcriptase-Cas1 Fusion Protein Contains a Cas6 Domain Required for Both CRISPR RNA Biogenesis and RNA Spacer Acquisition. Mol. Cell 72, 700-714.e8 (2018). [0826] Zhao, C., Liu, F. & Pyle, A. M. An ultraprocessive, accurate reverse transcriptase encoded by a metazoan group II intron. RNA 24, 183–195 (2018). [0827] Zimmerly, S. & Wu, L. An Unexplored Diversity of Reverse Transcriptases in Bacteria. Microbiol Spectr 3, MDNA3-0058–2014 (2015). [0828] Ostertag, E. M. & Kazazian Jr, H. H. Biology of Mammalian L1 Retrotransposons. Annual Review of Genetics 35, 501–538 (2001). [0829] Perach, M. & Hizi, A. Catalytic Features of the Recombinant Reverse Transcriptase of Bovine Leukemia Virus Expressed in Bacteria. Virology 259, 176–189 (1999). [0830] Lim, D. et al. Crystal structure of the moloney murine leukemia virus RNase H domain. J. Virol.80, 8379–8389 (2006). [0831] Zhao, C. & Pyle, A. M. Crystal structures of a group II intron maturase reveal a missing link in spliceosome evolution. Nature Structural & Molecular Biology 23, 558–565 (2016). [0832] Griffiths, D. J. Endogenous retroviruses in the human genome sequence. Genome Biol.2, REVIEWS1017 (2001). [0833] Baranauskas, A. et al. Generation and characterization of new highly thermostable and processive M-MuLV reverse transcriptase variants. Protein Eng Des Sel 25, 657–668 (2012). [0834] Zimmerly, S., Guo, H., Perlman, P. S. & Lambowltz, A. M. Group II intron mobility occurs by target DNA-primed reverse transcription. Cell 82, 545–554 (1995). [0835] Feng, Q., Moran, J. V., Kazazian, H. H. & Boeke, J. D. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87, 905–916 (1996). [0836] Berkhout, B., Jebbink, M. & Zsíros, J. Identification of an Active Reverse Transcriptase Enzyme Encoded by a Human Endogenous HERV-K Retrovirus. Journal of Virology 73, 2365–2375 (1999). [0837] Kotewicz, M. L., Sampson, C. M., D’Alessio, J. M. & Gerard, G. F. Isolation of cloned Moloney murine leukemia virus reverse transcriptase lacking ribonuclease H activity. Nucleic Acids Res 16, 265–277 (1988). [0838] Arezi, B. & Hogrefe, H. Novel mutations in Moloney Murine Leukemia Virus reverse transcriptase increase thermostability through tighter binding to template-primer. Nucleic Acids Res 37, 473–481 (2009). [0839] Blain, S. W. & Goff, S. P. Nuclease activities of Moloney murine leukemia virus reverse transcriptase. Mutants with altered substrate specificities. J. Biol. Chem.268, 23585– 23592 (1993). [0840] Xiong, Y. & Eickbush, T. H. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J 9, 3353–3362 (1990). [0841] Herschhorn, A. & Hizi, A. Retroviral reverse transcriptases. Cell. Mol. Life Sci. 67, 2717–2747 (2010). [0842] Taube, R., Loya, S., Avidan, O., Perach, M. & Hizi, A. Reverse transcriptase of mouse mammary tumour virus: expression in bacteria, purification and biochemical characterization. Biochem. J.329 ( Pt 3), 579–587 (1998). [0843] Liu, M. et al. Reverse Transcriptase-Mediated Tropism Switching in Bordetella Bacteriophage. Science 295, 2091–2094 (2002). [0844] Luan, D. D., Korman, M. H., Jakubczak, J. L. & Eickbush, T. H. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell 72, 595–605 (1993). [0845] Nottingham, R. M. et al. RNA-seq of human reference RNA samples using a thermostable group II intron reverse transcriptase. RNA 22, 597–613 (2016). [0846] Telesnitsky, A. & Goff, S. P. RNase H domain mutations affect the interaction between Moloney murine leukemia virus reverse transcriptase and its primer-template. Proc. Natl. Acad. Sci. U.S.A.90, 1276–1280 (1993). [0847] Halvas, E. K., Svarovskaia, E. S. & Pathak, V. K. Role of Murine Leukemia Virus Reverse Transcriptase Deoxyribonucleoside Triphosphate-Binding Site in Retroviral Replication and In Vivo Fidelity. Journal of Virology 74, 10349–10358 (2000). [0848] Nowak, E. et al. Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid. Nucleic Acids Res 41, 3874–3887 (2013). [0849] Stamos, J. L., Lentzsch, A. M. & Lambowitz, A. M. Structure of a Thermostable Group II Intron Reverse Transcriptase with Template-primer and Its Functional and Evolutionary Implications. Molecular Cell 68, 926-939.e4 (2017). [0850] Das, D. & Georgiadis, M. M. The Crystal Structure of the Monomeric Reverse Transcriptase from Moloney Murine Leukemia Virus. Structure 12, 819–829 (2004). [0851] Avidan, O., Meer, M. E., Oz, I. & Hizi, A. The processivity and fidelity of DNA synthesis exhibited by the reverse transcriptase of bovine leukemia virus. European Journal of Biochemistry 269, 859–867 (2002). [0852] Gerard, G. F. et al. The role of template-primer in protection of reverse transcriptase from thermal inactivation. Nucleic Acids Res 30, 3118–3129 (2002). [0853] Monot, C. et al. The Specificity and Flexibility of L1 Reverse Transcription Priming at Imperfect T-Tracts. PLOS Genetics 9, e1003499 (2013). [0854] Mohr, S. et al. Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing. RNA 19, 958–970 (2013). [0855] Any of the references noted above which relate to reverse transriptases are hereby incorporated by reference in their entireties, if not already stated so. PE fusion proteins [0856] The prime editor (PE) system described herein contemplate fusion proteins comprising a napDNAbp and a polymerase (e.g., DNA-dependent DNA polymerase or RNA- dependent DNA polymerase, such as, reverse transcriptase), and optionally joined by a linker. The application contemplates any suitable napDNAbp and polymerase (e.g., DNA-dependent DNA polymerase or RNA-dependent DNA polymerase, such as, reverse transcriptase) to be combined in a single fusion protein. Examples of napDNAbps and polymerases (e.g., DNA- dependent DNA polymerase or RNA-dependent DNA polymerase, such as, reverse transcriptase) are each defined herein. Since polymerases are well-known in the art, and the amino acid sequences are readily available, this disclosure is not meant in any way to be limited to those specific polymerases identified herein. [0857] In various embodiments, the fusion proteins may comprise any suitable structural configuration. For example, the fusion protein may comprise from the N-terminus to the C- terminus direction, a napDNAbp fused to a polymerase (e.g., DNA-dependent DNA polymerase or RNA-dependent DNA polymerase, such as, reverse transcriptase) . In other embodiments, the fusion protein may comprise from the N-terminus to the C-terminus direction, a polymerase (e.g., a reverse transcriptase) fused to a napDNAbp. The fused domain may optionally be joined by a linker, e.g., an amino acid sequence. In other embodiments, the fusion proteins may comprise the structure NH2-[napDNAbp]-[ polymerase]-COOH; or NH2-[polymerase]-[napDNAbp]-COOH, wherein each instance of indicates the presence of an optional linker sequence. In embodiments wherein the polymerase is a reverse transcriptase, the fusion proteins may comprise the structure NH2- [napDNAbp]-[RT]-COOH; or NH2-[RT]-[napDNAbp]-COOH, wherein each instance of “]- [“ indicates the presence of an optional linker sequence. [0858] In some embodiments, a fusion protein comprising an MLV reverse transcriptase (“MLV-RT”) fused to a nickase Cas9 (“Cas9(H840A)”) via a linker sequence. This example is not intended to limit scope of fusion proteins that may be utilized for the prime editor (PE) system described herein. [0859] In various embodiments, the prime editor fusion protein may have the following amino acid sequence (referred to herein as “PE1”), which includes a Cas9 variant comprising an H840A mutation (i.e., a Cas9 nickase) and an M-MLV RT wild type, as well as an N- terminal NLS sequence (19 amino acids) and an amino acid linker (32 amino acids) that joins the C-terminus of the Cas9 nickase domain to the N-terminus of the RT domain. The PE1 fusion protein has the following structure: [NLS]-[Cas9(H840A)]-[linker]-[MMLV_RT(wt)]. The amino acid sequence of PE1 and its individual components are shown in the Description of Sequences (Fusion Protein Sequences, SEQ ID NOs: 51, 86, 125-128 [0860] In another embodiment, the prime editor fusion protein and its individual components may comprise any amino acid sequence of SEQ ID NOs: 51, 116, 125-126, and 128-129 (referred to herein as “PE2”)(See Description of Sequences, Fusion Protein Sequences), which includes a Cas9 variant comprising an H840A mutation (i.e., a Cas9 nickase) and an M-MLV RT comprising mutations D200N, T330P, L603W, T306K, and W313F, as well as an N-terminal NLS sequence (19 amino acids) and an amino acid linker (33 amino acids) that joins the C-terminus of the Cas9 nickase domain to the N-terminus of the RT domain. The PE2 fusion protein has the following structure: [NLS]-[Cas9(H840A)]- [linker]-[MMLV_RT(D200N)(T330P)(L603W)(T306K)(W313F)]. In some embodiments, the amino acid sequence of PE2 comprises the amino acid sequene of SEQ ID NO: 129. [0861] In still other embodiments, the prime editor fusion protein may have the amino acid sequences of any one of SEQ ID NOs: 125, 129, 130-133, 135, 137-140 (see Description of Sequences, Fusion Protein Sequences). [0862] In other embodiments, the prime editor fusion proteins can be based on SaCas9 or on SpCas9 nickases with altered PAM specificities, such as the following exemplary sequences: SEQ ID NOs:137-139. [0863] In yet other embodiments, the prime editor fusion proteins contemplated herein may include a Cas9 nickase (e.g., Cas9 (H840A)) fused to a truncated version of M-MLV reverse transcriptase. In this embodiment, the reverse transcriptase also contains 4 mutations (D200N, T306K, W313F, T330P; noting that the L603W mutation present in PE2 is no longer present due to the truncation). The DNA sequence encoding this truncated editor is 522 bp smaller than PE2, and therefore makes its potentially useful for applications where delivery of the DNA sequence is challenging due to its size (i.e. adeno-associated virus and lentivirus delivery). This embodiment is referred to as Cas9(H840A)-MMLV-RT(trunc) or “PE2-short”or “PE2-trunc” and has the amino acid sequence of SEQ ID NO: 130 (see Description of Sequences, Fusion Protein Sequences). [0864] In various embodiments, the prime editor fusion proteins contemplated herein may also include any variants of the above-disclosed sequences having an amino acid sequence that is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to PE1, PE2, or any of the above indicated prime editor fusion sequences. [0865] In certain embodiments, linkers may be used to link any of the peptides or peptide domains or moieties of the invention (e.g., a napDNAbp linked or fused to a reverse transcriptase). Linkers and other domains [0866] The PE fusion proteins may comprise various other domains besides the napDNAbp (e.g., Cas9 domain) and the polymerase domain (e.g., RT domain). For example, in the case where the napDNAbp is a Cas9 and the polymerase is a RT, the PE fusion proteins may comprise one or more linkers that join the Cas9 domain with the RT domain. The linkers may also join other functional domains, such as nuclear localization sequences (NLS) or a FEN1 (or other flap endonuclease) to the PE fusion proteins or a domain thereof. [0867] In addition, in embodiments involving trans prime editing, linkers may be used to link tPERT recruitment protein to a prime editor, e.g., between the tPERt recruitment protein and the napDNAbp. Linkers [0868] The linker may be as simple as a covalent bond, or it may be a polymeric linker many atoms in length. In certain embodiments, the linker is a polpeptide or based on amino acids. In other embodiments, the linker is not peptide-like. In certain embodiments, the linker is a covalent bond (e.g., a carbon-carbon bond, disulfide bond, carbon-heteroatom bond, etc.). In certain embodiments, the linker is a carbon-nitrogen bond of an amide linkage. In certain embodiments, the linker is a cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic or heteroaliphatic linker. In certain embodiments, the linker is polymeric (e.g., polyethylene, polyethylene glycol, polyamide, polyester, etc.). In certain embodiments, the linker comprises a monomer, dimer, or polymer of aminoalkanoic acid. In certain embodiments, the linker comprises an aminoalkanoic acid (e.g., glycine, ethanoic acid, alanine, beta-alanine, 3-aminopropanoic acid, 4-aminobutanoic acid, 5- pentanoic acid, etc.). In certain embodiments, the linker comprises a monomer, dimer, or polymer of aminohexanoic acid (Ahx). In certain embodiments, the linker is based on a carbocyclic moiety (e.g., cyclopentane, cyclohexane). In other embodiments, the linker comprises a polyethylene glycol moiety (PEG). In other embodiments, the linker comprises amino acids. In certain embodiments, the linker comprises a peptide. In certain embodiments, the linker comprises an aryl or heteroaryl moiety. In certain embodiments, the linker is based on a phenyl ring. The linker may included funtionalized moieties to facilitate attachment of a nucleophile (e.g., thiol, amino) from the peptide to the linker. Any electrophile may be used as part of the linker. Exemplary electrophiles include, but are not limited to, activated esters, activated amides, Michael acceptors, alkyl halides, aryl halides, acyl halides, and isothiocyanates. [0869] In certain embodiments, linkers may be used to link any of the peptides or peptide domains or moieties of the invention (e.g., a napDNAbp linked or fused to a reverse transcriptase). [0870] As defined above, the term “linker,” as used herein, refers to a chemical group or a molecule linking two molecules or moieties, e.g., a binding domain and a cleavage domain of a nuclease. In some embodiments, a linker joins a gRNA binding domain of an RNA- programmable nuclease and the catalytic domain of a recombinase. In some embodiments, a linker joins a dCas9 and reverse transcriptase. Typically, the linker is positioned between, or flanked by, two groups, molecules, or other moieties and connected to each one via a covalent bond, thus connecting the two. In some embodiments, the linker is an amino acid or a plurality of amino acids (e.g., a peptide or protein). In some embodiments, the linker is an organic molecule, group, polymer, or chemical moiety. In some embodiments, the linker is 5-100 amino acids in length, for example, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 30-35, 35-40, 40-45, 45-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100-150, or 150-200 amino acids in length. Longer or shorter linkers are also contemplated. [0871] The linker may be as simple as a covalent bond, or it may be a polymeric linker many atoms in length. In certain embodiments, the linker is a polypeptide or based on amino acids. In other embodiments, the linker is not peptide-like. In certain embodiments, the linker is a covalent bond (e.g., a carbon-carbon bond, disulfide bond, carbon-heteroatom bond, etc.). In certain embodiments, the linker is a carbon-nitrogen bond of an amide linkage. In certain embodiments, the linker is a cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic or heteroaliphatic linker. In certain embodiments, the linker is polymeric (e.g., polyethylene, polyethylene glycol, polyamide, polyester, etc.). In certain embodiments, the linker comprises a monomer, dimer, or polymer of aminoalkanoic acid. In certain embodiments, the linker comprises an aminoalkanoic acid (e.g., glycine, ethanoic acid, alanine, beta-alanine, 3-aminopropanoic acid, 4-aminobutanoic acid, 5- pentanoic acid, etc.). In certain embodiments, the linker comprises a monomer, dimer, or polymer of aminoHEXAnoic acid (Ahx). In certain embodiments, the linker is based on a carbocyclic moiety (e.g., cyclopentane, cycloHEXAne). In other embodiments, the linker comprises a polyethylene glycol moiety (PEG). In other embodiments, the linker comprises amino acids. In certain embodiments, the linker comprises a peptide. In certain embodiments, the linker comprises an aryl or heteroaryl moiety. In certain embodiments, the linker is based on a phenyl ring. The linker may included funtionalized moieties to facilitate attachment of a nucleophile (e.g., thiol, amino) from the peptide to the linker. Any electrophile may be used as part of the linker. Exemplary electrophiles include, but are not limited to, activated esters, activated amides, Michael acceptors, alkyl halides, aryl halides, acyl halides, and isothiocyanates. [0872] The amino acid sequences of exemplary linkers are shown in the Description of Sequences (e.g., see Linkers, SEQ ID NOs:128, 134, 141-170). Nuclear localization sequence (NLS) [0873] In various embodiments, the PE fusion proteins may comprise one or more nuclear localization sequences (NLS), which help promote translocation of a protein into the cell nucleus. Such sequences are well-known in the art and can include any of the amino acid sequences of SEQ ID NOs: 126-127 and 156-170 [0874] The NLS examples above are non-limiting. The PE fusion proteins may comprise any known NLS sequence, including any of those described in Cokol et al., “Finding nuclear localization signals,” EMBO Rep., 2000, 1(5): 411-415 and Freitas et al., “Mechanisms and Signals for the Nuclear Import of Proteins,” Current Genomics, 2009, 10(8): 550-7, each of which are incorporated herein by reference. [0875] In various embodiments, the prime editors and constructs encoding the prime editors disclosed herein further comprise one or more, preferably, at least two nuclear localization signals. In certain embodiments, the prime editors comprise at least two NLSs. In embodiments with at least two NLSs, the NLSs can be the same NLSs or they can be different NLSs. In addition, the NLSs may be expressed as part of a fusion protein with the remaining portions of the prime editors. In some embodiments, one or more of the NLSs are bipartite NLSs (“bpNLS”). In certain embodiments, the disclosed fusion proteins comprise two bipartite NLSs. In some embodiments, the disclosed fusion proteins comprise more than two bipartite NLSs. [0876] The location of the NLS fusion can be at the N-terminus, the C-terminus, or within a sequence of a prime editor (e.g., inserted between the encoded napDNAbp component (e.g., Cas9) and a polymerase domain (e.g., a reverse transcriptase domain). [0877] The NLSs may be any known NLS sequence in the art. The NLSs may also be any future-discovered NLSs for nuclear localization. The NLSs also may be any naturally- occurring NLS, or any non-naturally occurring NLS (e.g., an NLS with one or more desired mutations). The amino acid sequence of exemplary NLSs are shown in SEQ ID NOs: 126- 127 and 156-170 (See Description of Sequences, Nuclear Localization Sequences). [0878] Nuclear localization signals appear at various points in the amino acid sequences of proteins. NLS’s have been identified at the N-terminus, the C-terminus and in the central region of proteins. Thus, the disclosure provides prime editors that may be modified with one or more NLSs at the C-terminus, the N-terminus, as well as at in internal region of the prime editor. The residues of a longer sequence that do not function as component NLS residues should be selected so as not to interfere, for example tonically or sterically, with the nuclear localization signal itself. Therefore, although there are no strict limits on the composition of an NLS-comprising sequence, in practice, such a sequence can be functionally limited in length and composition. [0879] The present disclosure contemplates any suitable means by which to modify a prime editor to include one or more NLSs. In one aspect, the prime editors may be engineered to express a prime editor protein that is translationally fused at its N-terminus or its C-terminus (or both) to one or more NLSs, i.e., to form a prime editor-NLS fusion construct. In other embodiments, the prime editor-encoding nucleotide sequence may be genetically modified to incorporate a reading frame that encodes one or more NLSs in an internal region of the encoded prime editor. In addition, the NLSs may include various amino acid linkers or spacer regions encoded between the prime editor and the N-terminally, C-terminally, or internally-attached NLS amino acid sequence, e.g, and in the central region of proteins. Thus, the present disclosure also provides for nucleotide constructs, vectors, and host cells for expressing fusion proteins that comprise a prime editor and one or more NLSs. [0880] The prime editors described herein may also comprise nuclear localization signals which are linked to a prime editor through one or more linkers, e.g., and polymeric, amino acid, nucleic acid, polysaccharide, chemical, or nucleic acid linker element. The linkers within the contemplated scope of the disclosure are not intented to have any limitations and can be any suitable type of molecule (e.g., polymer, amino acid, polysaccharide, nucleic acid, lipid, or any synthetic chemical linker domain) and be joined to the prime editor by any suitable strategy that effectuates forming a bond (e.g., covalent linkage, hydrogen bonding) between the prime editor and the one or more NLSs. Flap endonucleases (e.g., FEN1) [0881] In various embodiments, the PE fusion proteins may comprise one or more flap endonulceases (e.g., FEN1), which refers to an enzyme that catalyzes the removal of 5ʹ single strand DNA flaps. These are naturally occurring enzymes that process the removal of 5ʹ flaps formed during cellular processes, including DNA replication. The prime editing methods herein described may utilize endogenously supplied flap endonucleases or those provided in trans to remove the 5ʹ flap of endogenouse DNA formed at the target site during prime editing. Flap endonucleases are known in the art and can be found described in Patel et al., “Flap endonucleases pass 5ʹ-flaps through a flexible arch using a disorder-thread-order mechanism to confer specificity for free 5ʹ-ends,” Nucleic Acids Research, 2012, 40(10): 4507-4519 and Tsutakawa et al., “Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily,” Cell, 2011, 145(2): 198-211 (each of which are incorporated herein by reference). An exemplary flap endonuclease is FEN1, which may be represented by the amino acid sequence in SEQ ID NO: 171 (see Description of Sequences, Flap endonucleases): [0882] The flap endonucleases may also include any FEN1 variant, mutant, or other flap endonuclease ortholog, homolog, or variant. Non-limiting FEN1 variant examples are shown in SEQ ID NOs: 172-176 (see Description of Sequences, Flap endonucleases). [0883] In various embodiments, the prime editor fusion proteins contemplated herein may include any flap endonulcease variant described herein having an amino acid sequence that is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to any SEQ ID NOs: 171-176. [0884] Other endonucleases that may be utilized by the instant methods to facilitate removal of the 5’ end single strand DNA flap include, but are not limited to (1) trex 2, (2) exo1 endonuclease (e.g., Keijzers et al., Biosci Rep.2015, 35(3): e00206) Trex 2 [0885] Non-limiting Trex-2 variant examples are shown in SEQ ID NOs: 177-179 (see Description of Sequences, Trex). ExoI [0886] Human exonuclease 1 (EXO1) has been implicated in many different DNA metabolic processes, including DNA mismatch repair (MMR), micro-mediated end-joining, homologous recombination (HR), and replication. Human EXO1 belongs to a family of eukaryotic nucleases, Rad2/XPG, which also include FEN1 and GEN1. The Rad2/XPG family is conserved in the nuclease domain through species from phage to human. The EXO1 gene product exhibits both 5′ exonuclease and 5′ flap activity. Additionally, EXO1 contains an intrinsic 5′ RNase H activity. Human EXO1 has a high affinity for processing double stranded DNA (dsDNA), nicks, gaps, pseudo Y structures and can resolve Holliday junctions using its inherit flap activity. Human EXO1 is implicated in MMR and contain conserved binding domains interacting directly with MLH1 and MSH2. EXO1 nucleolytic activity is positively stimulated by PCNA, MutSα (MSH2/MSH6 complex), 14-3-3, MRN and 9-1-1 complex. [0887] Non-limiting Exol variant examples are shown in SEQ ID NOs: 180-182 (see Description of Sequences, Exol). Inteins and split-inteins [0888] It will be understood that in some embodiments (e.g., delivery of a prime editor in vivo using AAV particles), it may be advantageous to split a polypeptide (e.g., a deaminase or a napDNAbp) or a fusion protein (e.g., a prime editor) into an N-terminal half and a C- terminal half, delivery them separately, and then allow their colocalization to reform the complete protein (or fusion protein as the case may be) within the cell. Separate halves of a protein or a fusion protein may each comprise a split-intein tag to facilitate the reformation of the complete protein or fusion protein by the mechanism of protein trans splicing. [0889] Protein trans-splicing, catalyzed by split inteins, provides an entirely enzymatic method for protein ligation. A split-intein is essentially a contiguous intein (e.g. a mini-intein) split into two pieces named N-intein and C-intein, respectively. The N-intein and C-intein of a split intein can associate non-covalently to form an active intein and catalyze the splicing reaction essentially in same way as a contiguous intein does. Split inteins have been found in nature and also engineered in laboratories. As used herein, the term "split intein" refers to any intein in which one or more peptide bond breaks exists between the N-terminal and C- terminal amino acid sequences such that the N-terminal and C-terminal sequences become separate molecules that can non-covalently reassociate, or reconstitute, into an intein that is functional for trans-splicing reactions. Any catalytically active intein, or fragment thereof, may be used to derive a split intein for use in the methods of the invention. For example, in one aspect the split intein may be derived from a eukaryotic intein. In another aspect, the split intein may be derived from a bacterial intein. In another aspect, the split intein may be derived from an archaeal intein. Preferably, the split intein so-derived will possess only the amino acid sequences essential for catalyzing trans-splicing reactions. [0890] As used herein, the "N-terminal split intein (In)" refers to any intein sequence that comprises an N- terminal amino acid sequence that is functional for trans-splicing reactions. An In thus also comprises a sequence that is spliced out when trans-splicing occurs. An In can comprise a sequence that is a modification of the N-terminal portion of a naturally occurring intein sequence. For example, an In can comprise additional amino acid residues and/or mutated residues so long as the inclusion of such additional and/or mutated residues does not render the In non-functional in trans-splicing. Preferably, the inclusion of the additional and/or mutated residues improves or enhances the trans-splicing activity of the In. [0891] As used herein, the "C-terminal split intein (Ic)" refers to any intein sequence that comprises a C- terminal amino acid sequence that is functional for trans-splicing reactions. In one aspect, the Ic comprises 4 to 7 contiguous amino acid residues, at least 4 amino acids of which are from the last β-strand of the intein from which it was derived. An Ic thus also comprises a sequence that is spliced out when trans-splicing occurs. An Ic can comprise a sequence that is a modification of the C-terminal portion of a naturally occurring intein sequence. For example, an Ic can comprise additional amino acid residues and/or mutated residues so long as the inclusion of such additional and/or mutated residues does not render the In non-functional in trans-splicing. Preferably, the inclusion of the additional and/or mutated residues improves or enhances the trans-splicing activity of the Ic. [0892] In some embodiments of the invention, a peptide linked to an Ic or an In can comprise an additional chemical moiety including, among others, fluorescence groups, biotin, polyethylene glycol (PEG), amino acid analogs, unnatural amino acids, phosphate groups, glycosyl groups, radioisotope labels, and pharmaceutical molecules. In other embodiments, a peptide linked to an Ic can comprise one or more chemically reactive groups including, among others, ketone, aldehyde, Cys residues and Lys residues. The N-intein and C-intein of a split intein can associate non-covalently to form an active intein and catalyze the splicing reaction when an "intein-splicing polypeptide (ISP)" is present. As used herein, "intein- splicing polypeptide (ISP)" refers to the portion of the amino acid sequence of a split intein that remains when the Ic, In, or both, are removed from the split intein. In certain embodiments, the In comprises the ISP. In another embodiment, the Ic comprises the ISP. In yet another embodiment, the ISP is a separate peptide that is not covalently linked to In nor to Ic. [0893] Split inteins may be created from contiguous inteins by engineering one or more split sites in the unstructured loop or intervening amino acid sequence between the -12 conserved beta-strands found in the structure of mini-inteins. Some flexibility in the position of the split site within regions between the beta-strands may exist, provided that creation of the split will not disrupt the structure of the intein, the structured beta-strands in particular, to a sufficient degree that protein splicing activity is lost. [0894] In protein trans-splicing, one precursor protein consists of an N-extein part followed by the N-intein, another precursor protein consists of the C-intein followed by a C- extein part, and a trans-splicing reaction (catalyzed by the N- and C-inteins together) excises the two intein sequences and links the two extein sequences with a peptide bond. Protein trans-splicing, being an enzymatic reaction, can work with very low (e.g. micromolar) concentrations of proteins and can be carried out under physiological conditions. [0895] Exemplary sequences are shown in SEQ ID NOs: 2-9, 183-190, and 230 (see Description of Sequences, Intein sequences). [0896] Although inteins are most frequently found as a contiguous domain, some exist in a naturally split form. In this case, the two fragments are expressed as separate polypeptides and must associate before splicing takes place, so-called protein trans-splicing. [0897] An exemplary split intein is the Ssp DnaE intein, which comprises two subunits, namely, DnaE-N and DnaE-C. The two different subunits are encoded by separate genes, namely dnaE-n and dnaE-c, which encode the DnaE-N and DnaE-C subunits, respectively. DnaE is a naturally occurring split intein in Synechocytis sp. PCC6803 and is capable of directing trans-splicing of two separate proteins, each comprising a fusion with either DnaE- N or DnaE-C. [0898] Additional naturally occurring or engineered split-intein sequences are known in the or can be made from whole-intein sequences described herein or those available in the art. Examples of split-intein sequences can be found in Stevens et al., “A promiscuous split intein with expanded protein engineering applications,” PNAS, 2017, Vol.114: 8538-8543; Iwai et al., “Highly efficient protein trans-splicing by a naturally split DnaE intein from Nostc punctiforme, FEBS Lett, 580: 1853-1858, each of which are incorporated herein by reference. Additional split intein sequences can be found, for example, in WO 2013/045632, WO 2014/055782, WO 2016/069774, and EP2877490, the contents each of which are incorporated herein by reference. [0899] In addition, protein splicing in trans has been described in vivo and in vitro (Shingledecker, et al., [0076] Gene 207:187 (1998), Southworth, et al., EMBO J.17:918 (1998); Mills, et al., Proc. Natl. Acad. Sci. USA, 95:3543-3548 (1998); Lew, et al., J. Biol. Chem., 273:15887-15890 (1998); Wu, et al., Biochim. Biophys. Acta 35732:1 (1998b), Yamazaki, et al., J. Am. Chem. Soc.120:5591 (1998), Evans, et al., J. Biol. Chem.275:9091 (2000); Otomo, et al., Biochemistry 38:16040-16044 (1999); Otomo, et al., J. Biolmol. NMR 14:105-114 (1999); Scott, et al., Proc. Natl. Acad. Sci. USA 96:13638-13643 (1999)) and provides the opportunity to express a protein as to two inactive fragments that subsequently undergo ligation to form a functional product. RNA-protein interaction domain [0900] In various embodiments, two separate protein domains (e.g., a Cas9 domain and a polymerase domain) may be colocalized to one another to form a functional complex (akin to the function of a fusion protein comprising the two separate protein domains) by using an “RNA-protein recruitment system,” such as the “MS2 tagging technique.” Such systems generally tag one protein domain with an “RNA-protein interaction domain” (aka “RNA- protein recruitment domain”) and the other with an “RNA-binding protein” that specifically recognizes and binds to the RNA-protein interaction domain, e.g., a specific hairpin structure. These types of systems can be leveraged to colocalize the domains of a prime editor, as well as to recruitment additional functionalities to a prime editor, such as a UGI domain. In one example, the MS2 tagging technique is based on the natural interaction of the MS2 bacteriophage coat protein (“MCP” or “MS2cp”) with a stem-loop or hairpin structure present in the genome of the phage, i.e., the “MS2 hairpin.” In the case of the MS2 hairpin, it is recognized and bound by the MS2 bacteriophage coat protein (MCP). Thus, in one exemplarly scenario a deaminase-MS2 fusion can recruit a Cas9-MCP fusion. [0901] A review of other modular RNA-protein interaction domains are described in the art, for example, in Johansson et al., “RNA recognition by the MS2 phage coat protein,” Sem Virol., 1997, Vol.8(3): 176-185; Delebecque et al., “Organization of intracellular reactions with rationally designed RNA assemblies,” Science, 2011, Vol.333: 470-474; Mali et al., “Cas9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering,” Nat. Biotechnol., 2013, Vol.31: 833-838; and Zalatan et al., “Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds,” Cell, 2015, Vol.160: 339-350, each of which are incorporated herein by reference in their entireties. Other systems include the PP7 hairpin, which specifically recruits the PCP protein, and the “com” hairpin, which specifically recruits the Com protein. See Zalatan et al. [0902] Exemplary sequences are shown in SEQ ID NOs: 192-193 (see Description of Sequences, RNA-protein interaction domain). Additional PE elements [0903] In certain embodiments, the prime editors described herein may comprise an inhibitor of base repair. The term “inhibitor of base repair” or “IBR” refers to a protein that is capable in inhibiting the activity of a nucleic acid repair enzyme, for example a base excision repair enzyme. In some embodiments, the IBR is an inhibitor of OGG base excision repair. In some embodiments, the IBR is an inhibitor of base excision repair (“iBER”). Exemplary inhibitors of base excision repair include inhibitors of APE1, Endo III, Endo IV, Endo V, Endo VIII, Fpg, hOGG1, hNEIL1, T7 EndoI, T4PDG, UDG, hSMUG1, and hAAG. In some embodiments, the IBR is an inhibitor of Endo V or hAAG. In some embodiments, the IBR is an iBER that may be a catalytically inactive glycosylase or catalytically inactive dioxygenase or a small molecule or peptide inhibitor of an oxidase, or variants threreof. In some embodiments, the IBR is an iBER that may be a TDG inhibitor, MBD4 inhibitor or an inhibitor of an AlkBH enzyme. In some embodiments, the IBR is an iBER that comprises a catalytically inactive TDG or catalytically inactive MBD4. An exemplary catalytically inactive TDG is an N140A mutant of SEQ ID NO: 197 (human TDG). [0904] Exemplary glycosylases may comprise the amino acid sequence of any one of SEQ ID NOs: 194-197 (see Description of Sequences, Additional PE elements). [0905] In some embodiments, the fusion proteins described herein may comprise one or more heterologous protein domains (e.g., about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more domains in addition to the prime editor components). A fusion protein may comprise any additional protein sequence, and optionally a linker sequence between any two domains. Other exemplary features that may be present are localization sequences, such as cytoplasmic localization sequences, export sequences, such as nuclear export sequences, or other localization sequences, as well as sequence tags that are useful for solubilization, purification, or detection of the fusion proteins. [0906] Examples of protein domains that may be fused to a prime editor or component thereof (e.g., the napDNAbp domain, the polymerase domain, or the NLS domain) include, without limitation, epitope tags, and reporter gene sequences. Non-limiting examples of epitope tags include histidine (His) tags, V5 tags, FLAG tags, influenza hemagglutinin (HA) tags, Myc tags, VSV-G tags, and thioredoxin (Trx) tags. Examples of reporter genes include, but are not limited to, glutathione-5-transferase (GST), horseradish peroxidase (HRP), chloramphenicol acetyltransferase (CAT), beta-galactosidase, beta-glucuronidase, luciferase, green fluorescent protein (GFP), HcRed, DsRed, cyan fluorescent protein (CFP), yellow fluorescent protein (YFP), and autofluorescent proteins including blue fluorescent protein (BFP). A prime editor may be fused to a gene sequence encoding a protein or a fragment of a protein that bind DNA molecules or bind other cellular molecules, including, but not limited to, maltose binding protein (MBP), S-tag, Lex A DNA binding domain (DBD) fusions, GAL4 DNA binding domain fusions, and herpes simplex virus (HSV) BP16 protein fusions. Additional domains that may form part of a prime editor are described in US Patent Publication No.2011/0059502, published March 10, 2011 and incorporated herein by reference in its entirety. [0907] In an aspect of the disclosure, a reporter gene which includes, but is not limited to, glutathione-5-transferase (GST), horseradish peroxidase (HRP), chloramphenicol acetyltransferase (CAT) beta-galactosidase, beta-glucuronidase, luciferase, green fluorescent protein (GFP), HcRed, DsRed, cyan fluorescent protein (CFP), yellow fluorescent protein (YFP), and autofluorescent proteins including blue fluorescent protein (BFP), may be introduced into a cell to encode a gene product which serves as a marker by which to measure the alteration or modification of expression of the gene product. In certain embodiments of the disclosure the gene product is luciferase. In a further embodiment of the disclosure the expression of the gene product is decreased. [0908] Suitable protein tags provided herein include, but are not limited to, biotin carboxylase carrier protein (BCCP) tags, myc-tags, calmodulin-tags, FLAG-tags, hemagglutinin (HA)-tags, polyhistidine tags, also referred to as histidine tags or His-tags, maltose binding protein (MBP)-tags, nus-tags, glutathione-S-transferase (GST)-tags, green fluorescent protein (GFP)-tags, thioredoxin-tags, S-tags, Softags (e.g., Softag 1, Softag 3), strep-tags , biotin ligase tags, FlAsH tags, V5 tags, and SBP-tags. Additional suitable sequences will be apparent to those of skill in the art. In some embodiments, the fusion protein comprises one or more His tags. [0909] In some embodiments of the present disclosure, the activity of the prime editing system may be temporally regulated by adjusting the residence time, the amount, and/or the activity of the expressed components of the PE system. For example, as described herein, the PE may be fused with a protein domain that is capable of modifying the intracellular half-life of the PE. In certain embodiments involving two or more vectors (e.g., a vector system in which the components described herein are encoded on two or more separate vectors), the activity of the PE system may be temporally regulated by controlling the timing in which the vectors are delivered. For example, in some embodiments a vector encoding the nuclease system may deliver the PE prior to the vector encoding the template. In other embodiments, the vector encoding the PEgRNA may deliver the guide prior to the vector encoding the PE system. In some embodiments, the vectors encoding the PE system and PEgRNA are delivered simultaneously. In certain embodiments, the simultaneously delivered vectors temporally deliver, e.g., the PE, PEgRNA, and/or second strand guide RNA components. In further embodiments, the RNA (such as, e.g., the nuclease transcript) transcribed from the coding sequence on the vectors may further comprise at least one element that is capable of modifying the intracellular half-life of the RNA and/or modulating translational control. In some embodiments, the half-life of the RNA may be increased. In some embodiments, the half-life of the RNA may be decreased. In some embodiments, the element may be capable of increasing the stability of the RNA. In some embodiments, the element may be capable of decreasing the stability of the RNA. In some embodiments, the element may be within the 3' UTR of the RNA. In some embodiments, the element may include a polyadenylation signal (PA). In some embodiments, the element may include a cap, e.g., an upstream mRNA or PEgRNA end. In some embodiments, the RNA may comprise no PA such that it is subject to quicker degradation in the cell after transcription. In some embodiments, the element may include at least one AU-rich element (ARE). The AREs may be bound by ARE binding proteins (ARE-BPs) in a manner that is dependent upon tissue type, cell type, timing, cellular localization, and environment. In some embodiments the destabilizing element may promote RNA decay, affect RNA stability, or activate translation. In some embodiments, the ARE may comprise 50 to 150 nucleotides in length. In some embodiments, the ARE may comprise at least one copy of the sequence AUUUA. In some embodiments, at least one ARE may be added to the 3' UTR of the RNA. In some embodiments, the element may be a Woodchuck Hepatitis Virus (WHP). [0910] Posttranscriptional Regulatory Element (WPRE), which creates a tertiary structure to enhance expression from the transcript. In further embodiments, the element is a modified and/or truncated WPRE sequence that is capable of enhancing expression from the transcript, as described, for example in Zufferey et al., J Virol, 73(4): 2886-92 (1999) and Flajolet et al., J Virol, 72(7): 6175-80 (1998). In some embodiments, the WPRE or equivalent may be added to the 3' UTR of the RNA. In some embodiments, the element may be selected from other RNA sequence motifs that are enriched in either fast- or slow-decaying transcripts. [0911] In some embodiments, the vector encoding the PE or the PEgRNA may be self- destroyed via cleavage of a target sequence present on the vector by the PE system. The cleavage may prevent continued transcription of a PE or a PEgRNA from the vector. Although transcription may occur on the linearized vector for some amount of time, the expressed transcripts or proteins subject to intracellular degradation will have less time to produce off-target effects without continued supply from expression of the encoding vectors. PegRNAs [0912] The prime editing system described herein contemplates the use of any suitable PEgRNAs. The inventors have discovered that the mechanism of target-primed reverse transcription (TPRT) can be leveraged or adapted for conducting precision and versatile CRISPR/Cas-based genome editing through the use of a specially configured guide RNA comprising a reverse transcription (RT) template sequence that codes for the desired nucleotide change. The application refers to this specially configured guide RNA as an “extended guide RNA” or a “PEgRNA” since the RT template sequence can be provided as an extension of a standard or traditional guide RNA molecule. The application contemplates any suitable configuration or arrangement for the extended guide RNA. PegRNAs architecture [0913] An exemplary embodiment of an extended guide RNA usable in the prime editing system disclosed herein comprises a traditional guide RNA that includes a ~20 nt protospacer sequence and a gRNA core region, which binds with the napDNAbp. In this embodiment, the guide RNA includes an extended RNA segment at the 5´ end, i.e., a 5´ extension. In this embodiment, the 5´extension includes a reverse transcription template sequence, a reverse transcription primer binding site, and an optional 5-20 nucleotide linker sequence. In some embodiments, the RT primer binding site hybrizes to the free 3ʹ end that is formed after a nick is formed in the non-target strand of the R-loop, thereby priming reverse transcriptase for DNA polymerization in the 5´-3´ direction. [0914] Another exemplary embodiment of an extended guide RNA usable in the prime editing system disclosed herein comprise a traditional guide RNA that includes a ~20 nt protospacer sequence and a gRNA core, which binds with the napDNAbp. In this embodiment, the guide RNA includes an extended RNA segment at the 3´ end, i.e., a 3´ extension. In this embodiment, the 3´extension includes a reverse transcription template sequence, and a reverse transcription primer binding site. In some embodiments, the RT primer binding site hybrizes to the free 3´ end that is formed after a nick is formed in the non- target strand of the R-loop, thereby priming reverse transcriptase for DNA polymerization in the 5´-3´ direction. [0915] Another exemplary embodiment of an extend guide RNA usable in the prime editing system disclosed herein comprises a traditional guide RNA that includes a ~20 nt protospacer sequence and a gRNA core, which binds with the napDNAbp. In this embodiment, the guide RNA includes an extended RNA segment at an intermolecular position within the gRNA core, i.e., an intramolecular extension. In this embodiment, the intramolecular extension includes a reverse transcription template sequence, and a reverse transcription primer binding site. The RT primer binding site hybrizes to the free 3´ end that is formed after a nick is formed in the non-target strand of the R-loop, thereby priming reverse transcriptase for DNA polymerization in the 5´-3´ direction. [0916] In one embodiment, the position of the intermolecular RNA extension is not in the protospacer sequence of the guide RNA. In another embodiment, the position of the intermolecular RNA extension in the gRNA core. In still another embodiment, the position of the intermolecular RNA extension is any with the guide RNA molecule except within the protospacer sequence, or at a position which disrupts the protospacer sequence. [0917] In one embodiment, the intermolecular RNA extension is inserted downstream from the 3´ end of the protospacer sequence. In another embodiment, the intermolecular RNA extension is inserted at least 1 nucleotide, at least 2 nucleotides, at least 3 nucleotides, at least 4 nucleotides, at least 5 nucleotides, at least 6 nucleotides, at least 7 nucleotides, at least 8 nucleotides, at least 9 nucleotides, at least 10 nucleotides, at least 11 nucleotides, at least 12 nucleotides, at least 13 nucleotides, at least 14 nucleotides, at least 15 nucleotides, at least 16 nucleotides, at least 17 nucleotides, at least 18 nucleotides, at least 19 nucleotides, at least 20 nucleotides, at least 21 nucleotides, at least 22 nucleotides, at least 23 nucleotides, at least 24 nucleotides, at least 25 nucleotides downstream of the 3´ end of the protospacer sequence. [0918] In other embodiments, the intermolecular RNA extension is inserted into the gRNA, which refers to the portion of the guide RNA corresponding or comprising the tracrRNA, which binds and/or interacts with the Cas9 protein or equivalent thereof (i.e, a different napDNAbp). Preferably the insertion of the intermolecular RNA extension does not disrupt or minimally disrupts the interaction betweeen the tracrRNA portion and the napDNAbp. [0919] The length of the RNA extension can be any useful length. In various embodiments, the RNA extension is at least 5 nucleotides, at least 6 nucleotides, at least 7 nucleotides, at least 8 nucleotides, at least 9 nucleotides, at least 10 nucleotides, at least 11 nucleotides, at least 12 nucleotides, at least 13 nucleotides, at least 14 nucleotides, at least 15 nucleotides, at least 16 nucleotides, at least 17 nucleotides, at least 18 nucleotides, at least 19 nucleotides, at least 20 nucleotides, at least 21 nucleotides, at least 22 nucleotides, at least 23 nucleotides, at least 24 nucleotides, at least 25 nucleotides, at least 30 nucleotides, at least 40 nucleotides, at least 50 nucleotides, at least 60 nucleotides, at least 70 nucleotides, at least 80 nucleotides, at least 90 nucleotides, at least 100 nucleotides, at least 200 nucleotides, at least 300 nucleotides, at least 400 nucleotides, or at least 500 nucleotides in length. [0920] The RT template sequence can also be any suitable length. For example, the RT template sequence can be at least 3 nucleotides, at least 4 nucleotides, at least 5 nucleotides, at least 6 nucleotides, at least 7 nucleotides, at least 8 nucleotides, at least 9 nucleotides, at least 10 nucleotides, at least 11 nucleotides, at least 12 nucleotides, at least 13 nucleotides, at least 14 nucleotides, at least 15 nucleotides, at least 16 nucleotides, at least 17 nucleotides, at least 18 nucleotides, at least 19 nucleotides, at least 20 nucleotides, at least 30 nucleotides, at least 40 nucleotides, at least 50 nucleotides, at least 60 nucleotides, at least 70 nucleotides, at least 80 nucleotides, at least 90 nucleotides, at least 100 nucleotides, at least 200 nucleotides, at least 300 nucleotides, at least 400 nucleotides, or at least 500 nucleotides in length. [0921] In still other embodiments, wherein the reverse transcription primer binding site sequence is at least 3 nucleotides, at least 4 nucleotides, at least 5 nucleotides, at least 6 nucleotides, at least 7 nucleotides, at least 8 nucleotides, at least 9 nucleotides, at least 10 nucleotides, at least 11 nucleotides, at least 12 nucleotides, at least 13 nucleotides, at least 14 nucleotides, at least 15 nucleotides, at least 16 nucleotides, at least 17 nucleotides, at least 18 nucleotides, at least 19 nucleotides, at least 20 nucleotides, at least 30 nucleotides, at least 40 nucleotides, at least 50 nucleotides, at least 60 nucleotides, at least 70 nucleotides, at least 80 nucleotides, at least 90 nucleotides, at least 100 nucleotides, at least 200 nucleotides, at least 300 nucleotides, at least 400 nucleotides, or at least 500 nucleotides in length. [0922] In other embodiments, the optional linker or spacer sequence is at least 3 nucleotides, at least 4 nucleotides, at least 5 nucleotides, at least 6 nucleotides, at least 7 nucleotides, at least 8 nucleotides, at least 9 nucleotides, at least 10 nucleotides, at least 11 nucleotides, at least 12 nucleotides, at least 13 nucleotides, at least 14 nucleotides, at least 15 nucleotides, at least 16 nucleotides, at least 17 nucleotides, at least 18 nucleotides, at least 19 nucleotides, at least 20 nucleotides, at least 30 nucleotides, at least 40 nucleotides, at least 50 nucleotides, at least 60 nucleotides, at least 70 nucleotides, at least 80 nucleotides, at least 90 nucleotides, at least 100 nucleotides, at least 200 nucleotides, at least 300 nucleotides, at least 400 nucleotides, or at least 500 nucleotides in length. [0923] The RT template sequence, in certain embodiments, encodes a single-stranded DNA molecule which is homologous to the non-target strand (and thus, complementary to the corresponding site of the target strand) but includes one or more nucleotide changes. The least one nucleotide change may include one or more single-base nucleotide changes, one or more deletions, and one or more insertions. [0924] In some embodiments, the synthesized single-stranded DNA product of the RT template sequence is homologous to the non-target strand and contains one or more nucleotide changes. The single-stranded DNA product of the RT template sequence hybridizes in equilibrium with the complementary target strand sequence, thereby displacing the homologous endogenous target strand sequence. The displaced endogenous strand may be referred to in some embodiments as a 5´ endogenous DNA flap species. This 5´ endogenous DNA flap species can be removed by a 5´ flap endonuclease (e.g., FEN1) and the single-stranded DNA product, now hybridized to the endogenous target strand, may be ligated, thereby creating a mismatch between the endogenous sequence and the newly synthesized strand. The mismatch may be resolved by the cell’s innate DNA repair and/or replication processes. [0925] In various embodiments, the nucleotide sequence of the RT template sequence corresponds to the nucleotide sequence of the non-target strand which becomes displaced as the 5´ flap species and which overlaps with the site to be edited. [0926] In various embodiments of the extended guide RNAs, the reverse transcription template sequence may encode a single-strand DNA flap that is complementary to an endogenous DNA sequence adjacent to a nick site, wherein the single-strand DNA flap comprises a desired nucleotide change. The single-stranded DNA flap may displace an endogenous single-strand DNA at the nick site. The displaced endogenous single-strand DNA at the nick site can have a 5´ end and form an endogenous flap, which can be excised by the cell. In various embodiments, excision of the 5´ end endogenous flap can help drive product formation since removing the 5´ end endogenous flap encourages hybridization of the single-strand 3´ DNA flap to the corresponding complementary DNA strand, and the incorporation or assimilation of the desired nucleotide change carried by the single-strand 3´ DNA flap into the target DNA. [0927] In various embodiments of the extended guide RNAs, the cellular repair of the single-strand DNA flap results in installation of the desired nucleotide change, thereby forming a desired product. [0928] In still other embodiments, the desired nucleotide change is installed in an editing window that is between about -5 to +5 of the nick site, or between about -10 to +10 of the nick site, or between about -20 to +20 of the nick site, or between about -30 to +30 of the nick site, or between about -40 to + 40 of the nick site, or between about -50 to +50 of the nick site, or between about -60 to +60 of the nick site, or between about -70 to +70 of the nick site, or between about -80 to +80 of the nick site, or between about -90 to +90 of the nick site, or between about -100 to +100 of the nick site, or between about -200 to +200 of the nick site. [0929] In other embodiments, the desired nucleotide change is installed in an editing window that is between about +1 to +2 from the nick site, or about +1 to +3, +1 to +4, +1 to +5, +1 to +6, +1 to +7, +1 to +8, +1 to +9, +1 to +10, +1 to +11, +1 to +12, +1 to +13, +1 to +14, +1 to +15, +1 to +16, +1 to +17, +1 to +18, +1 to +19, +1 to +20, +1 to +21, +1 to +22, +1 to +23, +1 to +24, +1 to +25, +1 to +26, +1 to +27, +1 to +28, +1 to +29, +1 to +30, +1 to +31, +1 to +32, +1 to +33, +1 to +34, +1 to +35, +1 to +36, +1 to +37, +1 to +38, +1 to +39, +1 to +40, +1 to +41, +1 to +42, +1 to +43, +1 to +44, +1 to +45, +1 to +46, +1 to +47, +1 to +48, +1 to +49, +1 to +50, +1 to +51, +1 to +52, +1 to +53, +1 to +54, +1 to +55, +1 to +56, +1 to +57, +1 to +58, +1 to +59, +1 to +60, +1 to +61, +1 to +62, +1 to +63, +1 to +64, +1 to +65, +1 to +66, +1 to +67, +1 to +68, +1 to +69, +1 to +70, +1 to +71, +1 to +72, +1 to +73, +1 to +74, +1 to +75, +1 to +76, +1 to +77, +1 to +78, +1 to +79, +1 to +80, +1 to +81, +1 to +82, +1 to +83, +1 to +84, +1 to +85, +1 to +86, +1 to +87, +1 to +88, +1 to +89, +1 to +90, +1 to +90, +1 to +91, +1 to +92, +1 to +93, +1 to +94, +1 to +95, +1 to +96, +1 to +97, +1 to +98, +1 to +99, +1 to +100, +1 to +101, +1 to +102, +1 to +103, +1 to +104, +1 to +105, +1 to +106, +1 to +107, +1 to +108, +1 to +109, +1 to +110, +1 to +111, +1 to +112, +1 to +113, +1 to +114, +1 to +115, +1 to +116, +1 to +117, +1 to +118, +1 to +119, +1 to +120, +1 to +121, +1 to +122, +1 to +123, +1 to +124, or +1 to +125 from the nick site. [0930] In still other embodiments, the desired nucleotide change is installed in an editing window that is between about +1 to +2 from the nick site, or about +1 to +5, +1 to +10, +1 to +15, +1 to +20, +1 to +25, +1 to +30, +1 to +35, +1 to +40, +1 to +45, +1 to +50, +1 to +55, +1 to +100, +1 to +105, +1 to +110, +1 to +115, +1 to +120, +1 to +125, +1 to +130, +1 to +135, +1 to +140, +1 to +145, +1 to +150, +1 to +155, +1 to +160, +1 to +165, +1 to +170, +1 to +175, +1 to +180, +1 to +185, +1 to +190, +1 to +195, or +1 to +200, from the nick site. [0931] In various aspects, the extended guide RNAs are modified versions of a guide RNA. Guide RNAs maybe naturally occurring, expressed from an encoding nucleic acid, or synthesized chemically. Methods are well known in the art for obtaining or otherwise synthesizing guide RNAs and for determining the appropriate sequence of the guide RNA, including the protospacer sequence which interacts and hybridizes with the target strand of a genomic target site of interest. [0932] In various embodiments, the particular design aspects of a guide RNA sequence will depend upon the nucleotide sequence of a genomic target site of interest (i.e., the desired site to be edited) and the type of napDNAbp (e.g., Cas9 protein) present in prime editing systems described herein, among other factors, such as PAM sequence locations, percent G/C content in the target sequence, the degree of microhomology regions, secondary structures, etc. [0933] In general, a guide sequence is any polynucleotide sequence having sufficient complementarity with a target polynucleotide sequence to hybridize with the target sequence and direct sequence-specific binding of a napDNAbp (e.g., a Cas9, Cas9 homolog, or Cas9 variant) to the target sequence. In some embodiments, the degree of complementarity between a guide sequence and its corresponding target sequence, when optimally aligned using a suitable alignment algorithm, is about or more than about 50%, 60%, 75%, 80%, 85%, 90%, 95%, 97.5%, 99%, or more. Optimal alignment may be determined with the use of any suitable algorithm for aligning sequences, non-limiting example of which include the Smith-Waterman algorithm, the Needleman-Wunsch algorithm, algorithms based on the Burrows-Wheeler Transform (e.g., the Burrows Wheeler Aligner), ClustalW, Clustal X, BLAT, Novoalign (Novocraft Technologies, ELAND (Illumina, San Diego, Calif.), SOAP (available at soap.genomics.org.cn), and Maq (available at maq.sourceforge.net). In some embodiments, a guide sequence is about or more than about 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 75, or more nucleotides in length. [0934] In some embodiments, a guide sequence is less than about 75, 50, 45, 40, 35, 30, 25, 20, 15, 12, or fewer nucleotides in length. The ability of a guide sequence to direct sequence-specific binding of a prime editor (PE) to a target sequence may be assessed by any suitable assay. For example, the components of a prime editor (PE), including the guide sequence to be tested, may be provided to a host cell having the corresponding target sequence, such as by transfection with vectors encoding the components of a prime editor (PE) disclosed herein, followed by an assessment of preferential cleavage within the target sequence, such as by Surveyor assay as described herein. Similarly, cleavage of a target polynucleotide sequence may be evaluated in a test tube by providing the target sequence, components of a prime editor (PE), including the guide sequence to be tested and a control guide sequence different from the test guide sequence, and comparing binding or rate of cleavage at the target sequence between the test and control guide sequence reactions. Other assays are possible, and will occur to those skilled in the art. [0935] A guide sequence may be selected to target any target sequence. In some embodiments, the target sequence is a sequence within a genome of a cell. Exemplary target sequences include those that are unique in the target genome. Non-limiting target sequences include any of those with nucleic acid sequences of any SEQ ID NOs: 198-226 (see Description of Sequences, pegRNAs). [0936] In some embodiments, a guide sequence is selected to reduce the degree of secondary structure within the guide sequence. Secondary structure may be determined by any suitable polynucleotide folding algorithm. Some programs are based on calculating the minimal Gibbs free energy. An example of one such algorithm is mFold, as described by Zuker and Stiegler (Nucleic Acids Res.9 (1981), 133-148). Another example folding algorithm is the online webserver RNAfold, developed at Institute for Theoretical Chemistry at the University of Vienna, using the centroid structure prediction algorithm (see e.g. A. R. Gruber et al., 2008, Cell 106(1): 23-24; and PA Carr and GM Church, 2009, Nature Biotechnology 27(12): 1151-62). Further algorithms may be found in U.S. application Ser. No.61/836,080; Broad Reference BI-2013/004A); incorporated herein by reference. [0937] In general, a tracr mate sequence includes any sequence that has sufficient complementarity with a tracr sequence to promote one or more of: (1) excision of a guide sequence flanked by tracr mate sequences in a cell containing the corresponding tracr sequence; and (2) formation of a complex at a target sequence, wherein the complex comprises the tracr mate sequence hybridized to the tracr sequence. In general, degree of complementarity is with reference to the optimal alignment of the tracr mate sequence and tracr sequence, along the length of the shorter of the two sequences. Optimal alignment may be determined by any suitable alignment algorithm, and may further account for secondary structures, such as self-complementarity within either the tracr sequence or tracr mate sequence. In some embodiments, the degree of complementarity between the tracr sequence and tracr mate sequence along the length of the shorter of the two when optimally aligned is about or more than about 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97.5%, 99%, or higher. In some embodiments, the tracr sequence is about or more than about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, or more nucleotides in length. In some embodiments, the tracr sequence and tracr mate sequence are contained within a single transcript, such that hybridization between the two produces a transcript having a secondary structure, such as a hairpin. Preferred loop forming sequences for use in hairpin structures are four nucleotides in length, and most preferably have the sequence GAAA. However, longer or shorter loop sequences may be used, as may alternative sequences. The sequences preferably include a nucleotide triplet (for example, AAA), and an additional nucleotide (for example C or G). Examples of loop forming sequences include CAAA and AAAG. In an embodiment of the invention, the transcript or transcribed polynucleotide sequence has at least two or more hairpins. In preferred embodiments, the transcript has two, three, four or five hairpins. In a further embodiment of the invention, the transcript has at most five hairpins. In some embodiments, the single transcript further includes a transcription termination sequence; preferably this is a polyT sequence, for example six T nucleotides. Further non-limiting examples of single polynucleotides comprising a guide sequence, a tracr mate sequence, and a tracr sequence are shown in SEQ ID NOs: 210-215. [0938] In some embodiments, sequences (1) to (3) are used in combination with Cas9 from S. thermophilus CRISPR1. In some embodiments, sequences (4) to (6) are used in combination with Cas9 from S. pyogenes. In some embodiments, the tracr sequence is a separate transcript from a transcript comprising the tracr mate sequence. [0939] It will be apparent to those of skill in the art that in order to target any of the fusion proteins comprising a Cas9 domain and a single-stranded DNA binding protein, as disclosed herein, to a target site, e.g., a site comprising a point mutation to be edited, it is typically necessary to co-express the fusion protein together with a guide RNA, e.g., an sgRNA. As explained in more detail elsewhere herein, a guide RNA typically comprises a tracrRNA framework allowing for Cas9 binding, and a guide sequence, which confers sequence specificity to the Cas9:nucleic acid editing enzyme/domain fusion protein. [0940] In some embodiments, the guide RNA comprises a structure 5ʹ-[guide sequence]- guuuuagagcuagaaauagcaaguuaaaauaaaggcuaguccguuaucaacuugaaaaag uggcaccgagucggugcuu uuu-3ʹ (SEQ ID NO: 216), wherein the guide sequence comprises a sequence that is complementary to the target sequence. The guide sequence is typically 20 nucleotides long. The sequences of suitable guide RNAs for targeting Cas9:nucleic acid editing enzyme/domain fusion proteins to specific genomic target sites will be apparent to those of skill in the art based on the instant disclosure. Such suitable guide RNA sequences typically comprise guide sequences that are complementary to a nucleic sequence within 50 nucleotides upstream or downstream of the target nucleotide to be edited. Some exemplary guide RNA sequences suitable for targeting any of the provided fusion proteins to specific target sequences are provided herein. Additional guide sequences are well known in the art and can be used with the prime editor (PE) described herein. [0941] In other embodiments, the PEgRNAs include those disclosed in International Patent Application No. PCT/US2020/023721, filed March 19, 2020, entitled “Methods and Compositions for Editing Nucleotide Sequences,” by David Liu, et al., published as WO 2020/191239 on September 24, 2020. [0942] In some embodiments, the structure of an embodiment of a PEgRNA contemplated herein and which may be designed in accordance with the methodology defined in Example 2. The PEgRNA comprises three main component elements ordered in the 5ʹ to 3ʹ direction, namely: a spacer, a gRNA core, and an extension arm at the 3ʹ end. The extension arm may further be divided into the following structural elements in the 5ʹ to 3ʹ direction, namely: a primer binding site (A), an edit template (B), and a homology arm (C). In addition, the PEgRNA may comprise an optional 3ʹ end modifier region (e1) and an optional 5ʹ end modifier region (e2). Still further, the PEgRNA may comprise a transcriptional termination signal at the 3ʹ end of the PEgRNA (not depicted). These structural elements are further defined herein. The depiction of the structure of the PEgRNA is not meant to be limiting and embraces variations in the arrangement of the elements. For example, the optional sequence modifiers (e1) and (e2) could be positioned within or between any of the other regions shown, and not limited to being located at the 3ʹ and 5ʹ ends. [0943] In some embodiments, the structure of another embodiment of a PEgRNA contemplated herein and which may be designed in accordance with the methodology defined in Example 2. The PEgRNA comprises three main component elements ordered in the 5ʹ to 3ʹ direction, namely: a spacer, a gRNA core, and an extension arm at the 3ʹ end. The extension arm may further be divided into the following structural elements in the 5ʹ to 3ʹ direction, namely: a primer binding site (A), an edit template (B), and a homology arm (C). In addition, the PEgRNA may comprise an optional 3ʹ end modifier region (e1) and an optional 5ʹ end modifier region (e2). Still further, the PEgRNA may comprise a transcriptional termination signal on the 3ʹ end of the PEgRNA (not depicted). These structural elements are further defined herein. The depiction of the structure of the PEgRNA is not meant to be limiting and embraces variations in the arrangement of the elements. For example, the optional sequence modifiers (e1) and (e2) could be positioned within or between any of the other regions shown, and not limited to being located at the 3ʹ and 5ʹ ends. [0944] The PEgRNAs may also include additional design improvements that may modify the properties and/or characteristics of PEgRNAs thereby improving the efficacy of prime editing. In various embodiments, these improvements may belong to one or more of a number of different categories, including but not limited to: (1) designs to enable efficient expression of functional PEgRNAs from non-polymerase III (pol III) promoters, which would enable the expression of longer PEgRNAs without burdensome sequence requirements; (2) improvements to the core, Cas9-binding PEgRNA scaffold, which could improve efficacy; (3) modifications to the PEgRNA to improve RT processivity, enabling the insertion of longer sequences at targeted genomic loci; and (4) addition of RNA motifs to the 5ʹ or 3ʹ termini of the PEgRNA that improve PEgRNA stability, enhance RT processivity, prevent misfolding of the PEgRNA, or recruit additional factors important for genome editing. [0945] In one embodiment, PEgRNA could be designed with polIII promoters to improve the expression of longer-length PEgRNA with larger extension arms. sgRNAs are typically expressed from the U6 snRNA promoter. This promoter recruits pol III to express the associated RNA and is useful for expression of short RNAs that are retained within the nucleus. However, pol III is not highly processive and is unable to express RNAs longer than a few hundred nucleotides in length at the levels required for efficient genome editing. Additionally, pol III can stall or terminate at stretches of U’s, potentially limiting the sequence diversity that could be inserted using a PEgRNA. Other promoters that recruit polymerase II (such as pCMV) or polymerase I (such as the U1 snRNA promoter) have been examined for their ability to express longer sgRNAs. However, these promoters are typically partially transcribed, which would result in extra sequence 5ʹ of the spacer in the expressed PEgRNA, which has been shown to result in markedly reduced Cas9:sgRNA activity in a site-dependent manner. Additionally, while pol III-transcribed PEgRNAs can simply terminate in a run of 6-7 U’s, PEgRNAs transcribed from pol II or pol I would require a different termination signal. Often such signals also result in polyadenylation, which would result in undesired transport of the PEgRNA from the nucleus. Similarly, RNAs expressed from pol II promoters such as pCMV are typically 5ʹ-capped, also resulting in their nuclear export. [0946] Previously, Rinn and coworkers screened a variety of expression platforms for the production of long-noncoding RNA- (lncRNA) tagged sgRNAs183. These platforms include RNAs expressed from pCMV and that terminate in the ENE element from the MALAT1 ncRNA from humans184, the PAN ENE element from KSHV185, or the 3ʹ box from U1 snRNA186. Notably, the MALAT1 ncRNA and PAN ENEs form triple helices protecting the polyA-tail 184, 187. These constructs could also enhance RNA stability. It is contemplated that these expression systems will also enable the expression of longer PEgRNAs. [0947] In addition, a series of methods have been designed for the cleavage of the portion of the pol II promoter that would be transcribed as part of the PEgRNA, adding either a self- cleaving ribozyme such as the hammerhead188, pistol189, hatchet189, hairpin190, VS191, twister192, or twister sister192 ribozymes, or other self-cleaving elements to process the transcribed guide, or a hairpin that is recognized by Csy4193 and also leads to processing of the guide. Also, it is hypothesized that incorporation of multiple ENE motifs could lead to improved PEgRNA expression and stability, as previously demonstrated for the KSHV PAN RNA and element185. It is also anticipated that circularizing the PEgRNA in the form of a circular intronic RNA (ciRNA) could also lead to enhanced RNA expression and stability, as well as nuclear localization194. [0948] In various other embodiments, the PEgRNA may be improved by introducing improvements to the scaffold or core sequences. This can be done by introducing known [0949] The core, Cas9-binding PEgRNA scaffold can likely be improved to enhance PE activity. Several such approaches have already been demonstrated. For instance, the first pairing element of the scaffold (P1) contains a GTTTT-AAAAC pairing element. Such runs of Ts have been shown to result in pol III pausing and premature termination of the RNA transcript. Rational mutation of one of the T-A pairs to a G-C pair in this portion of P1 has been shown to enhance sgRNA activity, suggesting this approach would also be feasible for PEgRNAs195. Additionally, increasing the length of P1 has also been shown to enhance sgRNA folding and lead to improved activity195, suggesting it as another avenue for the improvement of PEgRNA activity. Example improvements to the core can include: [0950] PEgRNA containing a 6 nt extension to P1 [0951] GGCCCAGACTGAGCACGTGAGTTTTAGAGCTAGCTCATGAAAATGAGC TAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGGACCGAGT CGGTCCTCTGCCATCAAAGCGTGCTCAGTCTGTTTTTTT (SEQ ID NO: 228) [0952] PEgRNA containing a T-A to G-C mutation within P1 [0953] GGCCCAGACTGAGCACGTGAGTTTGAGAGCTAGAAATAGCAAGTTTA AATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGGACCGAGTCGGTCCTCTGCC ATCAAAGCGTGCTCAGTCTGTTTTTTT (SEQ ID NO: 231) [0954] In various other embodiments, the PEgRNA may be improved by introducing modifications to the edit template region. As the size of the insertion templated by the PEgRNA increases, it is more likely to be degraded by endonucleases, undergo spontaneous hydrolysis, or fold into secondary structures unable to be reverse-transcribed by the RT or that disrupt folding of the PEgRNA scaffold and subsequent Cas9-RT binding. Accordingly, it is likely that modification to the template of the PEgRNA might be necessary to affect large insertions, such as the insertion of whole genes. Some strategies to do so include the incorporation of modified nucleotides within a synthetic or semi-synthetic PEgRNA that render the RNA more resistant to degradation or hydrolysis or less likely to adopt inhibitory secondary structures196. Such modifications could include 8-aza-7-deazaguanosine, which would reduce RNA secondary structure in G-rich sequences; locked-nucleic acids (LNA) that reduce degradation and enhance certain kinds of RNA secondary structure; 2’-O-methyl, 2’- fluoro, or 2’-O-methoxyethoxy modifications that enhance RNA stability. Such modifications could also be included elsewhere in the PEgRNA to enhance stability and activity. Alternatively or additionally, the template of the PEgRNA could be designed such that it both encodes for a desired protein product and is also more likely to adopt simple secondary structures that are able to be unfolded by the RT. Such simple structures would act as a thermodynamic sink, making it less likely that more complicated structures that would prevent reverse transcription would occur. Finally, one could also split the template into two, separate PEgRNAs. In such a design, a PE would be used to initiate transcription and also recruit a separate template RNA to the targeted site via an RNA-binding protein fused to Cas9 or an RNA recognition element on the PEgRNA itself such as the MS2 aptamer. The RT could either directly bind to this separate template RNA, or initiate reverse transcription on the original PEgRNA before swapping to the second template. Such an approach could enable long insertions by both preventing misfolding of the PEgRNA upon addition of the long template and also by not requiring dissociation of Cas9 from the genome for long insertions to occur, which could possibly be inhibiting PE-based long insertions. [0955] In still other embodiments, the PEgRNA may be improved by introducing additional RNA motifs at the 5ʹ and 3ʹ termini of the PEgRNAs, or even at positions therein between (e.g., in the gRNA core region, or the the spacer). Several such motifs - such as the PAN ENE from KSHV and the ENE from MALAT1 were discussed above as possible means to terminate expression of longer PEgRNAs from non-pol III promoters. These elements form RNA triple helices that engulf the polyA tail, resulting in their being retained within the nucleus184, 187. However, by forming complex structures at the 3ʹ terminus of the PEgRNA that occlude the terminal nucleotide, these structures would also likely help prevent exonuclease-mediated degradation of PEgRNAs. [0956] Other structural elements inserted at the 3ʹ terminus could also enhance RNA stability, albeit without enabling termination from non-pol III promoters. Such motifs could include hairpins or RNA quadruplexes that would occlude the 3ʹ terminus197, or self- cleaving ribozymes such as HDV that would result in the formation of a 2’-3ʹ-cyclic phosphate at the 3ʹ terminus and also potentially render the PEgRNA less likely to be degraded by exonucleases198. Inducing the PEgRNA to cyclize via incomplete splicing - to form a ciRNA - could also increase PEgRNA stability and result in the PEgRNA being retained within the nucleus194. [0957] Additional RNA motifs could also improve RT processivity or enhance PEgRNA activity by enhancing RT binding to the DNA-RNA duplex. Addition of the native sequence bound by the RT in its cognate retroviral genome could enhance RT activity199. This could include the native primer binding site (PBS), polypurine tract (PPT), or kissing loops involved in retroviral genome dimerization and initiation of transcription199. [0958] Addition of dimerization motifs - such as kissing loops or a GNRA tetraloop/tetraloop receptor pair200 - at the 5ʹ and 3ʹ termini of the PEgRNA could also result in effective circularization of the PEgRNA, improving stability. Additionally, it is envisioned that addition of these motifs could enable the physical separation of the PEgRNA spacer and primer, prevention occlusion of the spacer which would hinder PE activity. Short 5ʹ extensions or 3’ extensions to the PEgRNA that form a small toehold hairpin in the spacer region or along the primer binding site could also compete favorably against the annealing of intracomplementary regions along the length of the PEgRNA, e.g., the interaction between the spacer and the primer binding site that can occur.Finally, kissing loops could also be used to recruit other template RNAs to the genomic site and enable swapping of RT activity from one RNA to the other. In some embodiments, a number secondary RNA structures that may be engineered into any region of the PEgRNA, including in the terminal portions of the extension arm (i.e., e1and e2). Exemplary embodiments are shown in SEQ ID NOs: 184, 198-226 and 231 (see Description of Sequences, pegRNAs) [0959] PEgRNA scaffold could be further improved via directed evolution, in an analogous fashion to how SpCas9 and prime editor (PE) have been improved. Directed evolution could enhance PEgRNA recognition by Cas9 or evolved Cas9 variants. Additionally, it is likely that different PEgRNA scaffold sequences would be optimal at different genomic loci, either enhancing PE activity at the site in question, reducing off-target activities, or both. Finally, evolution of PEgRNA scaffolds to which other RNA motifs have been added would almost certainly improve the activity of the fused PEgRNA relative to the unevolved, fusion RNA. For instance, evolution of allosteric ribozymes composed of c-di- GMP-I aptamers and hammerhead ribozymes led to dramatically improved activity202, suggesting that evolution would improve the activity of hammerhead-PEgRNA fusions as well. In addition, while Cas9 currently does not generally tolerate 5ʹ extension of the sgRNA, directed evolution will likely generate enabling mutations that mitigate this intolerance, allowing additional RNA motifs to be utilized. [0960] The present disclosure contemplates any such ways to further improve the efficacy of the prime editing systems disclosed here. [0961] In various embodiments, it may be advantageous to limit the appearance of consecutive sequence of Ts from the extension arm as consecutive series of T’s may limit the capacity of the PEgRNA to be transcribed. For example, strings of at least consecutive three T’s, at least consecutive four T’s, at least consecutive five T’s, at least consecutive six T’s, at least consecutive seven T’s, at least consecutive eight T’s, at least consecutive nine T’s, at least consecutive ten T’s, at least consecutive elevent T’s, at least consecutive twelve T’s, at least consecutive thirteen T’s , at least consecutive fourteen T’s, or at least consecutive fifteen T’s should be avoided when designing the PEgRNA, or should be at least removed from the final designed sequence. In one embodiment, one can avoid the includes of unwanted strings of consecutive T’s in PEgRNA extension arms but avoiding target sites that are rich in consecutive A:T nucleobase pairs. Split PegRNAs designs for trans prime editing [0962] The instant disclosure also contemplates trans prime editing, which refers to a modified version of prime editing which operates by separating the PEgRNA into two distinct molecules: a guide RNA and a tPERT molecule. The tPERT molecule is programmed to co-localize with the prime editor complex at a target DNA site, bringing the primer binding site and the DNA synthesis template to the prime editor in trans. In some embodiments, a trans prime editor (tPE) comprises a two-component system comprising (1) an recruiting protein (RP)-PE:gRNA complex and (2) a tPERT that includes a primer binding site and a DNA synthesis template joined to an RNA-protein recruitment domain (e.g., stem loop or hairpin), wherein the recruiting protein component of the RP-PE:gRNA complex recruits the tPERT to a target site to be edited, thereby associating the PBS and DNA synthesis template with the prime editor in trans. Said another way, the tPERT is engineered to contain (all or part of) the extension arm of a PEgRNA, which includes the primer binding site and the DNA synthesis template. One advantage of this approach is to separate the extension arm of a PEgRNA from the guide RNA, thereby minimizing annealing interactions that tend to occur between the PBS of the extension arm and the spacer sequence of the guide RNA. [0963] A key feature of trans prime editing is the ability of the trans prime editor to recruit the tPERT to the site of DNA editing, thereby effectively co-localizing all of the functions of a PEgRNA at the site of prime editing. Recruitment can be achieve by installing an RNA-protein recruitment domain, such as a MS2 aptamer, into the tPERT and fusing a corresponding recruiting protein to the prime editor (e.g., via a linker to the napDNAbp or via a linker to the polymerase) that is capable of specifically binding to the RNA-protein recruitment domain, thereby recruiting the tPERT molecule to the prime editor complex. In some embodiments, the RP-PE:gRNA complex binds to and nicks the target DNA sequence. Then, the recruiting protein (RP) recruits a tPERT to co-localize to the prime editor complex bound to the DNA target site, thereby allowing the primer binding site, located on the tPERT, to bind to the primer sequence on the nicked strand, and subsequently, allowing the polymerase (e.g., RT) to synthesize a single strand of DNA against the DNA synthesis template, located on the tPERT, up through the 5ʹ end of the tPERT. [0964] While the tPERT, in some embodiments, may comprise PBS and DNA synthesis template on the 5ʹ end of the RNA-protein recruitment domain, the tPERT in other configurations may be designed with the PBS and DNA synthesis template located on the 3ʹ end of the RNA-protein recruitment domain. However, the tPERT with the 5’ extension has the advantage that synthesis of the single strand of DNA will naturally terminate at the 5’ end of the tPERT and thus, does not risk using any portion of the RNA-protein recruitment domain as a template during the DNA synthesis stage of prime editing. PegRNAs design method [0965] The present disclosure also relates to methods for designing PEgRNAs. [0966] In one aspect of design, the design approach can take into account the particular application for which prime editing is being used. For instance, and as exemplied and discussed herein, prime editing can be used, without limitation, to (a) install mutation- correcting changes to a nucleotide sequence, (b) install protein and RNA tags, (c) install immunoepitopes on proteins of interest, (d) install inducible dimerization domains in proteins, (e) install or remove sequences to alter that activity of a biomolecule, (f) install recombinase target sites to direct specific genetic changes, and (g) mutagenesis of a target sequence by using an error-prone RT. In addition to these methods which, in general, insert, change, or delete nucleotide sequences at target sites of interest, prime editors can also be used to construct highly programmable libraries, as well as to conduct cell data recording and lineage tracing studies. In these various uses, there may be as described herein particular design aspects pertaining to the preparation of a PEgRNA that is particularly useful for any given of these applications. [0967] When designing a PEgRNA for any particular application or use of prime editing, a number of considerations may be taken into account, which include, but are not limited to: (a) the target sequence, i.e., the nucleotide sequence in which one or more nucleobase modifications are desired to be installed by the prime editor; (b) the location of the cut site within the target sequence, i.e., the specific nucleobase position at which the prime editor will induce a single-stand nick to create a 3ʹ end RT primer sequence on one side of the nick and the 5ʹ end endogenous flap on the other side of the nick (which ultimately is removed by FEN1 or equivalent thereto and replaced by the 3ʹ ssDNA flap. The cut site is analogous to the “edit location” since this what creates the 3ʹ end RT primer sequence which becomes extended by the RT during RNA-depending DNA polymerization to create the 3ʹ ssDNA flap containing the desired edit, which then replaces the 5ʹ endogenous DNA flap in the target sequence. (c) the available PAM sequences (including the canonical SpCas9 PAM sites, as well as non-canonical PAM sites recognized by Cas9 variants and equivalents with expanded or differing PAM specificities); (d) the spacing between the available PAM sequences and the location of the cut site in the target sequence; (e) the particular Cas9, Cas9 variant, or Cas9 equivalent of the prime editor being used; (f) the sequence and length of the primer binding site; (g) the sequence and length of the edit template; (h) the sequence and length of the homology arm; (i) the spacer sequence and length; and (j) the core sequence. [0968] The instant disclosure discusses these aspects above. [0969] In one embodiment, an approach to designing a suitable PEgRNA, and optionally a nicking-sgRNA design guide for second-site nicking, is hereby provided. This embodiment provides a step-by-step set of instructions for designing PEgRNAs and nicking-sgRNAs for prime editing which takes into account one or more of the above considerations. [0970] Define the target sequence and the edit. Retrieve the sequence of the target DNA region (~200bp) centered around the location of the desired edit (point mutation, insertion, deletion, or combination thereof). . [0971] Locate target PAMs. Identify PAMs in the proximity to the desired edit location. PAMs can be identified on either strand of DNA proximal to the desired edit location. While PAMs close to the edit position are preferred (i.e., wherein the nick site is less than 30 nt from the edit position, or less than 29 nt, 28 nt, 27 nt, 26 nt, 25 nt, 24 nt, 23 nt, 22 nt, 21 nt, 20 nt, 19 nt, 18 nt, 17 nt, 16 nt, 15 nt, 14 nt, 13 nt, 12 nt, 11 nt, 10 nt, 9 nt, 8 nt, 7 nt, 6 nt, 5 nt, 4 nt, 3 nt, or 2 nt from the edit position to the nick site), it is possible to install edits using protospacers and PAMs that place the nick ≥ 30 nt from the edit position. [0972] Locate the nick sites. For each PAM being considered, identify the corresponding nick site and on which strand. For Sp Cas9 H840A nickase, cleavage occurs in the PAM- containing strand between the 3rd and 4th bases 5ʹ to the NGG PAM. All edited nucleotides must exist 3ʹ of the nick site, so appropriate PAMs must place the nick 5ʹ to the target edit on the PAM-containing strand. In the example shown below, there are two possible PAMs. For simplicity, the remaining steps will demonstrate the design of a PEgRNA using PAM 1 only. [0973] Design the spacer sequence. The protospacer of Sp Cas9 corresponds to the 20 nucleotides 5ʹ to the NGG PAM on the PAM-containing strand. Efficient Pol III transcription initiation requires a G to be the first transcribed nucleotide. If the first nucleotide of the protospacer is a G, the spacer sequence for the PEgRNA is simply the protospacer sequence. If the first nucleotide of the protospacer is not a G, the spacer sequence of the PEgRNA is G followed by the protospacer sequence. [0974] Design a primer binding site (PBS). Using the starting allele sequence, identify the DNA primer on the PAM-containing strand. The 3ʹ end of the DNA primer is the nucleotide just upstream of the nick site (i.e. the 4th base 5ʹ to the NGG PAM for Sp Cas9). As a general design principle for use with PE2 and PE3, a PEgRNA primer binding site (PBS) containing 12 to 13 nucleotides of complementarity to the DNA primer can be used for sequences that contain ~40-60% GC content. For sequences with low GC content, longer (14- to 15-nt) PBSs should be tested. For sequences with higher GC content, shorter (8- to 11-nt) PBSs should be tested. Optimal PBS sequences should be determined empirically, regardless of GC content. To design a length-p PBS sequence, take the reverse complement of the first p nucleotides 5ʹ of the nick site in the PAM-containing strand using the starting allele sequence. [0975] Design an RT template (or DNA synthesis template). The RT template (or DNA synthesis template where the polymerase is not reverse transcriptase) encodes the designed edit and homology to the sequence adjacent to the edit. In one embodiment, these regions correspond to a DNA synthesis template, wherein the DNA synthesis template comprises the “edit template” and the “homology arm.” Optimal RT template lengths vary based on the target site. For short-range edits (positions +1 to +6), it is recommended to test a short (9 to 12 nt), a medium (13 to 16 nt), and a long (17 to 20 nt) RT template. For long-range edits (positions +7 and beyond), it is recommended to use RT templates that extend at least 5 nt (preferably 10 or more nt) past the position of the edit to allow for sufficient 3ʹ DNA flap homology. For long-range edits, several RT templates should be screened to identify functional designs. For larger insertions and deletions (≥5 nt), incorporation of greater 3ʹ homology (~20 nt or more) into the RT template is recommended. Editing efficiency is typically impaired when the RT template encodes the synthesis of a G as the last nucleotide in the reverse transcribed DNA product (corresponding to a C in the RT template of the PEgRNA). As many RT templates support efficient prime editing, avoidance of G as the final synthesized nucleotide is recommended when designing RT templates. To design a length-r RT template sequence, use the desired allele sequence and take the reverse complement of the first r nucleotides 3ʹ of the nick site in the strand that originally contained the PAM. Note that compared to SNP edits, insertion or deletion edits using RT templates of the same length will not contain identical homology. [0976] Assemble the full PEgRNA sequence. Concatenate the PEgRNA components in the following order (5ʹ to 3ʹ): spacer, scaffold, RT template and PBS. [0977] Designing nicking-sgRNAs for PE3. Identify PAMs on the non-edited strand upstream and downstream of the edit. Optimal nicking positions are highly locus-dependent and should be determined empirically. In general, nicks placed 40 to 90 nucleotides 5ʹ to the position across from the PEgRNA-induced nick lead to higher editing yields and fewer indels. A nicking sgRNA has a spacer sequence that matches the 20-nt protospacer in the starting allele, with the addition of a 5ʹ-G if the protospacer does not begin with a G. [0978] Designing PE3b nicking-sgRNAs. If a PAM exists in the complementary strand and its corresponding protospacer overlaps with the sequence targeted for editing, this edit could be a candidate for the PE3b system. In the PE3b system, the spacer sequence of the nicking-sgRNA matches the sequence of the desired edited allele, but not the starting allele. The PE3b system operates efficiently when the edited nucleotide(s) falls within the seed region (~10 nt adjacent to the PAM) of the nicking-sgRNA protospacer. This prevents nicking of the complementary strand until after installation of the edited strand, preventing competition between the PEgRNA and the sgRNA for binding the target DNA. PE3b also avoids the generation of simultaneous nicks on both strands, thus reducing indel formation significantly while maintaining high editing efficiency. PE3b sgRNAs should have a spacer sequence that matches the 20-nt protospacer in the desired allele, with the addition of a 5ʹ G if needed. [0979] The above step-by-step process for designing a suitable PEgRNA and a second- site nicking sgRNA is not meant to be limiting in any way. The disclosure contemplates variations of the above-described step-by-step process which would be derivable therefrom by a person of ordinary skill in the art. Host Cells [0980] Cells that may contain any of the compositions described herein include prokaryotic cells and eukaryotic cells. The methods described herein are used to deliver a prime editorinto a eukaryotic cell (e.g., a mammalian cell, such as a human cell). In some embodiments, the cell is in vitro (e.g., cultured cell. In some embodiments, the cell is in vivo (e.g., in a subject such as a human subject). In some embodiments, the cell is ex vivo (e.g., isolated from a subject and may be administered back to the same or a different subject). [0981] Mammalian cells of the present disclosure include human cells, primate cells (e.g., vero cells), rat cells (e.g., GH3 cells, OC23 cells) or mouse cells (e.g., MC3T3 cells). There are a variety of human cell lines, including, without limitation, human embryonic kidney (HEK) cells, HeLa cells, cancer cells from the National Cancer Institute's 60 cancer cell lines (NCI60), DU145 (prostate cancer) cells, Lncap (prostate cancer) cells, MCF-7 (breast cancer) cells, MDA-MB-438 (breast cancer) cells, PC3 (prostate cancer) cells, T47D (breast cancer) cells, THP-1 (acute myeloid leukemia) cells, U87 (glioblastoma) cells, SHSY5Y human neuroblastoma cells (cloned from a myeloma) and Saos-2 (bone cancer) cells. In some embodiments, rAAV vectors are delivered into human embryonic kidney (HEK) cells (e.g., HEK 293 or HEK 293T cells). In some embodiments, rAAV vectors are delivered into stem cells (e.g., human stem cells) such as, for example, pluripotent stem cells (e.g., human pluripotent stem cells including human induced pluripotent stem cells (hiPSCs)). A stem cell refers to a cell with the ability to divide for indefinite periods in culture and to give rise to specialized cells. A pluripotent stem cell refers to a type of stem cell that is capable of differentiating into all tissues of an organism, but not alone capable of sustaining full organismal development. A human induced pluripotent stem cell refers to a somatic (e.g., mature or adult) cell that has been reprogrammed to an embryonic stem cell-like state by being forced to express genes and factors important for maintaining the defining properties of embryonic stem cells (see, e.g., Takahashi and Yamanaka, Cell 126 (4): 663–76, 2006, incorporated by reference herein). Human induced pluripotent stem cell cells express stem cell markers and are capable of generating cells characteristic of all three germ layers (ectoderm, endoderm, mesoderm). [0982] Additional non-limiting examples of cell lines that may be used in accordance with the present disclosure include 293-T, 293-T, 3T3, 4T1, 721, 9L, A-549, A172, A20, A253, A2780, A2780ADR, A2780cis, A431, ALC, B16, B35, BCP-1, BEAS-2B, bEnd.3, BHK-21, BR 293, BxPC3, C2C12, C3H-10T1/2, C6, C6/36, Cal-27, CGR8, CHO, CML T1, CMT, COR-L23, COR-L23/5010, COR-L23/CPR, COR-L23/R23, COS-7, COV-434, CT26, D17, DH82, DU145, DuCaP, E14Tg2a, EL4, EM2, EM3, EMT6/AR1, EMT6/AR10.0, FM3, H1299, H69, HB54, HB55, HCA2, Hepa1c1c7, High Five cells, HL-60, HMEC, HT-29, HUVEC, J558L cells, Jurkat, JY cells, K562 cells, KCL22, KG1, Ku812, KYO1, LNCap, Ma-Mel 1, 2, 3....48, MC-38, MCF-10A, MCF-7, MDA-MB-231, MDA-MB-435, MDA- MB-468, MDCK II, MG63, MONO-MAC 6, MOR/0.2R, MRC5, MTD-1A, MyEnd, NALM- 1, NCI-H69/CPR, NCI-H69/LX10, NCI-H69/LX20, NCI-H69/LX4, NIH-3T3, NW-145, OPCN/OPCT Peer, PNT-1A/PNT 2, PTK2, Raji, RBL cells, RenCa, RIN-5F, RMA/RMAS, S2, Saos-2 cells, Sf21, Sf9, SiHa, SKBR3, SKOV-3, T-47D, T2, T84, THP1, U373, U87, U937, VCaP, WM39, WT-49, X63, YAC-1 and YAR cells. [0983] Without further elaboration, it is believed that one skilled in the art can, based on the above description, utilize the present disclosure to its fullest extent. The following specific embodiments are, therefore, to be construed as merely illustrative, and not limitative of the remainder of the disclosure in any way whatsoever. All publications cited herein are incorporated by reference for the purposes or subject matter referenced herein. Kits [0984] The compositions of the present disclosure may be assembled into kits. In some embodiments, the kit comprises nucleic acid vectors for the expression of the prime editors described herein. In some embodiments, the kit further comprises appropriate guide nucleotide sequences (e.g., gRNAs) or nucleic acid vectors for the expression of such guide nucleotide sequences, to target the prime editor to the desired target sequence. [0985] The kit described herein may include one or more containers housing components for performing the methods described herein and optionally instructions for use. Any of the kit described herein may further comprise components needed for performing the assay methods. Each component of the kits, where applicable, may be provided in liquid form (e.g., in solution) or in solid form, (e.g., a dry powder). In certain cases, some of the components may be reconstitutable or otherwise processible (e.g., to an active form), for example, by the addition of a suitable solvent or other species (for example, water), which may or may not be provided with the kit. [0986] In some embodiments, the kits may optionally include instructions and/or promotion for use of the components provided. As used herein, “instructions” can define a component of instruction and/or promotion, and typically involve written instructions on or associated with packaging of the disclosure. Instructions also can include any oral or electronic instructions provided in any manner such that a user will clearly recognize that the instructions are to be associated with the kit, for example, audiovisual (e.g., videotape, DVD, etc.), Internet, and/or web-based communications, etc. The written instructions may be in a form prescribed by a governmental agency regulating the manufacture, use, or sale of pharmaceuticals or biological products, which can also reflect approval by the agency of manufacture, use or sale for animal administration. As used herein, “promoted” includes all methods of doing business including methods of education, hospital and other clinical instruction, scientific inquiry, drug discovery or development, academic research, pharmaceutical industry activity including pharmaceutical sales, and any advertising or other promotional activity including written, oral and electronic communication of any form, associated with the disclosure. Additionally, the kits may include other components depending on the specific application, as described herein. [0987] The kits may contain any one or more of the components described herein in one or more containers. The components may be prepared sterilely, packaged in a syringe and shipped refrigerated. Alternatively it may be housed in a vial or other container for storage. A second container may have other components prepared sterilely. Alternatively the kits may include the active agents premixed and shipped in a vial, tube, or other container. [0988] The kits may have a variety of forms, such as a blister pouch, a shrink wrapped pouch, a vacuum sealable pouch, a sealable thermoformed tray, or a similar pouch or tray form, with the accessories loosely packed within the pouch, one or more tubes, containers, a box or a bag. The kits may be sterilized after the accessories are added, thereby allowing the individual accessories in the container to be otherwise unwrapped. The kits can be sterilized using any appropriate sterilization techniques, such as radiation sterilization, heat sterilization, or other sterilization methods known in the art. The kits may also include other components, depending on the specific application, for example, containers, cell media, salts, buffers, reagents, syringes, needles, a fabric, such as gauze, for applying or removing a disinfecting agent, disposable gloves, a support for the agents prior to administration, etc. Pharmaceutical compositions [0989] Other aspects of the present disclosure relate to pharmaceutical compositions comprising any of the various components of the prime editing system described herein (e.g., including, but not limited to, the napDNAbps, reverse transcriptases, fusion proteins (e.g., comprising napDNAbps and reverse transcriptases), extended guide RNAs, and complexes comprising fusion proteins and extended guide RNAs, as well as accessory elements, such as second strand nicking components and 5´ endogenous DNA flap removal endonucleases for helping to drive the prime editing process towards the edited product formation). [0990] The term “pharmaceutical composition”, as used herein, refers to a composition formulated for pharmaceutical use. In some embodiments, the pharmaceutical composition further comprises a pharmaceutically acceptable carrier. In some embodiments, the pharmaceutical composition comprises additional agents (e.g. for specific delivery, increasing half-life, or other therapeutic compounds). [0991] As used here, the term “pharmaceutically-acceptable carrier” means a pharmaceutically-acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, manufacturing aid (e.g., lubricant, talc magnesium, calcium or zinc stearate, or steric acid), or solvent encapsulating material, involved in carrying or transporting the compound from one site (e.g., the delivery site) of the body, to another site (e.g., organ, tissue or portion of the body). A pharmaceutically acceptable carrier is “acceptable” in the sense of being compatible with the other ingredients of the formulation and not injurious to the tissue of the subject (e.g., physiologically compatible, sterile, physiologic pH, etc.). Some examples of materials which can serve as pharmaceutically-acceptable carriers include: (1) sugars, such as lactose, glucose and sucrose; (2) starches, such as corn starch and potato starch; (3) cellulose, and its derivatives, such as sodium carboxymethyl cellulose, methylcellulose, ethyl cellulose, microcrystalline cellulose and cellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) lubricating agents, such as magnesium stearate, sodium lauryl sulfate and talc; (8) excipients, such as cocoa butter and suppository waxes; (9) oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols, such as propylene glycol; (11) polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol (PEG); (12) esters, such as ethyl oleate and ethyl laurate; (13) agar; (14) buffering agents, such as magnesium hydroxide and aluminum hydroxide; (15) alginic acid; (16) pyrogen-free water; (17) isotonic saline; (18) Ringer's solution; (19) ethyl alcohol; (20) pH buffered solutions; (21) polyesters, polycarbonates and/or polyanhydrides; (22) bulking agents, such as polypeptides and amino acids (23) serum component, such as serum albumin, HDL and LDL; (22) C2-C12 alcohols, such as ethanol; and (23) other non-toxic compatible substances employed in pharmaceutical formulations. Wetting agents, coloring agents, release agents, coating agents, sweetening agents, flavoring agents, perfuming agents, preservative and antioxidants can also be present in the formulation. The terms such as “excipient”, “carrier”, “pharmaceutically acceptable carrier” or the like are used interchangeably herein. [0992] In some embodiments, the pharmaceutical composition is formulated for delivery to a subject, e.g., for gene editing. Suitable routes of administrating the pharmaceutical composition described herein include, without limitation: topical, subcutaneous, transdermal, intradermal, intralesional, intraarticular, intraperitoneal, intravesical, transmucosal, gingival, intradental, intracochlear, transtympanic, intraorgan, epidural, intrathecal, intramuscular, intravenous, intravascular, intraosseus, periocular, intratumoral, intracerebral, and intracerebroventricular administration. [0993] In some embodiments, the pharmaceutical composition described herein is administered locally to a diseased site (e.g., tumor site). In some embodiments, the pharmaceutical composition described herein is administered to a subject by injection, by means of a catheter, by means of a suppository, or by means of an implant, the implant being of a porous, non-porous, or gelatinous material, including a membrane, such as a sialastic membrane, or a fiber. [0994] In other embodiments, the pharmaceutical composition described herein is delivered in a controlled release system. In one embodiment, a pump may be used (see, e.g., Langer, 1990, Science 249:1527-1533; Sefton, 1989, CRC Crit. Ref. Biomed. Eng.14:201; Buchwald et al., 1980, Surgery 88:507; Saudek et al., 1989, N. Engl. J. Med.321:574). In another embodiment, polymeric materials can be used. (See, e.g., Medical Applications of Controlled Release (Langer and Wise eds., CRC Press, Boca Raton, Fla., 1974); Controlled Drug Bioavailability, Drug Product Design and Performance (Smolen and Ball eds., Wiley, New York, 1984); Ranger and Peppas, 1983, Macromol. Sci. Rev. Macromol. Chem.23:61. See also Levy et al., 1985, Science 228:190; During et al., 1989, Ann. Neurol.25:351; Howard et al., 1989, J. Neurosurg.71:105). Other controlled release systems are discussed, for example, in Langer, supra. [0995] In some embodiments, the pharmaceutical composition is formulated in accordance with routine procedures as a composition adapted for intravenous or subcutaneous administration to a subject, e.g., a human. In some embodiments, pharmaceutical composition for administration by injection are solutions in sterile isotonic aqueous buffer. Where necessary, the pharmaceutical can also include a solubilizing agent and a local anesthetic such as lignocaine to ease pain at the site of the injection. Generally, the ingredients are supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water free concentrate in a hermetically sealed container such as an ampoule or sachette indicating the quantity of active agent. Where the pharmaceutical is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline. Where the pharmaceutical composition is administered by injection, an ampoule of sterile water for injection or saline can be provided so that the ingredients can be mixed prior to administration. [0996] A pharmaceutical composition for systemic administration may be a liquid, e.g., sterile saline, lactated Ringer’s or Hank’s solution. In addition, the pharmaceutical composition can be in solid forms and re-dissolved or suspended immediately prior to use. Lyophilized forms are also contemplated. [0997] The pharmaceutical composition can be contained within a lipid particle or vesicle, such as a liposome or microcrystal, which is also suitable for parenteral administration. The particles can be of any suitable structure, such as unilamellar or plurilamellar, so long as compositions are contained therein. Compounds can be entrapped in “stabilized plasmid-lipid particles” (SPLP) containing the fusogenic lipid dioleoylphosphatidylethanolamine (DOPE), low levels (5-10 mol%) of cationic lipid, and stabilized by a polyethyleneglycol (PEG) coating (Zhang Y. P. et al., Gene Ther.1999, 6:1438-47). Positively charged lipids such as N-[1-(2,3-dioleoyloxi)propyl]-N,N,N- trimethyl-amoniummethylsulfate, or “DOTAP,” are particularly preferred for such particles and vesicles. The preparation of such lipid particles is well known. See, e.g., U.S. Patent Nos. 4,880,635; 4,906,477; 4,911,928; 4,917,951; 4,920,016; and 4,921,757; each of which is incorporated herein by reference. [0998] The pharmaceutical composition described herein may be administered or packaged as a unit dose, for example. The term “unit dose” when used in reference to a pharmaceutical composition of the present disclosure refers to physically discrete units suitable as unitary dosage for the subject, each unit containing a predetermined quantity of active material calculated to produce the desired therapeutic effect in association with the required diluent; i.e., carrier, or vehicle. [0999] Further, the pharmaceutical composition can be provided as a pharmaceutical kit comprising (a) a container containing a compound of the invention in lyophilized form and (b) a second container containing a pharmaceutically acceptable diluent (e.g., sterile water) for injection. The pharmaceutically acceptable diluent can be used for reconstitution or dilution of the lyophilized compound of the invention. Optionally associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of manufacture, use or sale for human administration. [1000] In another aspect, an article of manufacture containing materials useful for the treatment of the diseases described above is included. In some embodiments, the article of manufacture comprises a container and a label. Suitable containers include, for example, bottles, vials, syringes, and test tubes. The containers may be formed from a variety of materials such as glass or plastic. In some embodiments, the container holds a composition that is effective for treating a disease described herein and may have a sterile access port. For example, the container may be an intravenous solution bag or a vial having a stopper pierce- able by a hypodermic injection needle. The active agent in the composition is a compound of the invention. In some embodiments, the label on or associated with the container indicates that the composition is used for treating the disease of choice. The article of manufacture may further comprise a second container comprising a pharmaceutically-acceptable buffer, such as phosphate-buffered saline, Ringer's solution, or dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, syringes, and package inserts with instructions for use. [1001] The following set of examples are intended to illustrate certain embodiments of the present disclosure, but do not exemplify the full scope of the disclosure. EXAMPLES [1002] EXAMPLE 1. Efficient AAV-Mediated In Vivo prime Editing in Multiple Organs [1003] Prime editing has the potential to facilitate the study or treatment of many genetic disorders caused by DNA substitutions, insertions, or deletions. Realizing this potential requires delivery methods that support efficient prime editing in vivo. By identifying and engineering solutions to bottlenecks limiting AAV-mediated in vivo prime editing efficiencies, optimized dual-AAV prime editor delivery systems (v1em and v3em PE-AAV) that enable therapeutically relevant editing in mouse brain (up to 42% in neocortex), liver (up to 46%), and heart (up to 9.1%) were developed. Prime editor expression is a bottleneck of in vivo editing efficiency that is largely overcome by the v3em PE-AAV system. these systems were applied to install putative protective mutations in vivo for Alzheimer’s disease in astrocytes and for coronary artery disease in hepatocytes, cell types of therapeutic relevance to the respective diseases. In vivo prime editing with v3em PE-AAV did not cause detectable off-target editing and did not result in significant liver enzyme or liver histology differences compared to untreated animals. Optimized PE-AAV systems support the highest levels of in vivo prime editing reported to date, facilitating the study and potential treatment of diseases with a genetic component. [1004] The ability to precisely correct pathogenic mutations or install protective ones in living cells and organisms has the potential to profoundly improve the quality of life for hundreds of millions of people worldwide ¹ . Programmable nucleases such as CRISPR-Cas9 can efficiently disrupt genes through double-strand break (DSB) formation and repair, but lack the inherent ability to convert a target DNA sequence into a specified variant. In the presence of donor DNA templates, nucleases can stimulate precise gene conversion through DSB-mediated homology-directed repair (HDR), but HDR is typically inefficient in non- dividing cells, including most therapeutically relevant cell types, and desired HDR products are frequently accompanied by a large proportion of uncontrolled insertions and deletions [1005] (indels) ^2-4 . In addition, gene editing approaches that rely on DSBs have been shown to generate undesired large deletions ^5,6 , translocations ^7-10 , chromothripsis ¹¹ , and other chromosomal abnormalities ¹² , as well as induce the p53 DNA damage response ¹³ . [1006] Base editors (BEs) ^2,3,14-16 enable direct installation or correction of transition point mutations (C•G-to-T•A, or A•G-to-G•C) or some C•G-to-G•C transversions without requiring DSBs or donor DNA templates, and with few indel byproducts. Multiple clinical trials are underway using base editors to treat diseases including hypercholesterolemia ¹⁷ , T- cell leukemia ¹⁸ , sickle-cell disease ¹⁹ , and β-thalassemia ²⁰ . Prime editors (PEs) are a complementary DSB-independent gene editing technology that can perform virtually any substitutions, small deletions, and small insertions at target DNA sites in living cells ²¹ . PEs comprise a programmable DNA nickase such as a catalytically impaired CRISPR-Cas9 fused to an engineered reverse transcriptase (RT). A prime editing guide RNA (pegRNA) contains a spacer that guides the PE to the target DNA site as well as a covalently or non-covalently associated 3’ extension that encodes the desired edit. Prime editors reverse transcribe the pegRNA extension directly into the genome using the nicked target DNA strand as a primer, leading to permanent and precise changes in genomic DNA with relatively few byproducts ²¹ . Like BEs, PEs do not require DSBs or donor DNA template, and have been used widely across many mammalian cell systems including mitotic and post-mitotic cells ^2,22-26 . [1007] Before prime editors can be translated into clinical settings, safe and efficient delivery methods capable of targeting therapeutically relevant tissue types are needed. Since ex vivo clinical gene editing thus far has been limited primarily to hematologic cells, in vivo delivery methods are needed to treat most genetic diseases. Adeno-associated viruses (AAVs) are clinically validated, FDA-approved, and widely used for in vivo gene therapy and gene editing applications ^27,28 . While not without potential risks ^29-31 , AAV AAV remains one of the few effective and clinically validated in vivo delivery vectors for a variety of non-liver organs and tissue types ^32,33 . At ~6.3 kb of encoded DNA sequence, however, prime editors are currently too large to fit in a single AAV vector, which has a cargo size limit of ~4.7 kb ^34,35 . [1008] Previously, the packaging capacity of AAV has been overcome to accommodate large genome editing agents including base editors by splitting editing proteins into two halves, each fused to a fast-splicing intein, such that each half can be packaged separately into individual AAV vectors ^36-38 . Simultaneous administration of both AAVs results in reconstitution of the functional editing agent in co-transduced cells via association of the split intein fusion proteins, triggering a partial or complete trans-protein splicing reaction. Existing in vivo PE delivery strategies with intein-split AAV or hydrodynamic DNA injection have thus far yielded modest in vivo editing efficiencies in postnatal animals, achieving maximum efficiencies corresponding to 1.7, 6.5, ~9, or 13.5% editing of bulk liver or retina) ^22-26 . Adenoviral transduction has yielded the most efficient in vivo prime editing reported to date ²³ (up to 58% editing in isolated hepatocytes, corresponding to ~35-40% editing of bulk liver since hepatocytes make up 60-70% of cells in murine liver ³⁹ ) in neonatal animals at the highest dose, but can be challenging to apply clinically due to the immunogenicity and toxicity of adenovirus ⁴⁰ . The efficient in vivo delivery of prime editors into therapeutically relevant cells using clinically validated delivery vectors such as AAV therefore remains a major bottleneck to the use of prime editing for animal research and therapeutic applications. [1009] Presented herein is the development, optimization, and application of intein-split PE-AAVs that mediate efficient in vivo prime editing in multiple mouse organs. factors that limit in vivo prime editing efficiency were systematically identified. To address these factors, the prime editor protein, pegRNA, and AAV genomic elements were optimized. The resulting optimized ‘v3em PE-AAV’ delivery strategies enabled therapeutically relevant levels of prime editing in mouse brain (42%), liver (46%), and heart (9.1%), representing the first reported prime editing in post-natal brain and heart, and substantially higher AAV- mediated in vivo prime editing efficiencies than has been previously reported in the liver. [1010] v3em PE3-AAV was applied to install mutations of biomedical interest in mice that are not currently accessible with other in vivo genome editing technologies. Using v3em PE3-AAV, the rare apolipoprotein E Christchurch (APOE3 R136S) variant that may alter Alzheimer’s disease risk, was installed in humanized APOE3 mice and confirmed expression of the edited allele in APOE-expressing cells in vivo. We also used v3em PE3-AAV in mice to install the mutation homologous to the dominant variant of human PCSK9 Q152H (mouse Pcsk9 Q155H)that is associated with a reduction in LDL cholesterol levels and protection from coronary artery disease. Using v3em PE3-AAV, APOE3 R136S was installed in humanized APOE3 mice in APOE-expressing cells in vivo. v3em PE3-AAV was also used to install in mice at the endogenous genomic locus the mutation homologous to human PCSK9 Q152H (mouse Pcsk9 Q155H), achieving 39% average bulk liver prime editing and on average 27% reduction in circulating LDL cholesterol levelsin adult mice. These results advance the potential of prime editing for basic research and therapeutic applications and establish optimized PE-AAV systems as an effective in vivo prime editor delivery method. EXAMPLE 1A. Design and evaluation of split prime editor architectures [1011] To deliver PE via AAV, the coding sequence of PE was split into two halves, one containing the N-terminus of the PE and the other containing the C-terminus, each fused to the N- or C-terminal intein from Nostoc punctiforme ^36-38,41 , respectively. positions within loop regions of SpCas9 were identified that might accommodate fusion to the intein halves with minimal disruption to function. these positions were chosen based on the analysis of crystal structures containing SpCas9 ⁴² , on reports of SpCas9 locations that support circular permutation ^43,44 , and on the presence of nucleophilic residues that might support the intein splicing mechanism ⁴¹ . positions 844 and 1024 were nominated as putative split sites that would allow splitting of the PE into two halves, each of which fit within the packaging limit of AAV while accommodating space for promoter and terminator sequences as well as pegRNA and sgRNA expression cassettes. To maximize splicing efficiency, mutation of the three N-terminal amino acids of the C-terminal extein from the native residues to the consensus Cys-Phe-Asn sequence were also assessed, or to intermediate sequence variants. [1012] plasmids encoding the two candidate halves or full-length PE2 along with pegRNA and nicking sgRNA were transfected into HEK293T cells and measured editing efficiencies across three sites by high-throughput sequencing (HTS) (Fig.1a). Among the eight split designs tested, average prime editing efficiencies ranged from 37-96% of full- length PE2 activity depending on the split. The 1024-CFN and 844-CFN split designs yielded robust editing efficiencies (FIG.1A). Prime editing activity of both the 1024 and 844 splits were dependent on splicing competency of the intein (FIG.24), with the catalytically inactive intein 1024-CFN split being on average 39% less active than the catalytically active 1024- CFN intein split, and the catalytically inactive 844-CFN split on average 95% less active than the catalytically active 844-CFN intein split. These data indicate that the inteins function partially as a dimerization domain but that splicing activity enhances editing, in contrast to intein-split base editors that do not require catalytically competent inteins. Because the association of the two halves of Cas9 can be driven by scaffolding of the sgRNA47, the 1024-CFN split without any inteins was also assessed and it was found that editing activity was almost completely lost (PE21024-CFN ∆intein resulted in only 2.6% of the activity of the catalytically competent PE21024-CFN intein split) (FIG.24), thus establishing the necessity of the inteins to enable split prime editor association. EXAMPLE 1B: Initial in vivo prime editing with intein-split dual PE-AAV [1013] the 1024-CFN PE split was chosen in the initial PE-AAV architecture since this split allows packaging of roughly equal halves of the PE gene across two AAV genomes along with a U6 promoter-driven guide RNA cassette on each vector for expression of both the pegRNA and the nicking sgRNA for PE3 applications (Fig.1b). To remain within the ~4.7-kb packaging capacity of AAV ^34,35 , the small ubiquitous EFS promoter with a bGH polyadenylation signal was used, a combination of promoter and terminator that was previously shown to support efficient AAV-mediated base editing in vivo ⁴⁵ . To assess whether mRNA transcript-stabilizing cis-elements on the AAV genome would increase PE efficiency, the effect of including W3 was tested, the minimized gamma portion of the woodchuck hepatitis virus post-transcriptional regulatory element (WPRE), to the 3' UTR of the PE gene ⁴⁶ . the resulting candidate PE-AAV constructs were tested for their ability to install the +5 G-to-T transversion in the endogenous genomic mouse Dnmt1 locus. It was previously shown that this edit can be installed by lentiviral delivery of PE in cultured mouse primary cortical neurons with modest efficiency (7.1%) ²¹ . Because Dnmt1 acts redundantly with Dnmt3a in the mammalian brain, it was reasoned that edits near the N-terminus of the protein such as +5 G-to-T (resulting in P2Q) are unlikely to result in a phenotypic impact in edited cells ⁴⁷ . [1014] To assess initial in vivo prime editing efficiency, PE-AAVs were administered at a total dose of 1×10 ¹¹ vg (5×10 ¹⁰ vg each of the N- and C-terminal PE-AAVs) packaged in AAV9 to C57BL/6 mice on postnatal day 0 (P0) via intracerebroventricular (ICV) injection, a method of direct injection into the cerebrospinal fluid that bypasses the blood-brain barrier. To enable the analysis of transduced cells, in addition to bulk tissue, a 1×10 ¹⁰ vg AAV9 expressing EGFP fused to a nuclear membrane-localized Klarsicht/ANC-1/Syne-1 homology (KASH) domain ^36,48 was co-injected (Fig.1c). Three weeks after injection, the neocortex was harvested from injected and untreated control mice, isolated both bulk nuclei and FACS- sorted GFP-positive nuclei, extracted genomic DNA, and analyzed Dnmt1 editing by high- throughput sequencing (HTS).2.8% and 4.7% editing was observed in bulk and GFP-positive nuclei, respectively, in brains treated with PE-AAV containing the W3 (Fig.1c). In mice treated with PE-AAV without W3 (bGH only), editing was very inefficient (≤0.2%, Fig.1c). These results establish that prime editing is feasible in the mammalian brain when delivered via AAV and that addition of W3 is essential to achieve even low levels of prime editing in the brain. The EFS-driven dual-AAV system with W3 (Fig.1b) is hereafter referred to as ‘v1 PE3-AAV’. EXAMPLE 1C. Impact of MMR on in vivo prime editing efficiency. [1015] Next, improvements to the in vivo editing efficiency of prime editing with AAV was investigated. It was recently discovered that DNA mismatch repair (MMR) impedes prime editing efficiency and product purity in cultured cells ⁴⁹ . It was sought to evaluate whether the identity of the installed edit and its susceptibility to MMR may limit prime editing in vivo. To characterize a diversity of prime edits in the same target gene in cultured cells, pegRNAs encoding six new edits (+1 C-to-G; + 1 C-to-G and +5 G-to-T; +2 G-to-C; +1 CTT insertion; +1 CCC insertion; and +1 GCA insertion) were screened at the Dnmt1 locus in mouse Neuro 2a cells (N2a) cells using PE3 (FIG.7A). Compared to the previously validated +5 G-to-T edit that yielded 7.6% average editing in N2a cells in vitro, the six new edits all exhibited higher average editing efficiencies ranging from 14% to 45% (FIG.7A). [1016] Recently MLH1dn, a dominant negative human mismatch repair protein that increases the efficiency of prime editing when transiently co-expressed with PE components, was developed ⁴⁹ . The PE4 system co-expresses MLH1dn with PE2 components, while the PE5 system co-expresses MLH1dn with PE3 components. To assess whether the observed differences in prime editing efficiency were due to the reversion of prime editing intermediates by MMR, N2a cells were transfected with either PE2 or PE4 and pegRNAs encoding the +5 G- to-T, +1 C-to-G, +1 CCC insertion, or +2 G-to-C edits. The efficiency of +5 G-to-T and +1 C- to-G edits were improved 5.8-fold and 3.2-fold, respectively, with the addition of MLH1dn (PE4), indicating that these edits are impeded by MMR ⁴⁹ (Fig.2a, FIG. 7B). In contrast, the +2 G-to-C and +1 CCC insertion edits both exhibited comparatively higher editing efficiencies of 20% and 52%, respectively, with PE2, and the efficiency of these edits was not improved by addition of MLH1dn (PE4) (Fig.2a, FIG.7B). These data are consistent with previous observations that prime editing intermediates containing C•C mismatches and multiple contiguous insertions are poor substrates for MMR, allowing the +2 G-to-C and +1 CCC insertion prime editing intermediates to natively evade MMR ⁵⁰ . Taken together, these results support previous observations that prime editing efficiencies in cultured cells are lower for edits that proceed through intermediates that are more readily recognized by cellular MMR proteins ^49,51 . [1017] To assess whether MMR-recognized and MMR-evading edits show similar trends in prime editing efficiency in vivo, ICV injections were performed at P0 of 1×10 ¹¹ vg of v1 PE3- AAV9 with W3 encoding +1 C-to-G, +1 CCC insertion, or +2 G-to-C edits.6.1%, 25%, and 42% prime editing was observed for +1 C-to-G, +1 CCC insertion, and +2 G-to-C edits, respectively (FIG.2b), consistent with their relative MMR evasion and efficiencies in cultured N2a cells (FIG.2a, FIGs.7A-7B). Although the activity of MMR in the mammalian brain is not well understood, Mlh1 is expressed in the mammalian brain and may limit prime editing in the CNS. These data suggest that MMR or related DNA repair pathways likely also impedes prime editing in vivo, and that designing edits to natively evade MMR by adding nearby benign or silent bystander mutations ⁴⁹ may enhance prime editing efficiency in the mammalian brain. These results also establish that it is possible to perform in vivo prime editing in a mammalian brain at efficiencies anticipated to be therapeutically relevant for a variety of serious genetic disorders. EXAMPLE 1D. Development of split-intein PE-AAV system for systemic administration [1018] To further explore the utility of split-intein PE-AAVs in vivo, their ability to mediate prime editing in adult animals, rather than neonates, was investigated via systemic injection. the Dnmt1 +5 G-to-T, +1 CCC insertion, and +2 G-to-C edits were chosen for systemic AAV administration. the v1 PE3-AAV9 was delivered at a dose of 1×10 ¹² vg (5×10 ¹¹ vg each of the N- and C-terminal AAV) via retro-orbital (RO) injections into 6- to 8- week-old adult C57BL/6J mice. liver, heart, and skeletal muscle were harvested three weeks after injection and analyzed on-target editing by HTS. The +5 G-to-T edit was undetectable (≤0.1%), but low prime editing in the liver for +1 CCC insertion (0.3%) and +2 G-to-C edits (0.9%) was observed, respectively (Fig.2c). No prime editing was observed (≤0.1%) in the heart and skeletal muscle for any of the three edits (Fig.2c). While the same v1 PE3-AAV architecture robustly edited the brain of P0 pups when administered by ICV injection, prime editing was greatly reduced in adult mice after systemic injection, suggesting the PE-AAV architecture required further optimization. [1019] Therefore, the bottlenecks limiting in vivo prime editing after systemic injection were identified and solutions to overcome these bottlenecks were developed. EXAMPLE 1E. Factors limiting systemic in vivo PE efficiency [1020] To understand the factors limiting systemic in vivo prime editing, the effect of post-injection incubation time on prime editing efficiencies was first assessed.v1 PE3- AAV9 with pegRNA encoding the Dnmt1 +2 G-to-C edit was administered to C57BL/6 mice by RO injection and harvested tissues three or six weeks post-injection. A significant increase in PE activity was not observed with increased incubation time, with editing for both conditions yielding ≤1.1%, indicating that incubation time was not the main factor limiting prime editing efficiency (FIG.8). [1021] It was recently reported that the addition of a 3' stabilizing motif to pegRNAs (epegRNAs) increases the stability of the pegRNA and substantially improves prime editing efficiency in vitro ⁵² . To assess whether epegRNAs also augment prime editing in vivo, 1×10 ¹² vg (5×10 ¹¹ vg each half) of v1 PE3-AAV9 was delivered either with pegRNA or epegRNA (tevopreQ1 fused on the 3' end of the pegRNA with an 8-nucleotide linker) via systemic RO injection. The use of an epegRNA resulted in an average of 1.7% +2 G-to-C prime editing of Dnmt1 in the liver, compared to 0.9% prime editing with unmodified pegRNAs (P=0.20) (Fig.3a). However, when assessed in the brain by P0 ICV administration of 1×10 ¹¹ vg of v1 PE3-AAV9, epegRNAs more strongly increased Dnmt1 +1 C-to-G editing efficiencies over pegRNAs from 6.1% to 21% prime editing in bulk cortex and 8.6% to 38% prime editing in GFP+ cortex (P=0.1 for both) (Fig.3b). Collectively, these results indicate that epegRNAs can support efficient prime editing in vivo. Although these findings also suggest that pegRNA stability is not the sole factor limiting the editing efficiency of systemically administered PEs, epegRNAs were used for all subsequent designs and hereafter indicate use of an epegRNA with an ‘e’ (v1e PE3-AAV). [1022] Next, whether insufficient prime editor protein expression driven by the EFS promoter may be a major limiting factor for efficient systemic in vivo prime editing, was considered. In an effort to improve PE expression, the Cbh promoter was tested, a strong and ubiquitous promoter that mediates efficient AAV-mediated base editing in mice when delivered systemically ^36,53 . To accommodate the 0.7-kb Cbh promoter, the pegRNA and sgRNA cassettes were moved to a third AAV vector containing a human U6 promoter that drives epegRNA expression and a mouse U6 promoter that drives nicking sgRNA expression to avoid long stretches of homology on the AAV genome that can lead to recombination ⁵⁴ . Thus, prime editing in this system requires co-transduction of three AAVs to deliver all PE3 components (Fig.3c). this system was designated ‘v2e PE3-AAV’. [1023] All three v2e PE3-AAV9 prime editor systems were delivered at a 1:1:0.5 ratio (5×10 ¹¹ vg each of the N- and C-terminal PE-AAVs and 2.5×10 ¹¹ vg pegRNA/sgRNA AAV) to 6- to 8- week-old C57BL/6 mice via systemic RO injection and evaluated prime editing of Dnmt1 +2 G-to-C edit (Fig.3d). This new strategy yielded 48% prime editing in the bulk liver and 7.2% prime editing in the heart, 27- and 70-fold higher editing compared to v1e PE3-AAV9 that uses the EFS promoter (FIG.3D). Prime editing in heart was 7.2% and muscle tissue was less than 1%, while Cas9 delivered at the same dose yielded 18% and 8.7% indels in heart and muscle respectively (FIG.3D), suggesting that intrinsic cell type-specific factors or insufficient prime editor expression may still limit prime editing in some tissues, which can potentially be overcome by increasing AAV dose or by changing delivery route or timing of injection. These data suggest that prime editor expression level is a major determinant of in vivo prime editing efficiency. The observed liver editing efficiencies, which correspond to prime editing in the majority of hepatocytes, would likely be relevant for the study or potential treatment of a variety of genetic diseases in the liver ^23,55,56 , and are similar to bulk liver editing efficiencies achieved with optimized AAV-delivered base editors and Cas9 nuclease systems ^36,37,45 . These data also represent by several-fold the highest AAV- mediated in vivo prime editing efficiencies in a post-natal animal reported thus far ^22-26 . [1024] To further improve efficiency, architectural improvements from PEmax prime editors ⁴⁹ were tested, including codon optimization of MMLV RT for improved expression, mutations in Cas9 for enhanced nickase activity, and optimized nuclear localization signals (NLSs) into the v2e PE-AAV design, resulting in v2em PE3-AAV. all three v2e or v2em PE3- AAV9 vectors were delivered in a 1:1:0.5 ratio (5×10 ¹¹ vg each of the N- and C- terminal PE-AAVs and 2.5×10 ¹¹ vg pegRNA/sgRNA AAV) to 6- to 8-week-old C57BL/6 mice via systemic RO injection and evaluated the efficiency of the Dnmt1 +1 C-to-G prime edit. These improvements from PEmax resulted in a similar level of editing efficiency in the well-edited liver, but 2.4-fold higher prime editing efficiency in the heart (P=0.017, Fig.3e), suggesting that the PEmax improvements improve in vivo editing in tissues that do not reach high editing levels with older PE architectures. In the brain, incorporation of epegRNA and PEmax together resulted in 41% prime editing, corresponding to a 6.8-fold increase in prime editing in bulk neocortex compared to PE3 (FIGs.9A-9B, P<0.0001). The PEmax architecture, hereafter designated with an ‘m’, were used in all subsequent experiments; thus the triple-AAV system with PEmax is v2em PE3-AAV. EXAMPLE 1F. Development of highly active dual-AAV PEs for systemic editing in adult mice. [1025] While the triple AAV v2em PE3 system can achieve therapeutically relevant levels of prime editing in vivo, it was sought to design a dual PE3-AAV system to simplify delivery and reduce the total AAV dose, while preserving the improvements that enhanced in vivo prime editing efficiency. Although the use of prime editors containing smaller Cas variants such as SaCas9 is one potential solution to accommodating PEs with larger promoters in a dual AAV system, previously it has been found that the activity of SaCas9- derived PEs to be lower overall than SpCas9-based PEs (FIG.10) ^22,57 . Therefore a dual- AAV platform for delivery of SpCas9-based PEs was developed, because they are more thoroughly characterized and offer increased targeting flexibility and higher editing efficiencies compared with SaCas9 PEs. [1026] To reduce the size of the prime editing system to fit into two AAV, truncated MMLV RT variants that lack the RNaseH domain were considered . Truncations of MMLV RT in the connection domain that separates the largely functionally distinct polymerase and RNaseH subunits have been shown to retain reverse transcriptase activity in PEs ^23,24,57,58 . HEK293T cells with RNaseH truncated PE (PE ∆RNaseH) were transfected. PE ∆RNaseH performed similarly to full-length PE across a variety of edits in HEK293T cells with and without nicking sgRNA (FIG.11), except for the HEK3 +1 LoxP insertion edit, where PE2 ∆RNaseH and PE3 ∆RNaseH yielded half the efficiency of full-length PE2 and PE3 editing efficiency, respectively (P=0.010 for PE3 vs PE3 ∆RNaseH; FIG.11). This result indicates that the RNaseH domain of MMLV RT is not an essential prime editor component in immortalized cells for most tested edits and can be removed to reduce PE size, consistent with other reports using ∆RNaseH PEs in vitro ^22,23,57 . [1027] To directly assess whether PE ∆RNaseH maintains its full-length activity in vivo after systemic injection, the v2em PE3-AAV system was used to compare full-length prime editor programmed to edit Dnmt1 +1 C-to-G to two variants of RNaseH-deleted PEs. The first ∆RNaseH variant uses a previously published truncation at residue 497 of MMLV RT that appends six additional amino acids likely arising from a restriction enzyme cloning artifact ⁵⁸ . The second RT ∆RNaseH variant is a clean truncation at residue 497 of MMLV RT without additional amino acids. All three PEmax variants (PEmax, PEmax ∆RNaseH+6AA, and PEmax ∆RNaseH) delivered systemically as v2em PE3-AAVs injected at 1.25×10 ¹² vg total with AAV9 (5×10 ¹¹ vg each of the N- and C-terminal PE-AAVs plus 2.5×10 ¹¹ vg pegRNA/sgRNA AAV) into 6- to 8-week-old mice were similarly active in the liver and heart (Fig.4a), indicating that PE3max ∆RNaseH maintains full-length prime editing efficiency in vivo at the target site assessed. Similarly, when PEmax or PEmax ∆RNaseH v2em PE3- AAVs were injected at 5×10 ¹⁰ vg total with AAV9 (2.5×10 ¹⁰ vg per N- and C- terminal halves plus 1.1×10 ¹⁰ vg pegRNA/sgRNA AAV), PEmax ∆RNaseH performed similarly to PEmax (Fig.4b), indicating that the RNaseH domain is also not necessary for prime editing in the brain. [1028] Having established that PEmax ∆RNaseH can maintain the editing efficiency of full- length PEmax in vivo, the AAV genome architecture was next optimized to enable packaging of intein-split PE3max ∆RNaseH into two AAV genomes, resulting in v3em PE3- AAV (FIGs.4C-4D). Expression of each protein half is driven by the Cbh promoter and terminated with the SV40 late polyA, the size of which allows the pegRNA and nicking sgRNA cassettes to both fit in the C-terminal PE-AAV (Fig.4c). the performance of v2em PE3-AAV9 was compared with v3em PE3-AAV9, each with an epegRNA programmed to install the +1 C-to-G edit at Dnmt1 in 6- to 8-week-old C57BL/6 mice via systemic RO injection. Doses were 1.25×10 ¹² vg total v2em PE3-AAV (5×10 ¹¹ vg N-terminal v2 PE3- AAV, 5×10 ¹¹ vg C-terminal v2 PE3-AAV, and 2.5×10 ¹¹ vg v2 epegRNA/sgRNA AAV) or 1×10 ¹² vg of total v3em PE3-AAV (5×10 ¹¹ vg each of the N- and C-terminal v3em PE3- AAVs). [1029] Three weeks after injection, tissues were harvested for analysis by HTS. In bulk liver tissue, v3em PE3-AAV9 yielded efficiencies similar to v2em PE3-AAV9 (35% for v3em PE3- AAV vs 36% for v2em PE3-AAV). In bulk heart and skeletal muscle tissue, prime editing increased 2.1-fold (9.1%, P=0.026) and 4.9-fold (1.3%, not significant by unpaired t-test), respectively, for v3em compared to v2em PE3-AAV (Fig.4d). The observation of largely unchanged editing efficiency in liver but strong improvement in extra- hepatic tissues upon reduction of the co-transduction requirement is consistent with a previous report comparing dual-AAV and single-AAV adenine base editors ⁴⁵ and likely reflects that transduction efficiency in liver is only modestly limiting for either AAV system, in contrast with less efficiently transduced tissues in which AAV delivery remains a key bottleneck and thus v3em improvements substantially increase prime editing efficiencies. EXAMPLE 1G: v3em PE-AAV architecture increases in vivo PE expression [1030] Next, in vivo prime editor expression from v1em and v3em PE3-AAV9 architectures was directly compared. To do so, 6- to 8-week-old C57BL/6 mice were injected retro-orbitally with v1em or v3em PE3-AAV9, each at a high dose of 1×10 ¹² vg total (5×10 ¹¹ vg N- and C- terminal halves) or a 10-fold lower dose of 1×10 ¹¹ vg total (5×10 ¹⁰ vg N- and C-terminal halves), and with each epegRNA encoding the Dnmt1 +2 G-to-C edit. Three weeks after injection, DNA and RNA were isolated from bulk liver tissue.46% and 14% prime editing was observed with v3em PE3-AAV9 at the high and low dose, respectively (Fig.4e), and 5.7% and 0.1% prime editing with v1em PE3-AAV9 in bulk liver, consistent with improvements from the stronger Cbh promoter driving expression of PE protein. [1031] Viral genomes were quantified from the N- and C-terminal AAVs using ddPCR with probes specific for SpCas9 amplicons on each half of PEmax and found that the average number of transduced viral genomes did not significantly differ between N- and C-terminal AAV halves or between v1em PE3-AAV and v3em PE3-AAV architectures at either dose by unpaired t-tests with correction for multiple comparisons (FIG.14). expression of both PE- AAV halves of v1em PE3-AAV and v3em PE3-AAV were analyzed in bulk liver mRNA by generating cDNA and performing ddPCR quantification of both N- and C- terminal halves, normalized to Gapdh expression levels (FIG.14). When analyzing RNA expression differences, higher expression was observed of both N- and C-terminal PE with v3em PE3- AAV (3.5-fold to 4.8-fold higher than that of v1em), consistent with the editing differences observed between the two architectures (Fig.4e). These data collectively suggest that prime editor expression is a bottleneck of editing efficiency in the liver that is largely overcome by the v3em PE3-AAV architecture. [1032] Notably, it was observed that expression of the N-terminal transcript was consistently lower than that of the C-terminal transcript across architectures and doses. For example, the N-terminal prime editor transcript was 13-fold less abundant than the C- terminal prime editor transcript with the v3em architecture at the 1×10 ¹² vg dose (P=0.0033). The consistently lower expression of the N-terminal half indicates that the N-terminal half of the prime editor may be more limiting than the C-terminal transcript in these contexts. To assess whether increasing the ratio of N-terminal PE half would result in additional in vivo editing efficiency gains, v3em PE3-AAV9, encoding the Dnmt +2 G to C edit was delivered at the same total dose of 1×10 ¹² vg but at a ratio of 2.5:1 (7.1×10 ¹¹ vg N-terminal half and 2.9×10 ¹¹ vg C-terminal half). Increasing the ratio of N-terminal PE half to C-terminal PE half did not significantly alter prime editing in the liver, with the 1:1 ratio yielding 46% prime editing and the 2.5:1 ratio yielding 38% (P=0.35), but decreased prime editing efficiency in heart, with the 1:1 ratio yielding 11% prime editing and the 2.5:1 ratio yielding 5.6% (P=0.037). Prime editing in muscle did not change significantly, with the 1:1 ratio yielding 1.1% and the 2.5:1 ratio yielding 0.7% (P=0.61) (FIG.25). These results indicate that either the N-terminal half is not limiting and expression may be limited at translation rather than transcription, or that reducing the amount of C-terminal transcript outweighs the benefit of increasing the amount of N-terminal transcript. These results suggest that a 1:1 ratio of v3em- PE AAVs should be used; however, additional experiments characterizing the expression of both prime editor protein halves could yield insights to further improve in vivo prime editing efficiencies. [1033] Finally, v3em PE3-AAVs were assessed using the 844-CFN intein split architecture that also yielded high efficiency prime editing similar to that of full-length PE3 in vitro (Fig.1A, FIG.3E).1×10 ¹² vg of total 1024-CFN or 844-CFN v3em PE3- AAV (5×10 ¹¹ vg each of the N- and C-terminal PE-AAVs) was delivered to 6- to 8-week-old C57BL/6 mice via systemic RO injection and analyzed prime editing three weeks post injection. Editing efficiency differences were statistically insignificant by multiple unpaired t- tests (FIG.3E), providing an alternate PE protein split that could be beneficial for accommodating tags, altered architectures, or different elements on the AAV genome that may be necessary for different applications. the 1024-CFN (v3em PE-AAV) was used for further characterization. EXAMPLE 1H: Improved PE-AAV in vivo prime editing in the central nervous system [1034] While v1 PE3-AAV supported robust central nervous system (CNS) prime editing when injected directly to the brain in neonatal mice (Fig.2b, Fig.3b), improvements in v3em PE3-AAV design might offer increased CNS editing efficiency over v1em PE3-AAV. To test this possibility, PE3max with epegRNA installing the Dnmt1 +1 C-to-G edit was delivered via P0 ICV injection using the v1em or v3em PE3-AAV9 architecture at a dose of 1×10 ¹¹ vg (5×10 ¹⁰ vg per half) with 1×10 ¹⁰ vg capsid-, promoter-, and terminator-matched EGFP:KASH to facilitate sorting of transduced cells. The capsid- and promoter-matched GFP AAVs yielded 50% and 61% GFP-positive nuclei for v1 and v3, respectively (Fig.5B) indicating that the Cbh promoter may be active in more cells across the CNS than the EFS promoter. Although both approaches led to similarly high levels of editing in bulk cortex (41% and 42% for v1em and v3em, respectively), v1em PE3-AAV yielded higher editing among GFP-positive nuclei (81% for v1em and 69% for v3em, P=0.0087) (Fig.5C). [1035] In the context of the optimized v1em PE-AAV architecture, the importance of including a nicking sgRNA in vivo (the PE3 strategy) was assessed. Inclusion of a nicking sgRNA in the PE3 system can greatly increase prime editing efficiencies in cultured cells by biasing cellular repair machinery to repair the non-edited strand ^21,49,52 . v1em PE2-AAV9 (lacking the nick-inducing sgRNA) or v1em PE3-AAV9 (with the nicking sgRNA) was injected at a total dose of 1×10 ¹¹ vg (5×10 ¹⁰ vg per half) with 1×10 ¹⁰ vg promoter-matched AAV9 EGFP:KASH by P0 ICV. Three weeks later, nuclei was isolated from neocortex, sorted nuclei by FACS, and analyzed genomic DNA by HTS. The addition of the nicking sgRNA greatly improved prime editing efficiency for both edits (FIG.14), with the Dnmt1 +1 C- to-G edits increasing in efficiency by 9.8-fold in bulk cortex and 12-fold in the GFP+ population for PE3 compared to PE2. Similarly, inclusion of a nicking sgRNA improved prime editing with the Dnmt1 +2 G-to-C edit by 2.8-fold in bulk cortex and 2.5-fold in the GFP- positive population. These results demonstrate the importance of including a nicking sgRNA when performing prime editing in vivo. [1036] The delivery of prime editors to the CNS of adult animals via systemic administration provides a valuable proof of concept for preclinical studies in which genome editing in the brain might provide therapeutic benefit. Given that direct injection into the brains of P0 mice resulted in efficient CNS editing and that systemic injection resulted in efficient editing in peripheral tissues, it was reasoned that a blood-brain barrier-crossing capsid such as AAV PHP.eB ⁵⁹ might enable efficient CNS editing by systemic injection in adult mice that natively express the LY6A receptor of PHP.eB AAV ⁶⁰ . To test this possibility, C57BL/6 mice were injected with a total dose of 1×10 ¹² vg of either v1em or v3em PE3-AAV PHP.eB encoding an epegRNA to install the Dnmt1 +2 G-to-C edit (5×10 ¹¹ vg each half) with promoter- and terminator-matched 1×10 ¹¹ vg AAV PHP.eB EGFP:KASH to facilitate enrichment of transduced nuclei (Fig.5D). With v1em PE3-AAV PHP.eB 14% prime editing was observed in bulk cortex and 30% prime editing among GFP-positive cells, with few indels (0.5%), while v3em PE3-AAV PHP.eB yielded 13% prime editing and 0.7% indels in bulk cortex and 20% prime editing and 0.5% indels in the GFP-positive population (Fig.5D). Taken together, these results demonstrate prime editing of the CNS in adult mice following a systemic injection of a blood-brain barrier-crossing AAV capsid. EXAMPLE 1I. Efficient in vivo installation of a mutation relevant to neurological disease [1037] To test the capabilities of PE-AAV systems to edit mutations of biomedical interest in vivo, PE-AAVs were used to install the putatively protective APOE Christchurch (APOE3 R136S) coding variant, a G-to-T transversion mutation that cannot be installed via base editing and that would be difficult to install in post-mitotic or slowly dividing cells via HDR. This mutation is of biological and therapeutic interest, as it has been observed in an individual who carried the risk-associated PSEN1 (presenilin 1) E280A mutation but who did not develop cognitive impairment until three decades after the expected age of clinical onset of Alzheimer’s Disease (AD) among PSEN1 E280A carriers ⁶¹ . A subsequent study suggests the APOE Christchurch variant may be deleterious in other genetic contexts ⁶² . The ability to precisely install the APOE Christchurch allele in relevant cells in vivo could help illuminate the mutation’s influence on AD pathology. [1038] To develop a strategy for the installation of APOE3 R136S, a prime editing strategy for this mutation was first optimized in HEK293T cells, achieving 40% prime editing by plasmid transfection (FIGs.15A-15C), and verified prime editing in cultured humanized mouse astrocytes, observing 15% prime editing with PE3 and 27% prime editing with PE5 (FIG.15D). These results indicate that prime editing is feasible in cultured astrocytes, the major APOE-expressing cells in the CNS and the primary cell type of interest for this mutation ^63,64 . To assess installation of APOE3 R136S in vivo, ICV injection of v3em PE3- AAV9 was performed. the impact of injection timing was also assessed by injecting via ICV at P1 or P3, as the extent of non-neuronal cell transduction is known to increase with age at the time of injection ^65-67 . a total of 1×10 ¹¹ vg (5×10 ¹⁰ vg per half) of v3em PE3- AAV9 carrying the optimized epegRNA and nicking sgRNA was injected in humanized APOE3 mice via ICV injection. Three weeks after injection, prime editing efficiencies were analyzed in bulk nuclei from neocortex and hippocampus, two brain regions relevant to AD pathology. DNA editing efficiencies in bulk cortical and hippocampal tissues for P1 injected mice were 12% prime editing with 5.0% indels, and 14% prime editing with 3.1% indels, respectively, while P3 injections resulted in 8.2% prime editing with 4.6% indels, and 7.1% prime editing with 3.8% indels in the bulk cortex and hippocampus tissues, respectively (Fig.5d). To measure installation of APOE3 R136S in APOE-expressing cells, total RNA was isolated from AAV- injected and control brain tissues three weeks post injection, generated cDNA, and observed 9.4% prime editing with 3.5% indels in cortex APOE cDNA and 11% prime editing with 2.8% indels in hippocampal APOE cDNA. Together, these data reveal that prime editing can install mutations of therapeutic interest in relevant CNS cell types in vivo. EXAMPLE 1J. prime editing of liver in adult mice to install a protective variant of PCSK9 [1039] To further assess in vivo editing activity of PE-AAV systems, their ability to mediate therapeutically relevant prime edits in adult animals was tested. proprotein convertase subtilisin/kexin type 9 (Pcsk9) was targeted, a therapeutically relevant gene involved in cholesterol homeostasis ^68,69 . Humans with loss-of-function PCSK9 mutations have lower levels of low-density lipoprotein (LDL) cholesterol in the blood and a reduced risk of atherosclerotic cardiovascular disease without any apparent adverse health consequences ^68,70-73 . Previously, base editing has been used to precisely install a premature stop codon or splice site mutation in Pcsk9, resulting in a reduction of Pcsk9 protein level in the liver and a drop in circulating LDL cholesterol ^45,74-76 . While these studies have yielded encouraging results, and base editing of PCSK9 to lower LDL cholesterol levels has recently entered clinical trials ¹⁷ , the ability of prime editing to precisely introduce virtually any small substitution, insertion, or deletion provides access to PCSK9 variants that could offer complementary strengths. [1040] To test whether PE-AAV could edit the liver of an adult animal to confer a protective phenotypic change, PE-AAV was designed and produced to install the mouse homolog of PCSK9 Q152H, a G-to-C loss-of-function substitution observed in certain families that blocks autocatalytic processing of PCSK9 ⁷⁷ , with retention of both the mutated protein as well as autocatalytically competent wild-type PCSK9 in the endoplasmic reticulum (ER) without inducing ER stress or the unfolded protein response in humans or in mice overexpressing PCSK9 Q152H ⁷⁸ . Individuals homozygous for PCSK9 Q152H show a marked reduction in LDL cholesterol levels, and heterozygous individuals also show a reduction in levels of circulating PCSK9 and LDL ^77,79 . The development of an in vivo prime editing strategy to install this mutation in postnatal animals may help illuminate its physiological consequences and test a potential therapeutic strategy to lower coronary heart disease risk in high-risk populations. [1041] Prime editing was first optimized in cultured cells to install the mouse homolog of PCSK9 Q152H (Pcsk9 Q155H) (FIGs.16A-16C). plasmids encoding PEmax, an epegRNA, and a nicking sgRNA were transfected, resulting in up to 17% prime editing in mouse N2a cells (FIGs.16A-16C). Next, whether the inclusion of MMR-evading silent mutations near the intended edit ⁴⁹ could improve installation of Pcsk9 Q155H was assessed and a 2.8-fold improvement was found when the silent mutation was incorporated with PE2 and 1.3-fold with PE3max (FIG.16D), achieving up to 25% prime editing with 5.5% indels in N2a cells. [1042] With an efficient Pcsk9 Q155H prime editing strategy in mouse cells in hand, v3em PE3-AAV9 was delivered into 6- to 8-week-old mice via systemic (RO) injection at a dose of 1×10 ¹² vg per mouse (4-5×10 ¹³ vg/kg for a 20-25 gram mouse) and compared epegRNAs encoding Pcsk9 Q155H with a PAM-disrupting edit or with MMR-evading silent edits (FIG.17), achieving 31% and 38% prime editing, respectively. Inclusion of MMR- evading silent edits modestly increased average liver editing efficiency eight weeks post- injection (P=0.06, unpaired t-test) (FIG.17). Together, these in vitro and in vivo findings demonstrate that MMR-evading edits can be a useful means of increasing prime editing efficiency and, when possible, should be considered for the design of prime editing experiments in cultured cells or in animals, although it will be important to validate that these silent edits do not induce any undesired consequences. [1043] In a separate cohort of mice, whether v3em PE3-AAV-mediated Pcsk9 prime editing with this MMR-evading strategy in liver reduces circulating lipid levels was assessed. v3em PE3-AAV9 was delivered, into 6- to 8-week-old mice via systemic RO injection at a dose of 1×10 ¹² vg per mouse (4-5×10 ¹³ vg/kg for a 20- to 25-gram mouse) and achieved 39% editing eight weeks post-injection (Fig.6A, FIG.18A). mice injected with v3em PE3-AAV9 programmed to install Pcsk9 Q155H as well as untreated mice were serially bled and total and LDL cholesterol level were measured over time. All PE-treated mice exhibited decreased circulating total and LDL cholesterol compared to untreated control animals (P<0.05 by two- way ANOVA) (FIGs.18C-18D). [1044] Loss-of-function PCSK9 mutations decrease the rate of LDL receptor (LDLR) degradation in the liver, thereby reducing the level of circulating LDL cholesterol. Total plasma cholesterol in Pcsk9-edited mice decreased by 20% on average compared to age- matched untreated mice two weeks post-injection, and this effect persisted until the end of the study at eight weeks (P=0.0217 by two-way ANOVA at eight weeks) (Fig.6c).27% reduction in plasma LDL cholesterol was observed at two weeks post-treatment compared to age-matched untreated controls and this effect also persisted until the end of the study at eight weeks (Fig.6d) (P=0.023 by two-way ANOVA). While the effect of Pcsk9 Q155H transgene overexpression has been reported ^78,79 , the installation of this mutation into the genome in vivo and the examination of the resulting physiological effect has not been previously described. [1045] In PE-treated male mice, the total plasma cholesterol was lowered by 30% compared to untreated control male mice at two weeks post-injection (P=0.0004 by two-way ANOVA), nearing the degree of total cholesterol-lowering observed in Pcsk9 knockout mice ⁸⁰ or in highly efficient base-editing mediated knockdown ^45,74,75 (FIG.18B, and FIG. 19B). In contrast, the reduction in total cholesterol in female mice was 15% compared to age- matched untreated female mice at two weeks post-injection (FIG.18C and FIG.19C). [1046] The effect on LDL cholesterol was also prominent in male mice with 38% reduction at two weeks post-injection, persisting over time (FIGs.18D-18E and FIGs.19D- 19E) (P=0.00035 by two-way ANOVA at eight weeks). Reduction of LDL cholesterol levels in male mice were supported by western blot analysis showing increases in LDLR expression in liver tissue of PE treated mice compared to untreated mice (FIGs.20A-20B) (P=0.01, unpaired t-test). Similar degrees of sex-dependent differences in lipid response in mice have been previously reported ^81-83 . Collectively, these results demonstrate that the optimized v3em PE3-AAV architecture can achieve robust and therapeutically relevant prime editing in vivo to install genomic mutations that cannot readily be installed in relevant tissues by other methods. EXAMPLE 1K. Characterization of in vivo off-target editing and PE-AAV toxicity [1047] To assess in vivo off-target prime editing in liver tissue from v3em PE3-AAV treatment, CIRCLE-seq ⁸⁴ was performed to nominate potential off-target loci that might be engaged by either the pegRNA or the nicking sgRNA. From the nominated loci, 10 candidate off-target sites were then selected based on the highest read counts from CIRCLE-seq to examine by HTS (Supplementary Table 1). No detected off-target editing above background levels was present at any of these loci in mice treated with v3em PE3-AAV9, indicating that prime editing at this site maintains a high degree of sequence specificity, consistent with several other reports ^21,85-94 (FIGs.6E-6F). [1048] Finally, toxicity associated with v3em PE3-AAV delivery was investigated by measuring serum alanine aminotransferase (ALT) and aspartate transaminase (AST) levels, biomarkers of hepatocellular and kidney injury ⁹⁵ . AAV8, a serotype that efficiently and specifically transduces murine hepatocytes ⁹⁶ , was used and delivered into a separate cohort of mice dose- and serotype-matched AAV8 encoding EGFP to control for toxicity induced by the AAV vector. a third cohort of mice was also treated with dose- and serotype-matched Cas9 nickase to control for toxicity caused by Cas9 nickase and sgRNA portion of the prime editor, and a fourth cohort with saline alone. Although a slight elevation of ALT and AST in AAV-injected mice at 5- and 7-weeks post-injection was observed compared to saline controls, the levels were within the normal physiological range for all conditions ^97,98 and there were no statistically significant differences between the saline-treated mice and the PE- AAV-treated mice (P=0.28 by two-way ANOVA) (FIGs.21B-21C). Additionally, liver histology was performed eight weeks post-injection and found no evident histological or morphological changes compared to saline-treated mice (FIG.21A). Together, these results demonstrate that optimized v3em PE3-AAV can mediate efficient prime editing in the mouse liver (FIG.21D) with no detected off-target editing and without causing substantial toxicity. EXAMPLE 1L. Discussion [1049] By systematically identifying and addressing the factors limiting in vivo prime editing via AAV, a platform for the delivery of prime editors to neonatal and adult mouse organs was developed including CNS, liver, and heart. Optimized PE-AAVs are capable of installing a variety of edits across these tissue types with therapeutically relevant efficiencies. In both CNS and liver, PE-AAVs can achieve ≥40% precise installation of substitutions and small insertions, substantially outperforming previously reported platforms for in vivo PE delivery.These results represent the most efficient in vivo prime editing delivery using AAV, a clinically validated vector, achieving prime editing efficiencies in postnatal animals sufficient to be useful for a range of basic science and therapeutic applications. These results are also the first to establish prime editing in the mammalian brain, which may facilitate the study and treatment of neurological disorders. PE-AAVs can facilitate the installation of various therapeutic edits including protective alleles associated with Alzheimer’s disease and coronary artery disease. It is anticipated that properties of optimized v1em and v3em PE- AAV systems will advance the study and potential treatment of a wide variety of diseases with a genetic component. [1050] These findings also demonstrate that in vivo prime editing is feasible across multiple tissues and cell types. They highlight promoter choice and prime editor expression as key bottlenecks of PE performance in vivo that can be overcome through vector engineering. It is also shown that recent improvements in prime editing such as epegRNAs, PEmax, and the use of MMR-evading bystander edits can each improve prime editing in cultured cells and in vivo. The doses of systemically delivered AAV in this study were limited to a maximum of 1×10 ¹² vg per animal, corresponding to 4-5×10 ¹³ vg/kg for a 20-25 gram mouse, a dose considered to be well tolerated in clinical trials involving AAV. It is likely that higher AAV doses will yield higher levels of prime editing, though with potentially decreased therapeutic relevance due to dose-limiting AAV toxicity. Prime editing efficiency in extrahepatic tissues may be further increased by improvements in prime editor expression using tissue-specific optimization such as delivery route that increases AAV transduction in relevant tissues and the use of capsids with enhanced tropism for a given tissue. [1051] In vivo prime editing via AAVs currently relies on the use of two or more AAVs to encode all necessary prime editing components. Additionally, for prime editing applications that require additional proteins, such as installing site-specific recombinase landing sites for gene-sized genomic insertions further size reduction of the components could facilitate a dual-AAV PE strategy or delivery via a single adenoviral genome. Substantial size reduction of PE-AAV components to enable a single-AAV PE would further simplify use and enhance therapeutic relevance. Such a single-AAV PE could further improve in vivo editing efficiency in extrahepatic tissues or at lower doses, by reducing the requirement for co-transduction, similar to the improvements we recently observed from single-AAV base editor delivery. [1052] In vivo PE resulted in no detected off-target editing and no significant increase in markers of liver damage compared to saline, AAV-GFP, or AAV-Cas9 nickase treatment, suggesting that expression of the prime editor in vivo does not induce apparent hepatotoxicity. An adaptive immune response to AAV-delivered prime editors is possible ²³ , and thus measures to minimize inflammation and the immune response should be investigated for therapeutic applications. Additional improvements that reduce the immunogenicity of the vector, temporally control expression of prime editor components, and further enhance potency may improve the safety profile of prime editor delivery via AAV. Delivery methods such as lipid nanoparticles (LNP) or virus-like particles (VLP) that offer more transient delivery of prime editor mRNA or ribonucleoprotein may also overcome these challenges for in vivo applications that are well-suited to LNP or VLP tissue tropisms. EXAMPLE 1M. Methods Molecular biology [1053] All editor plasmids used for mammalian cell transfection were generated using Gibson assembly or USER assembly using pCMV-PE2 (Addgene #132775) and pCMV- PEmax (Addgene #174820) plasmids. All pegRNA and epegRNA constructs were cloned by Golden Gate assembly using custom pU6-pegRNA-GG-acceptor (Addgene #132777) and pU6-tevopreQ1-GG-acceptor (Addgene #174038) plasmids as described previously ^21,58 . All nicking sgRNA plasmids were generated by KLD assembly or Golden Gate assembly using pFYF1320 (Addgene #47511) as a template plasmid. rAAV vector plasmids were cloned restriction digestion of v5 AAV CBE (Addgene #137176) or v5 AAV ABE (Addgene #137177) followed by Gibson assembly with eBlocks or PCR amplicons. All plasmids used for mammalian tissue culture were purified from MACH1, DH5alpha or NEBstable E. coli using Plasmid Plus Maxiprep or Midiprep kits (Qiagen), ZymoPURE II Midiprep kit (Zymo Research) or PureYield plasmid miniprep kits (Promega). Key plasmids developed in this study will be made available through Addgene. Cell culture [1054] HEK293T cells (ATCC CRL-3216) and Neuro-2A cells (ATCC CCL-131) were grown in Dulbecco’s Modified Eagle’s Medium plus GlutaMax (Thermo Fisher Scientific) supplemented with 10% (v/v) FBS at 37 °C with 5% CO ₂ . Immortalized mouse astrocytes containing the APOE4 isoform of the human APOE gene (Taconic Biosciences) were grown in Dulbecco’s Modified Eagle’s Medium plus GlutaMax (Thermo Fisher Scientific) supplemented with 10% (v/v) fetal bovine serum (FBS) and 200 μg mL ⁻¹ Geneticin (Thermo Fisher Scientific). Cell lines were authenticated by their suppliers and were verified to be negative for mycoplasma during the study. Transfections of HEK293T and Neuro-2A cells [1055] 16–24 h before transfection, HEK293T and Neuro-2A cells at >90% viability were seeded on 48-well Poly-(D)-Lysine coated plates (BioCoat plates, Corning) at a density of 30,000– 40,000 cells per well. Cells were transfected with 1 μL of Lipofectamine 2000 (Thermo Fisher Scientific) and 750 ng PE plasmid, 250 ng pegRNA plasmid, and 83 ng sgRNA plasmid. For 96-well plate (Corning) transfections, 15,000-20,000 cells were plated 16-24 h before transfection and 200 ng PE, 40 ng pegRNA, and 13.3 ng nicking guide with 0.5 μL of Lipofectamine 2000 (Thermo Fisher Scientific) was used. For intein-split prime editor plasmid transfections in HEK293T cells, total prime editor plasmid was reduced to 50 ng.72 h post- transfection cellular genomic DNA was isolated with 75-150 μL of lysis buffer (10 mM Tris- HCl pH 8.0, 9.05% SDS, 25 μg mL ^-1 Proteinase K (Thermo Fisher Scientific) at 37 °C for 1h followed by heat inactivation at 80 °C for 30 min. In vitro transcription of PE2 and MLH1dn mRNA [1056] PE2 and hMLH1dn mRNA were in vitro transcribed as previously described ⁵¹ . In brief, plasmid templates for in vitro transcription carry an inactivated T7 promoter, 5' UTR, Kozak sequence, coding sequences, and 3' UTR. Next, transcription templates were PCR amplified from these plasmids using Phusion U Green Multiplex Master Mix (Thermo Fisher Scientific) with primers that correct the T7 promoter and add a 119-nt poly(A) tail to the 3' UTR. Following purification of the product with QIAquick PCR Purification Kit (Thermo Fisher Scientific), PE2 and hMLH1dn mRNAs were transcribed from these templates using HiScribe T7 High-Yield RNA Synthesis Kit (New England BioLabs) with full replacement of UTP with N1-Methylpseudouridine-5'-triphosphate (TriLink Biotechnologies) and co- transcriptional capping by CleanCap AG (TriLink Biotechnologies). mRNA products were precipitated in 2.5 M lithium chloride, washed twice with 70% ethanol, dissolved in nuclease- free water, and stored at –80 °C. Nucleofection of APOE4 murine astrocytes [1057] Astrocytes were nucleofected using program EN-150 with SF Cell Line 4D- Nucleofector X Kit (Lonza). Briefly, 200,000 astrocytes were resuspended in 20 μL of buffer with 1 μg PE2 mRNA, 90 pmol synthetic pegRNA (Integrated DNA Technologies), and 60 pmol synthetic nicking sgRNA (Synthego). For PE5 experiments, 2 μg of hMLH1dn mRNA were also included in the nucleofection. After nucleofection, the cells were diluted to 100 μL of pre- warmed media and recovered for 10 mins at 37 °C followed by plating in 12-well plates.72 h following nucleofection, gDNA was harvested from these cells as previously described. High-throughput sequencing and data analysis [1058] High-throughput sequencing library were prepared as previously described ^52,83 . Briefly, genomic loci of interest were amplified from the genomic DNA via two rounds of PCR with PhusionU or PhusionHS polymerase (Thermo Fisher Scientific). Initial PCR step (PCR1) was done using primers with Illumina adapter overhangs (Supplementary Table 1) with following conditions: 95 ºC for 3 min; 27-30 cycles of 95 ºC for 15 s, 61-70 ºC (corresponding to the experimentally optimized T _m ) for 20 s, and 72 ºC for 30s followed by 72ºC for 1 min. For tissue samples, PCR1 reactions were monitored with SYBR Green fluorescence to avoid over-amplification. Unique Illumina sequencing barcodes were added in subsequent PCR2 step, using 1-2 μl of PCR1 as a template with following conditions: 95 ºC for 3 min; 9 cycles of 95 ºC for 15 s, 61 ºC for 20 s, and 72 ºC for 30s followed by 72ºC for 1 min. Following PCR2, samples were pooled according to amplicon size and gel purified in a 1% agarose gel using a Qiaquick Gel Extraction Kit (Qiagen). Pooled library concentration was quantified (Qubit dsDNA HS assay kit, Thermo Fisher Scientific) and run on Illumina Miseq 300 v2 Kit (Illumina) with 280-300 single read cycles according to the manufacturer’s instructions. [1059] Sequencing reads were demultiplexed using MiSeq Reporter (Illumina). For prime editing where the specified edit was a single base change, alignment of amplicon sequences to reference sequence was performed using CRISPResso2 ¹¹⁰ in batch mode with ‘- q30’, ‘discard indel reads TRUE’ and ‘qwc’ coordinates spanning the sequence between pegRNA- and nicking sgRNA- directed Cas9 cut sites. Indels were calculated as percentage of (discarded reads)/(total aligned reads). Prime editing at a given position was calculated explicitly as: (frequency of specified point mutation in non-discarded reads) × 100 × (100 – (indel reads))/100)). For prime edits that were insertions, CRISPResso2 was executed in HDR mode using identical parameters as described above but with an additional parameter ‘e’ specifying sequence of the edited “desired” amplicon. Indels were calculated as percentage of (discarded reads from the reference-aligned sequences and HDR-aligned sequences)/(total aligned reads). In HDR mode, prime editing efficiency was quantified as (HDR-aligned reads without indels)/(number of total reads aligned to the reference amplicon) × 100 × (100 – (indel reads))/100)). AAV production [1060] AAV was produced as previously described ^36,45 . HEK293T clone 17 cells (ATCC CRL-11268) were maintained in DMEM plus GlutaMax (Thermo Fisher Scientific) with 10% (v/v) heat inactivated FBS without antibiotic in 150 mm ² dishes (Thermo Fisher Scientific) at 37 °C with 5% CO ₂ and passaged every 2-3 days. Cells were split 1:318-22 h before polyethyleneimine transfection (PEI MAX, Polysciences) with 5.7 μg AAV genome plasmid, 11.4 μg pHelper (Clontech) and 22.8 μg rep-cap plasmid per plate. Four days post- transfection, cells were harvested using a cell scraper (Corning), pelleted by centrifugation at 2,000 g for 10 min, resuspended in 500 µl hypertonic lysis buffer per plate (40 mM Tris base, 500 mM NaCl, 2 mM MgCl2 and 100 U mL ⁻¹ salt active nuclease (ArcticZymes)) and incubated at 37 °C for 1 h. Media was then decanted 5× solution of poly(ethylene glycol) 8,000 (PEG 8k; Sigma- Aldrich) and NaCl to a final concentration of 8% PEG and 500 mM NaCl, incubated on ice for 2h or overnight then centrifuged at 3,200 g for 30 min. The supernatant was removed and the pellet was resuspended in 500 μL of hypertonic lysis buffer per plate and added to the cell lysate. Cell lysates were either incubated at 4 °C overnight or taken immediately forward to ultracentrifugation. [1061] Cell lysates were centrifuged at 3,400 g for 10 min and added to Beckman Coulter Quick-seal tubes via 16-gauge 5” needles (Air-Tite N165) in a discontinuous gradient of iodixanol in sequentially floating layers: 9 mL 15% iodixanol in 500 mM NaCl and 1× PBS- _MK (1× PBS plus 1 mM MgCl ₂ and 2.5 mM KCl), 6 mL 25% iodixanol in 1× PBS-MK, and ^{5 mL} each of 40% and 60% iodixanol in 1× PBS-MK with Phenol red at a concentration of 1 μg mL ^{- 1} in the 15, 25, and 60% layers to visualize layers. Ultracentrifugation was performed using a Ti 70 rotor in a Optima XPN-100 Ultracentrifuge (Beckman Coulter) at 68,000 RPM for 1 h or 58,600 RPM for 2 h 15 min at 18 °C. Immediately following centrifugation, 3 mL of solution was removed from the 40–60% iodixanol interface via an 18-gauge needle. The buffer was exchanged for cold PBS with 0.001% F-68 using PES 100 kD MWCO columns (Thermo Fisher Scientific) and concentrated. The AAV solution was sterile filtered using a 0.22 μm filter, then quantified by qPCR (AAVpro titration kit version 2, Clontech) and stored at 4 °C until use. Animal care [1062] All experiments involving live animals were approved by the Broad Institute Institutional Animal Care and Use Committee and were consistent with local, state, and federal regulations as applicable, including the National Institutes of Health Guide for the Care and Use of Laboratory Animals. C57BL/6 mice for use in experiments were purchased as adults from The Jackson Laboratory or were born from pregnant females purchased from Charles River Laboratory. All mice were housed in a room maintained on a 12 h light and dark cycle with ad libitum access to standard rodent diet and water except for 6 h fasts just before submandibular bleeding for plasma analysis when access to water was still maintained. Retro-orbital injections [1063] For retro-orbital injections, AAV was diluted into 100 μL sterile 0.9% NaCl USP (Fresenius Kabi) before injection. Anesthesia was induced with 3-4% isoflurane. Under anesthesia, as verified by unresponsiveness to bilateral toe pinch, the right eye was protruded, the needle of the loaded insulin syringe was inserted into the retro-orbital sinus, bevel faced away from the eye, and the syringe was slowly advanced. Directly following injection, a drop of proparacaine hydrochloride ophthalmic solution (Patterson Veterinary) was applied to the eye as an analgesic. P0, P1 and P3 ventricle injections [1064] For neonatal intracerebroventricular injections, Drummond PCR pipettes were pulled at the ramp test value of a Sutter P1000 micropipette puller and passed through a Kimwipe three times for a tip diameter size of approximately 100 μm. The injection solution of 4 μL including a small amount of Fast Green dye was front-loaded. Mice were anesthetized by cryoanesthesia verified by color and unresponsiveness to bilateral toe pinch. 2 μL was then freehand injected into each ventricle. Transillumination of the head was then used to verify successful ventricle targeting. Mice tissue collection _[1065] At harvest, mice in this Example were sacrificed by CO ₂ asphyxiation and ^{unperfused tissues} were immediately dissected. Bulk tissue was harvested unless otherwise noted. For harvest of brain tissue, hemispheres were split sagittally by razor blade, then cerebellum, neocortex, and hippocampus were isolated from the underlying midbrain with a micro spatula. All animal tissues were harvested in DNAdvance lysis buffer, and the genomic DNA was purified according to the manufacturer’s protocol (Beckman Coulter). Nuclear isolation and sorting [1066] Nuclei were isolated from the cortex and the mid-brain as previously described. Dissected brain sections were homogenized in 2 mL of ice-cold EZ-PREP buffer (Sigma- Aldrich) using a glass Dounce homogenizer (Sigma-Aldrich) with 20 strokes of pestle A followed by 20 strokes of pestle B. Homogenized samples were then decanted into a new tube containing an additional 2 mL of EZ-PREP buffer on ice. After 5 min incubation, samples were centrifuged for 5 min at 500 g at 4 °C. Following centrifugation, supernatant was decanted and the nuclei pellet was resuspended in 4 mL of ice-cold Nuclei Suspension Buffer (NSB) comprising 100 µg/mL BSA (New England Biolabs) and 3.33 µM Vybrant DyeCycle Ruby (Thermo Fisher) in PBS followed. This was followed by a centrifugation step at 500 g for 5 min at 4 °C. After centrifugation, the supernatant was removed, and nuclei were resuspended in 1-2 mL of NSB, passed through 35-µm cell strainer, followed by flow sorting using the Sony MA900 Cell Sorter (Sony Biotechnology) at the Broad Institute flow cytometry core. See FIG.22 for example FACS gating. Nuclei were sorted into DNAdvance lysis buffer, and the genomic DNA was purified according to the manufacturer’s protocol (Beckman Coulter). Off-target analysis [1067] Circularization for In vitro Reporting of Cleavage Effects by sequencing (CIRCLE-seq) was performed and analyzed as described previously ⁸⁴ save for the following modifications: For the Cas9 cleavage step, guide denaturation, incubation, and proteinase K treatment was conducted using the more efficient method described in the CHANGE-seq protocol ¹⁰⁰ .Specifically, the sgRNAs with the spacer sequences “GCAUGGCUGUCUGGUUCUGU” (SEQ ID NO: 431) (the PCKS9 nicking sgRNA) and “GCCAGGUUCCAUGGGAUGCUC” (SEQ ID NO: 432) (used in the PCKS9 pegRNA) were ordered from Synthego with their standard chemical modifications, 2’O-Methyl for the first three and last three bases, and phosphorothioate bonds between the first three and last two bases. A 5' “G” nucleotide was included with the 20-nucleotide pegRNA spacer sequence to recapitulate the sequence expressed from AAVs. The sgRNAs were diluted to 9 µM in nuclease-free water and re-folded by incubation at 90 °C for 5 min followed by a slow annealing down to 25 °C at a ramp rate of 0.1 °C per second. The sgRNA was complexed with Cas9 nuclease (New England Biolabs) via a 10 min room temperature incubation after mixing 5 µL of 10x Cas9 Nuclease Reaction Buffer provided with the nuclease, 4.5 µL of 1 µM Cas9 nuclease (diluted from the 20µM stock in 1x Cas9 Nuclease Reaction Buffer), and 1.5 µL of 9 µM annealed sgRNA. Circular DNA from mouse N2A cells was added to a total mass of 125ng and diluted to a final volume of 50 µL. Following 1 h of incubation at 37 °C, Proteinase K (New England Biolabs) was diluted 4-fold in water and 5 uL of the diluted mixture was added to the cleavage reaction. Following a 15 min Proteinase K treatment at 37°C, DNA was A-tailed, adapter ligated, and USER-treated, and PCR-amplified as described in the CIRCLE-seq protocol ⁸⁴ . Following PCR, samples were loaded on a preparative 1% agarose gel and DNA was extracted between the 300 bp and 1 kb range to eliminate primer dimers before sequencing on an Illumina MiSeq. Data was processed using the CIRCLE-seq analysis pipeline and aligned to the mouse genome “mm10” with parameters: “read_threshold: 4; window_size: 3; mapq_threshold: 50; start_threshold: 1; gap_threshold:3; mismatch_threshold: 6; search_radius: 30; PAM: NGG; merged_analysis: True”. Analysis of prime editor activity at Cas9 off-target sites [1068] For detailed off-target analysis, the top 10 sites each for pegRNA and sgRNA spacer (20 total sites) with highest read counts were deep sequenced from liver tissues of untreated or v3em PE-AAV treated mice. The sequencing reads were then aligned to reference off-target amplicons using CRISPResso2 (cite Clement et al.2019) in batch mode with ‘-q30’, ‘discard indel reads TRUE’, ‘plot_window_size 80’, ‘-w25’, ‘min_alleles_around_cut_to_plot 0.1’, ‘max_rows_alleles_around_cut_to_plot 600’. Off- target reads were called as leniently as possible to capture all potential reverse transcription product including point mutations, insertions, or deletions at the Cas9 nick site. For off-target sites nominated by pegRNA spacer, the six nucleotide sequences 3' of Cas9 nick site (prime- editable target) was compared to the 3' DNA flap sequence encoded by pegRNA reverse transcription. Any aligned reads with nucleotide sequence within prime-editing target window that matches to the nucleotide encoded by pegRNA reverse transcription was noted as off-target reads. Off- target editing efficiencies were thus quantified as a percentage of (number of off-target reads)/(number of reference-aligned reads). For off-target sites nominated by nicking sgRNA spacer, insertions, or deletions at the Cas9 nick site was quantified as a percentage of (discarded reads)/(total aligned reads). To avoid differences in sequencing errors, samples that were sequenced in the same MiSeq run were compared. Alanine aminotransferase (ALT) and aspartate aminotransferase (AST) assay [1069] Blood was collected via submandibular bleeding in serum separator tube. The serum was then separated by centrifugation at 2000 g for 15 min and stored at -80 °C until the end of the experiment. The samples were sent to IDEXX Bioanalytics, MA, for analysis. Plasma measurements for total cholesterol and LDL cholesterol [1070] To track total cholesterol and LDL cholesterol levels in plasma, blood was collected using a submandibular bleed in heparin coated tube. Plasma was recovered by centrifugation at 2000 g for 15 min and stored at -80 °C in one-time use aliquots until the end of the experiment. Total cholesterol levels were determined by colorimetric assay using the Total Cholesterol Reagents (Thermo Fisher Scientific) with cholesterol standards from Pointe Scientific Inc following the manufacturer’s instructions. Plasma LDL cholesterol levels were measured using LDL Cholesterol kit (WakoChemical) following the manufacturer’s instructions. Western blot of liver tissues [1071] For Western blot analysis, liver samples were lysed in a homogenization buffer (Cell Signaling Technology) containing protease inhibitor cocktail (Sigma-Aldrich). Samples were run on Mini-Protean TGX Gel, 4-15% gradient gels (Bio-Rad), followed by transfer of proteins to nitrocellulose. Antibodies against LDLR (Proteintech) and β-actin (Cell Signaling Technology) were used. The western blot data was quantified through densitometry of the bands using LI-COR Odyssey analyzer software. Tissue fixation and histology _[1072] Mice were sacrificed by CO ₂ asphyxiation and tissues were immediately ^{harvested. For liver} histology, the left medial lobe was dissected and fixed in freshly prepared 4% paraformaldehyde in 1× PBS. For determination of transduced cell types, brain hemispheres were fixed in freshly prepared 4% paraformaldehyde in 1× PBS. Tissues were rocked at 4 °C for 24 h, washed once with PBS with 10mM Glycine, then rocked again at 4 °C in PBS with 10mM Glycine for another 24 h. Fixed tissues were then stored at 4 °C until further analysis. Liver histopathology was carried out by the Rodent Histopathology Core of Harvard Medical School. Fixed liver tissue was embedded in paraffin, then cut into 5 μm sections, and stained with hematoxylin and eosin stain for histopathological examination. Samples were analyzed by a blinded mouse histopathologist. Digital droplet PCR [1073] Total DNA was isolated from flash frozen liver tissue (DNeasy Blood and Tissue Kit, Qiagen) and total RNA was isolated from flash-frozen liver tissue (RNeasy Plus Mini Kit, Qiagen), according to manufacturer’s instructions. Isolated RNA was reverse transcribed into cDNA with SuperScript III first-strand synthesis mix with oligo dT primer (Invitrogen). For vg/dg calculation, ddPCR was carried out using ddPCR Supermix for Probes (BioRad) with 10 ng of isolated DNA used as template and 6.25 units HindIII-HF (NEB) per 25 uL reaction. Droplets were autogenerated and PCR was performed with an annealing temperature of 57 °C for 2 min for a total of 40 cycles. Droplets were analyzed on a QX200 droplet analyzer and fluorescence was quantified using QuantaSoft (BioRad). RNA expression analysis was carried out in the same manner but with Gapdh expression reference assay kit (BioRad). Reference probes were included in the same reaction and numbers reported are normalized to reference probes. Primer and probe sequences are available in Supplementary Table 8. To ensure minimal DNA contamination in RNA expression analysis, reverse transcriptase negative controls were included and verified to yield positive droplets indistinguishable from background. Statistical analysis [1074] Data are presented as mean and standard error of the mean (SEM). The sample size and the statistical tests used for each experiment are described in the figure legends. No statistical methods were used to predetermine sample size. Statistical analysis was performed using GraphPad Prism software. References [1075] Korf, B.R., Pyeritz, R.E. & Grody, W.W.3 - Nature and Frequency of Genetic Disease. in Emery and Rimoin's Principles and Practice of Medical Genetics and Genomics (Seventh Edition) (eds. Pyeritz, R.E., Korf, B.R. & Grody, W.W.) 47-51 (Academic Press, 2019). [1076] Anzalone, A.V., Koblan, L.W. & Liu, D.R. Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors. Nature Biotechnology 38, 824-844 (2020). [1077] Newby, G.A. & Liu, D.R. In vivo somatic cell base editing and prime editing. Molecular Therapy 29, 3107-3124 (2021). [1078] Rees, H.A. & Liu, D.R. Base editing: precision chemistry on the genome and transcriptome of living cells. Nature Reviews Genetics 19, 770-788 (2018). [1079] Kosicki, M., Tomberg, K. & Bradley, A. Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements. Nature Biotechnology 36, 765-771 (2018). [1080] Song, C.-Q., et al. Adenine base editing in an adult mouse model of tyrosinaemia. Nature biomedical engineering 4, 125-130 (2020). [1081] Giannoukos, G., et al. UDiTaS™, a genome editing detection method for indels and genome rearrangements. BMC Genomics 19, 212 (2018). [1082] Stadtmauer, E.A., et al. CRISPR-engineered T cells in patients with refractory cancer. Science 367, eaba7365 (2020). [1083] Turchiano, G., et al. Quantitative evaluation of chromosomal rearrangements in gene-edited human stem cells by CAST-Seq. Cell Stem Cell 28, 1136-1147.e1135 (2021). [1084] Webber, B.R., et al. Highly efficient multiplex human T cell engineering without double-strand breaks using Cas9 base editors. in Nat Commun, Vol.105222 (2019). [1085] Leibowitz, M.L., et al. Chromothripsis as an on-target consequence of CRISPR– Cas9 genome editing. Nature Genetics 53, 895-905 (2021). [1086] Alanis-Lobato, G., et al. Frequent loss of heterozygosity in CRISPR- Cas9&#x2013;edited early human embryos. Proceedings of the National Academy of Sciences 118, e2004832117 (2021). [1087] Haapaniemi, E., Botla, S., Persson, J., Schmierer, B. & Taipale, J. CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response. Nature Medicine 24, 927- 930 (2018). [1088] Komor, A.C., Kim, Y.B., Packer, M.S., Zuris, J.A. & Liu, D.R. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420-424 (2016). [1089] Gaudelli, N.M., et al. Programmable base editing of A• T to G• C in genomic DNA without DNA cleavage. Nature 551, 464 (2017). [1090] Koblan, L.W., et al. Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning. Nat Biotechnol 39, 1414-1425 (2021). [1091] Verve takes base editors into humans. Nature Biotechnology 40, 1159-1159 (2022). [1092] CAR T cells to fight T cell leukaemia. Vol.2022 (ISRCTN registry, 2022). [1093] BEACON: A Study Evaluating the Safety and Efficacy of BEAM-101 in Patients With Severe Sickle Cell Disease (BEACON). (clinicaltrials.gov, 2022). [1094] Li, W. Safety and Efficacy Evaluation of BRL-101 in Subjects With Transfusion Dependent β-Thalassemia. (2022).- [1095] Anzalone, A.V., et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149-157 (2019). [1096] Liu, P., et al. Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice. Nat Commun 12, 2121 (2021). [1097] Böck, D., et al. In vivo prime editing of a metabolic liver disease in mice. Science Translational Medicine 14, eabl9238 (2022). [1098] Zheng, C., et al. A flexible split prime editor using truncated reverse transcriptase improves dual-AAV delivery in mouse liver. Molecular Therapy 30, 1343-1351 (2022). [1099] Zhi, S., et al. Dual-AAV delivering split prime editor system for in vivo genome editing. Molecular Therapy 30, 283-294 (2022). [1100] Gao, Z., et al. A truncated reverse transcriptase enhances prime editing by split AAV vectors. Molecular Therapy 30, 2942-2951 (2022). [1101] Frangoul, H., et al. CRISPR-Cas9 Gene Editing for Sickle Cell Disease and β- Thalassemia. New England Journal of Medicine 384, 252-260 (2020). [1102] Mendell, J.R., et al. Single-Dose Gene-Replacement Therapy for Spinal Muscular Atrophy. New England Journal of Medicine 377, 1713-1722 (2017). [1103] Russell, S., et al. Efficacy and safety of voretigene neparvovec (AAV2- hRPE65v2) in patients with <em>RPE65</em>-mediated inherited retinal dystrophy: a randomised, controlled, open-label, phase 3 trial. The Lancet 390, 849-860 (2017). [1104] Paulk, N. Gene Therapy: It Is Time to Talk about High-Dose AAV: The deaths of two children with X-linked myotubular myopathy in the ASPIRO trial prompts a reexamination of vector safety. Genetic Engineering & Biotechnology News 40, 14-16 (2020). [1105] Chand, D.H., et al. Thrombotic Microangiopathy Following Onasemnogene Abeparvovec for Spinal Muscular Atrophy: A Case Series. J Pediatr 231, 265-268 (2021). [1106] Morales, L., Gambhir, Y., Bennett, J. & Stedman, H.H. Broader Implications of Progressive Liver Dysfunction and Lethal Sepsis in Two Boys following Systemic High- Dose AAV. Mol Ther 28, 1753-1755 (2020). [1107] Hinderer, C., et al. Severe Toxicity in Nonhuman Primates and Piglets Following High-Dose Intravenous Administration of an Adeno-Associated Virus Vector Expressing Human SMN. Human Gene Therapy 29, 285-298 (2018). [1108] Kuzmin, D.A., et al. The clinical landscape for AAV gene therapies. Nat Rev Drug Discov 20, 173-174 (2021). [1109] Au, H.K.E., Isalan, M. & Mielcarek, M. Gene Therapy Advances: A Meta- Analysis of AAV Usage in Clinical Settings. Frontiers in Medicine 8(2022). [1110] . Naso, M.F., Tomkowicz, B., Perry, W.L. & Strohl, W.R. Adeno-Associated Virus (AAV) as a Vector for Gene Therapy. Biodrugs 31, 317-334 (2017). [1111] Wu, Z., Yang, H. & Colosi, P. Effect of genome size on AAV vector packaging. Molecular therapy : the journal of the American Society of Gene Therapy 18, 80- 86 (2010). [1112] . Levy, J.M., et al. Cytosine and adenine base editing of the brain, liver, retina, heart and skeletal muscle of mice via adeno-associated viruses. Nat Biomed Eng 4, 97-110 (2020). [1113] Villiger, L., et al. Treatment of a metabolic liver disease by in vivo genome base editing in adult mice. Nat Med 24, 1519-1525 (2018). [1114] Truong, D.J., et al. Development of an intein-mediated split-Cas9 system for gene therapy. Nucleic acids research 43, 6450-6458 (2015). [1115] Racanelli, V. & Rehermann, B. The liver as an immunological organ. Hepatology 43, S54-S62 (2006). [1116] Varnavski, A.N., Calcedo, R., Bove, M., Gao, G. & Wilson, J.M. Evaluation of toxicity from high-dose systemic administration of recombinant adenovirus vector in vector-naive and pre-immunized mice. Gene Ther 12, 427-436 (2005). [1117] Zettler, J., Schutz, V. & Mootz, H.D. The naturally split Npu DnaE intein exhibits an extraordinarily high rate in the protein trans-splicing reaction. FEBS letters 583, 909-914 (2009). [1118] Lapinaite, A., et al. DNA capture by a CRISPR-Cas9-guided adenine base editor. Science 369, 566-571 (2020). [1119] Huang, T.P., et al. Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors. Nature Biotechnology 37, 626-631 (2019). [1120] Oakes, B.L., et al. CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification. Cell 176, 254-267.e216 (2019). [1121] Wright, A.V., et al. Rational design of a split-Cas9 enzyme complex. Proceedings of the National Academy of Sciences 112, 2984-2989 (2015). [1122] Davis, J.R., et al. Efficient in vivo base editing via single adeno-associated viruses with size-optimized genomes encoding compact adenine base editors. Nature Biomedical Engineering (2022). [1123] Choi, J.H., et al. Optimization of AAV expression cassettes to improve packaging capacity and transgene expression in neurons. Mol Brain 7, 17 (2014). [1124] Feng, J., et al. Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons. Nature Neuroscience 13, 423-430 (2010). [1125] Swiech, L., et al. In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9. Nat Biotechnol 33, 102-106 (2015). [1126] Chen, P.J., et al. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell 184, 5635-5652.e5629 (2021). [1127] Thomas, D.C., Roberts, J.D. & Kunkel, T.A. Heteroduplex repair in extracts of human HeLa cells. Journal of Biological Chemistry 266, 3744-3751 (1991). [1128] Doman, J.L., Sousa, A.A., Randolph, P.B., Chen, P.J. & Liu, D.R. Designing and executing prime editing experiments in mammalian cells. Nat Protoc (2022). [1129] Uhlén, M., et al. Proteomics. Tissue-based map of the human proteome. Science 347, 1260419 (2015). [1130] Brooks, P.J. DNA repair in neural cells: basic science and clinical implications. Mutat Res 509, 93-108 (2002). [1131] Pinto, R.M., et al. Mismatch Repair Genes Mlh1 and Mlh3 Modify CAG Instability in Huntington's Disease Mice: Genome-Wide and Candidate Approaches. PLOS Genetics 9, e1003930 (2013). [1132] Nelson, J.W., et al. Engineered pegRNAs improve prime editing efficiency. Nat Biotechnol 40, 402-410 (2022). [1133] Gray, S.J., et al. Optimizing promoters for recombinant adeno-associated virus-mediated gene expression in the peripheral and central nervous system using self- complementary vectors. Hum Gene Ther 22, 1143-1153 (2011). [1134] Vidigal, J.A. & Ventura, A. Rapid and efficient one-step generation of paired gRNA CRISPR-Cas9 libraries. Nat Commun 6, 8083 (2015). [1135] Koblan, L.W., et al. In vivo base editing rescues Hutchinson-Gilford progeria syndrome in mice. Nature 589, 608-614 (2021). [1136] Packer, M.S., et al. Evaluation of cytosine base editing and adenine base editing as a potential treatment for alpha-1 antitrypsin deficiency. Mol Ther 30, 1396-1406 (2022). [1137] Murillo, O., et al. Long-term metabolic correction of Wilson&#x2019;s disease in a murine model by gene therapy. Journal of Hepatology 64, 419-426 (2016). [1138] Grünewald, J., et al. Engineered CRISPR prime editors with compact, untethered reverse transcriptases. Nature Biotechnology (2022). [1139] Kotewicz, M.L., Sampson, C.M., D'Alessio, J.M. & Gerard, G.F. Isolation of cloned Moloney murine leukemia virus reverse transcriptase lacking ribonuclease H activity. Nucleic acids research 16, 265-277 (1988). [1140] Chan, K.Y., et al. Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems. Nat Neurosci 20, 1172-1179 (2017). [1141] Huang, Q., et al. Delivering genes across the blood-brain barrier: LY6A, a novel cellular receptor for AAV-PHP.B capsids. bioRxiv, 538421 (2019). [1142] Arboleda-Velasquez, J.F., et al. Resistance to autosomal dominant Alzheimer's disease in an APOE3 Christchurch homozygote: a case report. Nat Med 25, 1680-1683 (2019). [1143] Hernandez, I., et al. Heterozygous APOE Christchurch in familial Alzheimer's disease without mutations in other Mendelian genes. Neuropathol Appl Neurobiol 47, 579- 582 (2021). [1144] Boyles, J.K., Pitas, R.E., Wilson, E., Mahley, R.W. & Taylor, J.M. Apolipoprotein E associated with astrocytic glia of the central nervous system and with nonmyelinating glia of the peripheral nervous system. J Clin Invest 76, 1501-1513 (1985). [1145] Poirier, J., Hess, M., May, P.C. & Finch, C.E. Astrocytic apolipoprotein E mRNA and GFAP mRNA in hippocampus after entorhinal cortex lesioning. Molecular Brain Research 11, 97-106 (1991). [1146] Kim, J.Y., et al. Viral transduction of the neonatal brain delivers controllable genetic mosaicism for visualising and manipulating neuronal circuits in vivo. Eur J Neurosci 37, 1203-1220 (2013). [1147] Foust, K.D., et al. Intravascular AAV9 preferentially targets neonatal neurons and adult astrocytes. Nat Biotechnol 27, 59-65 (2009). [1148] Zhang, H., et al. Several rAAV Vectors Efficiently Cross the Blood&#x2013;brain Barrier and Transduce Neurons and Astrocytes in the Neonatal Mouse Central Nervous System. Molecular Therapy 19, 1440-1448 (2011). [1149] Abifadel, M., et al. Mutations in PCSK9 cause autosomal dominant hypercholesterolemia. Nature Genetics 34, 154-156 (2003). [1150] Fitzgerald, K., et al. Effect of an RNA interference drug on the synthesis of proprotein convertase subtilisin/kexin type 9 (PCSK9) and the concentration of serum LDL cholesterol in healthy volunteers: a randomised, single-blind, placebo-controlled, phase 1 trial. The Lancet 383, 60-68 (2014). [1151] Cohen, J., et al. Low LDL cholesterol in individuals of African descent resulting from frequent nonsense mutations in PCSK9. Nature Genetics 37, 161-165 (2005). [1152] Cohen, J.C., Boerwinkle, E., Mosley, T.H. & Hobbs, H.H. Sequence Variations in PCSK9, Low LDL, and Protection against Coronary Heart Disease. New England Journal of Medicine 354, 1264-1272 (2006). [1153] Hooper, A.J., Marais, A.D., Tanyanyiwa, D.M. & Burnett, J.R. The C679X mutation in PCSK9 is present and lowers blood cholesterol in a Southern African population. Atherosclerosis 193, 445-448 (2007). [1154] Rao, A.S., et al. Large-Scale Phenome-Wide Association Study of PCSK9 Variants Demonstrates Protection Against Ischemic Stroke. Circ Genom Precis Med 11, e002162 (2018). [1155] Musunuru, K., et al. In vivo CRISPR base editing of PCSK9 durably lowers cholesterol in primates. Nature 593, 429-434 (2021). [1156] Rothgangl, T., et al. In vivo adenine base editing of PCSK9 in macaques reduces LDL cholesterol levels. Nature Biotechnology 39, 949-957 (2021). [1157] Banskota, S., et al. Engineered virus-like particles for efficient <em>in&#xa0;vivo</em> delivery of therapeutic proteins. Cell 185, 250-265.e216 (2022). [1158] Mayne, J., et al. Novel Loss-of-Function PCSK9 Variant Is Associated with Low Plasma LDL Cholesterol in a French-Canadian Family and with Impaired Processing and Secretion in Cell Culture. Clinical Chemistry 57, 1415-1423 (2011). [1159] Lebeau, P., et al. Loss-of-function PCSK9 mutants evade the unfolded protein response sensor GRP78 and fail to induce endoplasmic reticulum stress when retained. J Biol Chem 293, 7329-7343 (2018). [1160] Lebeau, P.F., et al. The loss-of-function PCSK9Q152H variant increases ER chaperones GRP78 and GRP94 and protects against liver injury. The Journal of Clinical Investigation 131(2021). [1161] Zaid, A., et al. Proprotein convertase subtilisin/kexin type 9 (PCSK9): hepatocyte-specific low-density lipoprotein receptor degradation and critical role in mouse liver regeneration. Hepatology 48, 646-654 (2008). [1162] Vozenilek, A.E., et al. AAV8-mediated overexpression of mPCSK9 in liver differs between male and female mice. Atherosclerosis 278, 66-72 (2018). [1163] Jarrett, K.E., et al. Somatic Editing of Ldlr With Adeno-Associated Viral- CRISPR Is an Efficient Tool for Atherosclerosis Research. Arterioscler Thromb Vasc Biol 38, 1997-2006 (2018). [1164] Robinet, P., et al. Consideration of Sex Differences in Design and Reporting of Experimental Arterial Pathology Studies—Statement From ATVB Council. Arteriosclerosis, Thrombosis, and Vascular Biology 38, 292-303 (2018). [1165] Lazzarotto, C.R., et al. Defining CRISPR–Cas9 genome-wide nuclease activities with CIRCLE-seq. Nature Protocols 13, 2615-2642 (2018). [1166] Kim, D.Y., Moon, S.B., Ko, J.-H., Kim, Y.-S. & Kim, D. Unbiased investigation of specificities of prime editing systems in human cells. Nucleic acids research 48, 10576-10589 (2020). [1167] Liu, Y., et al. Efficient generation of mouse models with the prime editing system. Cell Discov 6, 27 (2020). [1168] Schene, I.F., et al. Prime editing for functional repair in patient-derived disease models. Nat Commun 11, 5352 (2020). [1169] Jin, S., et al. Genome-wide specificity of prime editors in plants. Nature Biotechnology 39, 1292-1299 (2021). [1170] Geurts, M.H., et al. Evaluating CRISPR-based prime editing for cancer modeling and CFTR repair in organoids. Life Sci Alliance 4(2021). [1171] Park, S.J., et al. Targeted mutagenesis in mouse cells and embryos using an enhanced prime editor. Genome Biol 22, 170 (2021). [1172] Lin, J., et al. Modeling a cataract disorder in mice with prime editing. Mol Ther Nucleic Acids 25, 494-501 (2021). [1173] Gao, P., et al. Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression. Genome Biol 22, 83 (2021). [1174] Habib, O., Habib, G., Hwang, G.H. & Bae, S. Comprehensive analysis of prime editing outcomes in human embryonic stem cells. Nucleic acids research 50, 1187- 1197 (2022). [1175] Gao, R., et al. Genomic and Transcriptomic Analyses of Prime Editing Guide RNA–Independent Off-Target Effects by Prime Editors. The CRISPR Journal 5, 276-293 (2022). [1176] Meunier, L. & Larrey, D. Drug-Induced Liver Injury: Biomarkers, Requirements, Candidates, and Validation. Front Pharmacol 10, 1482 (2019). [1177] Gao, G.-P., et al. Novel adeno-associated viruses from rhesus monkeys as vectors for human gene therapy. Proceedings of the National Academy of Sciences of the United States of America 99, 11854-11859 (2002). [1178] Thakore, P.I., et al. RNA-guided transcriptional silencing in vivo with S. aureus CRISPR-Cas9 repressors. Nat Commun 9, 1674 (2018). [1179] Ran, F.A., et al. In vivo genome editing using Staphylococcus aureus Cas9. Nature 520, 186-191 (2015). [1180] Meyer, K., et al. Improving single injection CSF delivery of AAV9-mediated gene therapy for SMA: a dose-response study in mice and nonhuman primates. Mol Ther 23, 477-487 (2015). [1181] Kishimoto, T.K. & Samulski, R.J. Addressing high dose AAV toxicity – ‘one and done’ or ‘slower and lower’? Expert Opinion on Biological Therapy 22, 1067-1071 (2022). [1182] Anzalone, A.V., et al. Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing. Nat Biotechnol 40, 731-740 (2022). [1183] Yarnall, M.T.N., et al. Drag-and-drop genome insertion of large sequences without double-strand DNA cleavage using CRISPR-directed integrases. Nat Biotechnol (2022). [1184] Clement, K., et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nature Biotechnology 37, 224-226 (2019). [1185] Lazzarotto, C.R., et al. CHANGE-seq reveals genetic and epigenetic effects on CRISPR–Cas9 genome-wide activity. Nature Biotechnology 38, 1317-1327 (2020

Tables referenced in Example 1 [1187] Table 1. Primers used for genomic DNA amplification and their corresponding amplicons. [1189] Table 2. pegRNA optimization for Dnmt1 site associated with Fig.7. All sequences are shown in 5' to 3' orientation. pegRNAs are a concatenation of the spacer sequence, the sgRNA scaffold, and the 3' extension (contains PBS and RT template, and a 3' motif in the case of epegRNAs). sgRNA scaffold sequence (5' to 3') [1190] Table 3. Sequences of nicking sgRNAs used in this study for Dnmt1, HEK3, PRNP, HBB, EMX1, RNF2 and FANCF loci. All sequences are shown in 5' to 3' orientation. Nicking sgRNAs are a concatenation of the spacer sequence and the sgRNA scaffold. sgRNA scaffold sequence (5' to 3')

[1191] Table 4. pegRNA optimization for APOE3 R136S associated with Fig.16. All sequences are shown in 5' to 3' orientation. pegRNAs are a concatenation of the spacer sequence, the sgRNA scaffold, and the 3' extension (contains PBS and RT template, and a 3' motif in the case of epegRNAs). sgRNA scaffold sequence (5' to 3')

[1193] Table 5. Nicking sgRNA optimization for APOE3 R136S associated with FIG. 15. All sequences are shown in 5' to 3' orientation. Nicking sgRNAs are a concatenation of the spacer sequence and the sgRNA scaffold. SgRNA scaffold sequence (5' to 3')

[1195] Table 6. pegRNA optimization for Pcsk9 Q155H associated with FIG.16. All sequences are shown in 5' to 3' orientation. pegRNAs are a concatenation of the spacer sequence, the sgRNA scaffold, and the 3' extension (contains PBS and RT template, and a 3' motif in the case of epegRNAs). SgRNA scaffold sequence (5’ to 3’)

[1198] Table 7. Nicking sgRNA optimization for Pcsk9 Q155H associated with FIG.16. All sequences are shown in 5' to 3' orientation. Nicking sgRNAs are a concatenation of the spacer sequence and the sgRNA scaffold. SRNA scaffold sequence (5' to 3') [1199] Table 8. Probes and primers used to quantify viral genomes in liver tissues. Table 9. Sequences of Pcsk9 pegRNA off-target sites identified by CIRCLE-seq

Table 10. Sequences of Psck9 nicking sgRNA off-target sites identified by CIRCLE-seq

[1201] While several embodiments of the present disclosure have been described and illustrated herein, those of ordinary skill in the art will readily envision a variety of other means and/or structures for performing the functions and/or obtaining the results and/or one or more of the advantages described herein, and each of such variations and/or modifications is deemed to be within the scope of the present disclosure. More generally, those skilled in the art will readily appreciate that all parameters, dimensions, materials, and configurations described herein are meant to be exemplary and that the actual parameters, dimensions, materials, and/or configurations will depend upon the specific application or applications for which the teachings of the present disclosure is/are used. Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the disclosure described herein. It is, therefore, to be understood that the foregoing embodiments are presented by way of example only and that, within the scope of the appended claims and equivalents thereto, the disclosure may be practiced otherwise than as specifically described and claimed. The present disclosure is directed to each individual feature, system, article, material, kit, and/or method described herein. In addition, any combination of two or more such features, systems, articles, materials, kits, and/or methods, if such features, systems, articles, materials, kits, and/or methods are not mutually inconsistent, is included within the scope of the present disclosure. [1202] In cases where the present specification and a document incorporated by reference include conflicting and/or inconsistent disclosure, the present specification shall control. If two or more documents incorporated by reference include conflicting and/or inconsistent disclosure with respect to each other, then the document having the later effective date shall control. [1203] All definitions, as defined and used herein, should be understood to control over dictionary definitions, definitions in documents incorporated by reference, and/or ordinary meanings of the defined terms. [1204] The indefinite articles “a” and “an,” as used herein in the specification and in the claims, unless clearly indicated to the contrary, should be understood to mean “at least one.” [1205] The phrase “and/or,” as used herein in the specification and in the claims, should be understood to mean “either or both” of the elements so conjoined, i.e., elements that are conjunctively present in some cases and disjunctively present in other cases. Multiple elements listed with “and/or” should be construed in the same fashion, i.e., “one or more” of the elements so conjoined. Other elements may optionally be present other than the elements specifically identified by the “and/or” clause, whether related or unrelated to those elements specifically identified. Thus, as a non-limiting example, a reference to “A and/or B”, when used in conjunction with open-ended language such as “comprising” can refer, in one embodiment, to A only (optionally including elements other than B); in another embodiment, to B only (optionally including elements other than A); in yet another embodiment, to both A and B (optionally including other elements); etc. [1206] As used herein in the specification and in the claims, “or” should be understood to have the same meaning as “and/or” as defined above. For example, when separating items in a list, “or” or “and/or” shall be interpreted as being inclusive, i.e., the inclusion of at least one, but also including more than one, of a number or list of elements, and, optionally, additional unlisted items. Only terms clearly indicated to the contrary, such as “only one of” or “exactly one of,” or, when used in the claims, “consisting of,” will refer to the inclusion of exactly one element of a number or list of elements. In general, the term “or” as used herein shall only be interpreted as indicating exclusive alternatives (i.e. “one or the other but not both”) when preceded by terms of exclusivity, such as “either,” “one of,” “only one of,” or “exactly one of.” [1207] As used herein in the specification and in the claims, the phrase “at least one,” in reference to a list of one or more elements, should be understood to mean at least one element selected from any one or more of the elements in the list of elements, but not necessarily including at least one of each and every element specifically listed within the list of elements and not excluding any combinations of elements in the list of elements. This definition also allows that elements may optionally be present other than the elements specifically identified within the list of elements to which the phrase “at least one” refers, whether related or unrelated to those elements specifically identified. Thus, as a non-limiting example, “at least one of A and B” (or, equivalently, “at least one of A or B,” or, equivalently “at least one of A and/or B”) can refer, in one embodiment, to at least one, optionally including more than one, A, with no B present (and optionally including elements other than B); in another embodiment, to at least one, optionally including more than one, B, with no A present (and optionally including elements other than A); in yet another embodiment, to at least one, optionally including more than one, A, and at least one, optionally including more than one, B (and optionally including other elements); etc. [1208] When the word “about” is used herein in reference to a number, it should be understood that still another embodiment of the disclosure includes that number not modified by the presence of the word “about.” [1209] It should also be understood that, unless clearly indicated to the contrary, in any methods claimed herein that include more than one step or act, the order of the steps or acts of the method is not necessarily limited to the order in which the steps or acts of the method are recited. [1210] In the claims, as well as in the specification above, all transitional phrases such as “comprising,” “including,” “carrying,” “having,” “containing,” “involving,” “holding,” “composed of,” and the like are to be understood to be open-ended, i.e., to mean including but not limited to. Only the transitional phrases “consisting of” and “consisting essentially of” shall be closed or semi-closed transitional phrases, respectively, as set forth in the United States Patent Office Manual of Patent Examining Procedures, Section 2111.03.