DNA Repair Profiling Reveals Nonrandom Outcomes at Cas9-Mediated Breaks

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 and have been thought to result in random outcomes. In this study, the DNA repair profiles of over 200 sites in the human genome are presented and demonstrate that the pattern of DNA repair following Cas9 cutting at each site is, in fact, nonrandom and consistent across experimental replicates, cell lines, and reagent delivery methods. Furthermore, genomic context does not dictate repair outcomes; outcomes are determined by the targeted DNA sequence, elucidating a strategy to anticipate the functional outcome of gene editing experiments and to use â??error-proneâ?Â DNA-repair machinery to generate precise edits.