The reverse transcriptase domain of prime editors contributes to DNA repair in mammalian cells – Nature Biotechnology

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  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Jin, S. et al. Genome-wide specificity of prime editors in plants. Nat. Biotechnol. 39, 1292–1299 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Fiumara, M. et al. Genotoxic effects of base and prime editing in human hematopoietic stem cells. Nat. Biotechnol. 42, 877–891 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bannert, N. & Kurth, R. Retroelements and the human genome: new perspectives on an old relation. Proc. Natl Acad. Sci. USA 101, 14572–14579 (2004).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Kazazian, H. H. Jr & Moran, J. V. Mobile DNA in health and disease. N. Engl. J. Med. 377, 361–370 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wells, J. N. & Feschotte, C. A field guide to eukaryotic transposable elements. Annu. Rev. Genet. 54, 539–561 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Moore, J. K. & Haber, J. E. Capture of retrotransposon DNA at the sites of chromosomal double-strand breaks. Nature 383, 644–646 (1996).

    Article 
    PubMed 

    Google Scholar 

  • Teng, S. C., Kim, B. & Gabriel, A. Retrotransposon reverse-transcriptase-mediated repair of chromosomal breaks. Nature 383, 641–644 (1996).

    Article 
    PubMed 

    Google Scholar 

  • Morrish, T. A. et al. DNA repair mediated by endonuclease-independent LINE-1 retrotransposition. Nat. Genet. 31, 159–165 (2002).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Liu, B. et al. A split prime editor with untethered reverse transcriptase and circular RNA template. Nat. Biotechnol. 40, 1388–1393 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Grunewald, J. et al. Engineered CRISPR prime editors with compact, untethered reverse transcriptases. Nat. Biotechnol. 41, 337–343 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • van Overbeek, M. et al. DNA repair profiling reveals nonrandom outcomes at Cas9-mediated breaks. Mol. Cell 63, 633–646 (2016).

    Article 
    PubMed 

    Google Scholar 

  • Xue, C. & Greene, E. C. DNA repair pathway choices in CRISPR–Cas9-mediated genome editing. Trends Genet. 37, 639–656 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Li, Y. et al. A versatile reporter system for CRISPR-mediated chromosomal rearrangements. Genome Biol. 16, 111 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Doman, J. L. et al. Phage-assisted evolution and protein engineering yield compact, efficient prime editors. Cell 186, 3983–4002.e26 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Jones, S. K. Jr et al. Massively parallel kinetic profiling of natural and engineered CRISPR nucleases. Nat. Biotechnol. 39, 84–93 (2021).

    Article 
    PubMed 

    Google Scholar 

  • 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).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hussmann, J. A. et al. Mapping the genetic landscape of DNA double-strand break repair. Cell 184, 5653–5669.e25 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Onn, L. et al. SIRT6 is a DNA double-strand break sensor. eLife 9, e51636 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Rass, E. et al. Role of MRE11 in chromosomal nonhomologous end joining in mammalian cells. Nat. Struct. Mol. Biol. 16, 819–824 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ulrich, H. D. Timing and spacing of ubiquitin-dependent DNA damage bypass. FEBS Lett. 585, 2861–2867 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Taylor, M. S. et al. Affinity proteomics reveals human host factors implicated in discrete stages of LINE-1 retrotransposition. Cell 155, 1034–1048 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Zong, Y. et al. An engineered prime editor with enhanced editing efficiency in plants. Nat. Biotechnol. 40, 1394–1402 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Bock, D. et al. In vivo prime editing of a metabolic liver disease in mice. Sci. Transl. Med. 14, eabl9238 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Zabrady, M., Zabrady, K., Li, A. W. H. & Doherty, A. J. Reverse transcriptases prime DNA synthesis. Nucleic Acids Res. 51, 7125–7142 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Davis, J. R. et al. Efficient prime editing in mouse brain, liver and heart with dual AAVs. Nat. Biotechnol. 42, 253–264 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Lee, J. et al. Prime editing with genuine Cas9 nickases minimizes unwanted indels. Nat. Commun. 14, 1786 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bebenek, K., Pedersen, L. C. & Kunkel, T. A. Structure–function studies of DNA polymerase lambda. Biochemistry 53, 2781–2792 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Liu, P. et al. Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice. Nat. Commun. 12, 2121 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Clement, K. et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat. Biotechnol. 37, 224–226 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 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).

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