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Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing

  • 1.

    Auton, A. et al. A global reference for human genetic variation. Nature 526, 68–74 (2015).

    Google Scholar 

  • 2.

    Landrum, M. J. et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 42, D980–D985 (2014).

    CAS 
    PubMed 

    Google Scholar 

  • 3.

    Weischenfeldt, J., Symmons, O., Spitz, F. & Korbel, J. O. Phenotypic impact of genomic structural variation: insights from and for human disease. Nat. Rev. Genet. 14, 125–138 (2013).

    CAS 
    PubMed 

    Google Scholar 

  • 4.

    Cox, D. B., Platt, R. J. & Zhang, F. Therapeutic genome editing: prospects and challenges. Nat. Med. 21, 121–131 (2015).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 5.

    Doudna, J. A. The promise and challenge of therapeutic genome editing. Nature 578, 229–236 (2020).

    CAS 
    PubMed 

    Google Scholar 

  • 6.

    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).

    CAS 
    PubMed 

    Google Scholar 

  • 7.

    Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 8.

    Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 9.

    Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823–826 (2013).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 10.

    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).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 11.

    Gaudelli, N. M. et al. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature 551, 464–471 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 12.

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

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 13.

    Canver, M. C. et al. Characterization of genomic deletion efficiency mediated by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 nuclease system in mammalian cells. J. Biol. Chem. 289, 21312–21324 (2014).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 14.

    Suzuki, K. et al. In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration. Nature 540, 144–149 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 15.

    Wang, B. et al. Highly efficient CRISPR/HDR-mediated knock-in for mouse embryonic stem cells and zygotes. Biotechniques 59, 201–202, 204, 206–208 (2015).

    CAS 
    PubMed 

    Google Scholar 

  • 16.

    Pawelczak, K. S., Gavande, N. S., VanderVere-Carozza, P. S. & Turchi, J. J. Modulating DNA repair pathways to improve precision genome engineering. ACS Chem. Biol. 13, 389–396 (2018).

    CAS 
    PubMed 

    Google Scholar 

  • 17.

    Branzei, D. & Foiani, M. Regulation of DNA repair throughout the cell cycle. Nat. Rev. Mol. Cell Biol. 9, 297–308 (2008).

    CAS 
    PubMed 

    Google Scholar 

  • 18.

    Heyer, W. D., Ehmsen, K. T. & Liu, J. Regulation of homologous recombination in eukaryotes. Annu. Rev. Genet. 44, 113–139 (2010).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 19.

    Gasperini, M. et al. CRISPR/Cas9-mediated scanning for regulatory elements required for HPRT1 expression via thousands of large, programmed genomic deletions. Am. J. Hum. Genet. 101, 192–205 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 20.

    Kosicki, M., Tomberg, K. & Bradley, A. Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements. Nat. Biotechnol. 36, 765–771 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 21.

    Alanis-Lobato, G. et al. Frequent loss of heterozygosity in CRISPR–Cas9-edited early human embryos. Proc. Natl Acad. Sci. USA 118, e2004832117 (2021).

  • 22.

    Song, Y. et al. Large-fragment deletions induced by Cas9 cleavage while not in the BEs system. Mol. Ther. Nucleic Acids 21, 523–526 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 23.

    Brunet, E. & Jasin, M. Induction of chromosomal translocations with CRISPR–Cas9 and other nucleases: understanding the repair mechanisms that give rise to translocations. Adv. Exp. Med. Biol. 1044, 15–25 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 24.

    Nahmad, A. D. et al. Frequent aneuploidy in primary human T cells following CRISPR–Cas9 cleavage. Preprint at https://www.biorxiv.org/content/10.1101/2021.08.20.457092v1.abstract (2021).

  • 25.

    Leibowitz, M. L. et al. Chromothripsis as an on-target consequence of CRISPR–Cas9 genome editing. Nat. Genet. 53, 895–905 (2021).

  • 26.

    Haapaniemi, E., Botla, S., Persson, J., Schmierer, B. & Taipale, J. CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response. Nat. Med. 24, 927–930 (2018).

    CAS 
    PubMed 

    Google Scholar 

  • 27.

    Ihry, R. J. et al. p53 inhibits CRISPR–Cas9 engineering in human pluripotent stem cells. Nat. Med. 24, 939–946 (2018).

    CAS 
    PubMed 

    Google Scholar 

  • 28.

    Enache, O. M. et al. Cas9 activates the p53 pathway and selects for p53-inactivating mutations. Nat. Genet. 52, 662–668 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 29.

    Merrick, C. A., Zhao, J. & Rosser, S. J. Serine integrases: advancing synthetic biology. ACS Synth. Biol. 7, 299–310 (2018).

    CAS 
    PubMed 

    Google Scholar 

  • 30.

    Karpinski, J. et al. Directed evolution of a recombinase that excises the provirus of most HIV-1 primary isolates with high specificity. Nat. Biotechnol. 34, 401–409 (2016).

    CAS 
    PubMed 

    Google Scholar 

  • 31.

    Chaikind, B., Bessen, J. L., Thompson, D. B., Hu, J. H. & Liu, D. R. A programmable Cas9-serine recombinase fusion protein that operates on DNA sequences in mammalian cells. Nucleic Acids Res. 44, 9758–9770 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 32.

    Gaj, T. et al. Enhancing the specificity of recombinase-mediated genome engineering through dimer interface redesign. J. Am. Chem. Soc. 136, 5047–5056 (2014).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 33.

    Kim, A. I. et al. Mycobacteriophage Bxb1 integrates into the Mycobacterium smegmatis groEL1 gene. Mol. Microbiol. 50, 463–473 (2003).

    CAS 
    PubMed 

    Google Scholar 

  • 34.

    Choi, J. et al. Precise genomic deletions using paired prime editing. Nat. Biotechnol. https://doi.org/10.1038/s41587-020 (2021).

  • 35.

    Lin, Q. et al. High-efficiency prime editing with optimized, paired pegRNAs in plants. Nat. Biotechnol. https://doi.org/10.1038/s41587-021-00868-w (2021).

  • 36.

    Scriver, C. R. The PAH gene, phenylketonuria, and a paradigm shift. Hum. Mutat. 28, 831–845 (2007).

    CAS 
    PubMed 

    Google Scholar 

  • 37.

    Nelson, J. W. et al. Engineered pegRNAs improve prime editing efficiency. Nat. Biotechnol. https://doi.org/10.1038/s41587-021-01039-7 (2021).

  • 38.

    Flanigan, K. M. et al. Mutational spectrum of DMD mutations in dystrophinopathy patients: application of modern diagnostic techniques to a large cohort. Hum. Mutat. 30, 1657–1666 (2009).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 39.

    Aartsma-Rus, A. et al. Development of exon skipping therapies for duchenne muscular dystrophy: a critical review and a perspective on the outstanding issues. Nucleic Acid Ther. 27, 251–259 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 40.

    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).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 41.

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

  • 42.

    Duportet, X. et al. A platform for rapid prototyping of synthetic gene networks in mammalian cells. Nucleic Acids Res. 42, 13440–13451 (2014).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 43.

    Jusiak, B. et al. Comparison of integrases identifies Bxb1-GA mutant as the most efficient site-specific integrase system in mammalian cells. ACS Synth. Biol. 8, 16–24 (2019).

    CAS 
    PubMed 

    Google Scholar 

  • 44.

    Sharma, R. et al. In vivo genome editing of the albumin locus as a platform for protein replacement therapy. Blood 126, 1777–1784 (2015).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 45.

    Nathwani, A. C. et al. Long-term safety and efficacy of factor IX gene therapy in hemophilia B. N. Engl. J. Med. 371, 1994–2004 (2014).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 46.

    Bessen, J. L. et al. High-resolution specificity profiling and off-target prediction for site-specific DNA recombinases. Nat. Commun. 10, 1937 (2019).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 47.

    Bondeson, M. L. et al. Inversion of the IDS gene resulting from recombination with IDS-related sequences is a common cause of the Hunter syndrome. Hum. Mol. Genet. 4, 615–621 (1995).

    CAS 
    PubMed 

    Google Scholar 

  • 48.

    Chen, X. et al. In trans paired nicking triggers seamless genome editing without double-stranded DNA cutting. Nat. Commun. 8, 657 (2017).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 49.

    Park, C. Y. et al. Targeted inversion and reversion of the blood coagulation factor 8 gene in human iPS cells using TALENs. Proc. Natl Acad. Sci. USA 111, 9253–9258 (2014).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 50.

    Li, J. et al. Efficient inversions and duplications of mammalian regulatory DNA elements and gene clusters by CRISPR/Cas9. J. Mol. Cell. Biol. 7, 284–298 (2015).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 51.

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

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 52.

    Clement, K., Farouni, R., Bauer, D. E. & Pinello, L. AmpUMI: design and analysis of unique molecular identifiers for deep amplicon sequencing. Bioinformatics 34, i202–i210 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 53.

    Shen, W., Le, S., Li, Y. & Hu, F. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS ONE 11, e0163962 (2016).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 54.

    Levy, J. M. & Nicoll, R. A. Membrane-associated guanylate kinase dynamics reveal regional and developmental specificity of synapse stability. J. Physiol. 595, 1699–1709 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 55.

    Koblan, L. W. et al. In vivo base editing rescues Hutchinson–Gilford progeria syndrome in mice. Nature 589, 608–614 (2021).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 56.

    Gaudelli, N. M. et al. Directed evolution of adenine base editors with increased activity and therapeutic application. Nat. Biotechnol. 38, 892–900 (2020).

    CAS 
    PubMed 

    Google Scholar 

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