DNA Repair Profiling Reveals Nonrandom Outcomes at Cas9-Mediated Breaks

Mol Cell. 2016 Aug 18;63(4):633-646. doi: 10.1016/j.molcel.2016.06.037. Epub 2016 Aug 4.


The repair outcomes at site-specific DNA double-strand breaks (DSBs) generated by the RNA-guided DNA endonuclease Cas9 determine how gene function is altered. Despite the widespread adoption of CRISPR-Cas9 technology to induce DSBs for genome engineering, the resulting repair products have not been examined in depth. Here, the DNA repair profiles of 223 sites in the human genome demonstrate that the pattern of DNA repair following Cas9 cutting at each site is nonrandom and consistent across experimental replicates, cell lines, and reagent delivery methods. Furthermore, the repair outcomes are determined by the protospacer sequence rather than genomic context, indicating that DNA repair profiling in cell lines can be used to anticipate repair outcomes in primary cells. Chemical inhibition of DNA-PK enabled dissection of the DNA repair profiles into contributions from c-NHEJ and MMEJ. Finally, this work elucidates a strategy for using "error-prone" DNA-repair machinery to generate precise edits.

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • CRISPR-Associated Protein 9
  • CRISPR-Cas Systems*
  • DNA Breaks, Double-Stranded*
  • DNA End-Joining Repair*
  • Endonucleases / genetics
  • Endonucleases / metabolism*
  • Gene Editing*
  • Gene Expression Profiling / methods*
  • HCT116 Cells
  • HEK293 Cells
  • Humans
  • K562 Cells
  • RNA Interference
  • RNA, Guide, CRISPR-Cas Systems / genetics
  • RNA, Guide, CRISPR-Cas Systems / metabolism
  • Time Factors
  • Transfection


  • Bacterial Proteins
  • RNA, Guide, CRISPR-Cas Systems
  • CRISPR-Associated Protein 9
  • Cas9 endonuclease Streptococcus pyogenes
  • Endonucleases