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Characterization of the interplay between DNA repair and CRISPR/Cas9-induced DNA lesions at an endogenous locus

Bothmer, Anne, Phadke, Tanushree, Barrera, Luis A., Margulies, Carrie M, Lee, Christina S., Buquicchio, Frank, Moss, Sean, Abdulkerim, Hayat S., Selleck, William, Jayaram, Hariharan, Myer, Vic E., Cotta-Ramusino, Cecilia·2017·Nature Communications
DOI 10.1038/ncomms13905PMC PMC5227551
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Abstract

The CRISPR–Cas9 system provides a versatile toolkit for genome engineering that can introduce various DNA lesions at specific genomic locations. However, a better understanding of the nature of these lesions and the repair pathways engaged is critical to realizing the full potential of this technology. Here we characterize the different lesions arising from each Cas9 variant and the resulting repair pathway engagement. We demonstrate that the presence and polarity of the overhang structure is a critical determinant of double-strand break repair pathway choice. Similarly, single nicks deriving from different Cas9 variants differentially activate repair: D10A but not N863A-induced nicks are repaired by homologous recombination. Finally, we demonstrate that homologous recombination is required for repairing lesions using double-stranded, but not single-stranded DNA as a template. This detailed characterization of repair pathway choice in response to CRISPR–Cas9 enables a more deterministic approach for designing research and therapeutic genome engineering strategies.

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  1. Hsu, P. D., Lander, E. S. & Zhang, F. Development and applications of CRISPR-Cas9 for genome engineering. Cell 157, 1262–1278 (2014). · DOI · Paper page
  2. Gasiunas, G., Barrangou, R., Horvath, P. & Siksnys, V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc. Natl. Acad Sci. USA 109, E2579–E2586 (2012). · DOI · Paper page
  3. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012). · DOI · Paper page
  4. Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013). · DOI · Paper page
  5. Sapranauskas, R. et al. The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic Acids Res. 39, 9275–9282 (2011). · DOI
  6. Sternberg, S. H., LaFrance, B., Kaplan, M. & Doudna, J. A. Conformational control of DNA target cleavage by CRISPR–Cas9. Nature 527, 1–14 (2015). · DOI · Paper page
  7. Ciccia, A. & Elledge, S. J. The DNA damage response: making it safe to play with knives. Mol. Cell 40, 179–204 (2010). · DOI · Paper page
  8. Symington, L. S. End resection at double-strand breaks: mechanism and regulation. Cold Spring Harb. Perspect. Biol. 6, a016436–a016436 (2014). · DOI
  9. McVey, M. & Lee, S. E. MMEJ repair of double-strand breaks (director’s cut): deleted sequences and alternative endings. Trends Genet. 24, 529–538 (2008). · DOI
  10. Deriano, L. & Roth, D. B. Modernizing the nonhomologous end-joining repertoire: alternative and classical NHEJ share the stage. Annu. Rev. Genet. 47, 433–455 (2013). · DOI
  11. Bétermier, M., Bertrand, P. & Lopez, B. S. Is Non-Homologous End-Joining Really an Inherently Error-Prone Process? PLoS Genet. 10, e1004086–e1004089 (2014). · DOI
  12. Ceccaldi, R., Rondinelli, B. & D’Andrea, A. D. Repair pathway choices and consequences at the double-strand break. Trends Cell Biol. 26, 1–13 (2015).
  13. Mehta, A. & Haber, J. E. Sources of DNA double-strand breaks and models of recombinational DNA repair. Cold Spring Harb. Perspect. Biol. 6, a016428–a016428 (2014). · DOI
  14. Saleh-Gohari, N. et al. Spontaneous homologous recombination is induced by collapsed replication forks that are caused by endogenous dna single-strand breaks. Mol. Cell Biol. 25, 7158–7169 (2005). · DOI
  15. Mayle, R. et al. DNA REPAIR. Mus81 and converging forks limit the mutagenicity of replication fork breakage. Science 349, 742–747 (2015). · DOI
  16. Neelsen, K. J. & Lopes, M. Replication fork reversal in eukaryotes: from dead end to dynamic response. Nat. Rev. Mol. Cell Biol. 16, 207–220 (2015). · DOI
  17. Vriend, L. E. M., Jasin, M. & Krawczyk, P. M. Assaying break and nick-induced homologous recombination in mammalian cells using the DR-GFP reporter and Cas9 nucleases. Meth. Enzymol. 546, 175–191 (2014). · DOI
  18. Vriend, L. E. M. et al. Distinct genetic control of homologous recombination repair of Cas9-induced double-strand breaks, nicks and paired nicks. Nucleic Acids Res. 44, 179–14 (2016). · DOI
  19. Ran, F. A. et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154, 1380–1389 (2013). · DOI · Paper page
  20. Liang, P. et al. CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes. Protein Cell 6, 1–10 (2015). · DOI
  21. Bennardo, N., Cheng, A., Huang, N. & Stark, J. M. Alternative-NHEJ is a mechanistically distinct pathway of mammalian chromosome break repair. PLoS Genet. 4, e1000110–e1000110 (2008). · DOI
  22. Certo, M. T. et al. Coupling endonucleases with DNA end–processing enzymes to drive gene disruption. Nat. Methods 9, 973–975 (2012). · DOI
  23. Muñoz, M. C., Yanez, D. A. & Stark, J. M. An RNF168 fragment defective for focal accumulation at DNA damage is proficient for inhibition of homologous recombination in BRCA1 deficient cells. Nucleic Acids Res. 42, 7720–7733 (2014). · DOI
  24. Davis, L. & Maizels, N. Homology-directed repair of DNA nicks via pathways distinct from canonical double-strand break repair. Proc. Natl Acad. Sci. USA 111, E924–E932 (2014). · DOI
  25. Robert, F., Barbeau, M., Éthier, S., Dostie, J. & Pelletier, J. Pharmacological inhibition of DNA-PK stimulates Cas9-mediated genome editing. Genome Med. 27, 1–11 (2015).
  26. Jasin, M. & Haber, J. E. The democratization of gene editing: insights from site-specific cleavage and double-strand break repair. DNA Repair 44, 6–16 (2016). · DOI
  27. Yousefzadeh, M. J. et al. Mechanism of suppression of chromosomal instability by DNA polymerase POLQ. PLoS Genet. 10, e1004654–15 (2014). · DOI
  28. Yu, A. M. & McVey, M. Synthesis-dependent microhomology-mediated end joining accounts for multiple types of repair junctions. Nucleic Acids Res. 38, 5706–5717 (2010). · DOI
  29. Richardson, C. D., Ray, G. J., DeWitt, M. A., Curie, G. L. & Corn, J. E. Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA. Nat. Biotechnol. 34, 1–7 (2016). · DOI · Paper page
  30. Hashimoto, Y., Ray Chaudhuri, A., Lopes, M. & Costanzo, V. Rad51 protects nascent DNA from Mre11-dependent degradation and promotes continuous DNA synthesis. Nat. Struct Mol. Biol. 17, 1305–1311 (2010). · DOI
  31. Schlacher, K. et al. Double-Strand break repair-independent role for BRCA2 in blocking stalled replication fork degradation by MRE11. Cell 145, 529–542 (2011). · DOI
  32. Zellweger, R. et al. Rad51-mediated replication fork reversal is a global response to genotoxic treatments in human cells. J. Cell Biol. 208, 563–579 (2015). · DOI
  33. Zhang, J., Kobert, K., Flouri, T. & Stamatakis, A. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30, 614–620 (2014). · DOI · Paper page
  34. Rice, P., Longden, I. & Bleasby, A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 16, 276–277 (2000). · DOI · Paper page
  35. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009). · DOI · Paper page

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Metadata

Authors
Bothmer, A., Phadke, T., Barrera, L. A., Margulies, C. M., Lee, C. S., Buquicchio, F., Moss, S., Abdulkerim, H. S., Selleck, W., Jayaram, H., Myer, V. E., & Cotta-Ramusino, C.
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2017-01-09
Volume
8
Issue
1
ISSN
2041-1723
DOI
10.1038/ncomms13905
PMC
PMC5227551
Cited by
187
References
9
Language
en
Licence

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