Anzalone, A. V., Koblan, L. W. & Liu, D. R. Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors. Nat. Biotechnol. 38, 824–844 (2020).
Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019).
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 Res. 48, 10576–10589 (2020).
Liang, S. Q. et al. Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag. Nat. Methods 20, 898–907 (2023).
Jin, S. et al. Genome-wide specificity of prime editors in plants. Nat. Biotechnol. 39, 1292–1299 (2021).
Gao, R. et al. Genomic and transcriptomic analyses of prime editing guide RNA-independent off-target effects by prime editors. CRISPR J. 5, 276–293 (2022).
Fiumara, M. et al. Genotoxic effects of base and prime editing in human hematopoietic stem cells. Nat. Biotechnol. 42, 877–891 (2023).
Bannert, N. & Kurth, R. Retroelements and the human genome: new perspectives on an old relation. Proc. Natl Acad. Sci. USA 101, 14572–14579 (2004).
Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).
Kazazian, H. H. Jr & Moran, J. V. Mobile DNA in health and disease. N. Engl. J. Med. 377, 361–370 (2017).
Wells, J. N. & Feschotte, C. A field guide to eukaryotic transposable elements. Annu. Rev. Genet. 54, 539–561 (2020).
Moore, J. K. & Haber, J. E. Capture of retrotransposon DNA at the sites of chromosomal double-strand breaks. Nature 383, 644–646 (1996).
Teng, S. C., Kim, B. & Gabriel, A. Retrotransposon reverse-transcriptase-mediated repair of chromosomal breaks. Nature 383, 641–644 (1996).
Morrish, T. A. et al. DNA repair mediated by endonuclease-independent LINE-1 retrotransposition. Nat. Genet. 31, 159–165 (2002).
Tao, J., Wang, Q., Mendez-Dorantes, C., Burns, K. H. & Chiarle, R. Frequency and mechanisms of LINE-1 retrotransposon insertions at CRISPR/Cas9 sites. Nat. Commun. 13, 3685 (2022).
Park, S. K., Mohr, G., Yao, J., Russell, R. & Lambowitz, A. M. Group II intron-like reverse transcriptases function in double-strand break repair. Cell 185, 3671–3688.e23 (2022).
Liu, B. et al. A split prime editor with untethered reverse transcriptase and circular RNA template. Nat. Biotechnol. 40, 1388–1393 (2022).
Grunewald, J. et al. Engineered CRISPR prime editors with compact, untethered reverse transcriptases. Nat. Biotechnol. 41, 337–343 (2023).
van Overbeek, M. et al. DNA repair profiling reveals nonrandom outcomes at Cas9-mediated breaks. Mol. Cell 63, 633–646 (2016).
Xue, C. & Greene, E. C. DNA repair pathway choices in CRISPR–Cas9-mediated genome editing. Trends Genet. 37, 639–656 (2021).
Shou, J., Li, J., Liu, Y. & Wu, Q. Precise and predictable CRISPR chromosomal rearrangements reveal principles of Cas9-mediated nucleotide insertion. Mol. Cell 71, 498–509 (2018).
Li, Y. et al. A versatile reporter system for CRISPR-mediated chromosomal rearrangements. Genome Biol. 16, 111 (2015).
Ohtsubo, Y., Sasaki, H., Nagata, Y. & Tsuda, M. Optimization of single strand DNA incorporation reaction by Moloney murine leukaemia virus reverse transcriptase. DNA Res. 25, 477–487 (2018).
Kaushik, N., Chowdhury, K., Pandey, V. N. & Modak, M. J. Valine of the YVDD motif of Moloney murine leukemia virus reverse transcriptase: role in the fidelity of DNA synthesis. Biochemistry 39, 5155–5165 (2000).
Kaushik, N., Singh, K., Alluru, I. & Modak, M. J. Tyrosine 222, a member of the YXDD motif of MuLV RT, is catalytically essential and is a major component of the fidelity center. Biochemistry 38, 2617–2627 (1999).
Doman, J. L. et al. Phage-assisted evolution and protein engineering yield compact, efficient prime editors. Cell 186, 3983–4002.e26 (2023).
Jones, S. K. Jr et al. Massively parallel kinetic profiling of natural and engineered CRISPR nucleases. Nat. Biotechnol. 39, 84–93 (2021).
Shi, X. et al. Cas9 has no exonuclease activity resulting in staggered cleavage with overhangs and predictable di- and tri-nucleotide CRISPR insertions without template donor. Cell Discov. 5, 53 (2019).
Hussmann, J. A. et al. Mapping the genetic landscape of DNA double-strand break repair. Cell 184, 5653–5669.e25 (2021).
Onn, L. et al. SIRT6 is a DNA double-strand break sensor. eLife 9, e51636 (2020).
Chu, V. T. et al. Increasing the efficiency of homology-directed repair for CRISPR–Cas9-induced precise gene editing in mammalian cells. Nat. Biotechnol. 33, 543–548 (2015).
Rass, E. et al. Role of MRE11 in chromosomal nonhomologous end joining in mammalian cells. Nat. Struct. Mol. Biol. 16, 819–824 (2009).
Sherman, B. T. et al. DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update). Nucleic Acids Res. 50, W216–W221 (2022).
Li, L. et al. DEAD box 1 facilitates removal of RNA and homologous recombination at DNA double-strand breaks. Mol. Cell. Biol. 36, 2794–2810 (2016).
Ulrich, H. D. Timing and spacing of ubiquitin-dependent DNA damage bypass. FEBS Lett. 585, 2861–2867 (2011).
Taylor, M. S. et al. Affinity proteomics reveals human host factors implicated in discrete stages of LINE-1 retrotransposition. Cell 155, 1034–1048 (2013).
Jiang, T., Zhang, X. O., Weng, Z. & Xue, W. Deletion and replacement of long genomic sequences using prime editing. Nat. Biotechnol. 40, 227–234 (2022).
Zheng, C. et al. A flexible split prime editor using truncated reverse transcriptase improves dual-AAV delivery in mouse liver. Mol. Ther. 30, 1343–1351 (2022).
Zong, Y. et al. An engineered prime editor with enhanced editing efficiency in plants. Nat. Biotechnol. 40, 1394–1402 (2022).
Bock, D. et al. In vivo prime editing of a metabolic liver disease in mice. Sci. Transl. Med. 14, eabl9238 (2022).
Zabrady, M., Zabrady, K., Li, A. W. H. & Doherty, A. J. Reverse transcriptases prime DNA synthesis. Nucleic Acids Res. 51, 7125–7142 (2023).
Davis, J. R. et al. Efficient prime editing in mouse brain, liver and heart with dual AAVs. Nat. Biotechnol. 42, 253–264 (2024).
Lee, J. et al. Prime editing with genuine Cas9 nickases minimizes unwanted indels. Nat. Commun. 14, 1786 (2023).
Bebenek, K., Pedersen, L. C. & Kunkel, T. A. Structure–function studies of DNA polymerase lambda. Biochemistry 53, 2781–2792 (2014).
Liu, P. et al. Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice. Nat. Commun. 12, 2121 (2021).
Clement, K. et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat. Biotechnol. 37, 224–226 (2019).
Liu, B., et al. Targeted genome editing with a DNA-dependent DNA polymerase and exogenous DNA-containing templates. Nat. Biotechnol. 42, 1039–1045 (2023).
Zheng, C., Zhang, G., Dean, L., Sontheimer, E. & Xue, W. The reverse transcriptase domain of prime editors contributes to DNA repair in mammalian cells. NCBI BioProject https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1209104 (2025).