DNA targeting specificity of RNA-guided Cas9 nucleases
Author(s)Hsu, Patrick; Scott, David Arthur; Weinstein, Joshua; Ran, F. Ann; Konermann, Silvana M.; Agarwala, Vineeta; Li, Yinqing; Fine, Eli J.; Wu, Xavier; Shalem, Ophir; Cradick, Thomas J.; Marraffini, Luciano A.; Bao, Gang; Zhang, Feng; ... Show more Show less
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The Streptococcus pyogenes Cas9 (SpCas9) nuclease can be efficiently targeted to genomic loci by means of single-guide RNAs (sgRNAs) to enable genome editing1, 2, 3, 4, 5, 6, 7, 8, 9, 10. Here, we characterize SpCas9 targeting specificity in human cells to inform the selection of target sites and avoid off-target effects. Our study evaluates >700 guide RNA variants and SpCas9-induced indel mutation levels at >100 predicted genomic off-target loci in 293T and 293FT cells. We find that SpCas9 tolerates mismatches between guide RNA and target DNA at different positions in a sequence-dependent manner, sensitive to the number, position and distribution of mismatches. We also show that SpCas9-mediated cleavage is unaffected by DNA methylation and that the dosage of SpCas9 and sgRNA can be titrated to minimize off-target modification. To facilitate mammalian genome engineering applications, we provide a web-based software tool to guide the selection and validation of target sequences as well as off-target analyses.
DepartmentMassachusetts Institute of Technology. Department of Biological Engineering; Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences; McGovern Institute for Brain Research at MIT
Nature Publishing Group
Hsu, Patrick D., David A. Scott, Joshua A. Weinstein, et al. "DNA targeting specificity of RNA-guided Cas9 nucleases." Nature Biotechnology 31:9 (2013) p.827-834.
Author's final manuscript