Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq

Published on Mar 1, 2016in Genome Research9.94
· DOI :10.1101/gr.199588.115
Daesik Kim14
Estimated H-index: 14
(SNU: Seoul National University),
Sojung Kim11
Estimated H-index: 11
(SNU: Seoul National University)
+ 2 AuthorsJin-Soo Kim53
Estimated H-index: 53
(SNU: Seoul National University)
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We present multiplex Digenome-seq to profile genome-wide specificities of up to 11 CRISPR-Cas9 nucleases simultaneously, saving time and reducing cost. Cell-free human genomic DNA was digested using multiple sgRNAs combined with the Cas9 protein and then subjected to whole-genome sequencing. In vitro cleavage patterns, characteristic of on- and off-target sites, were computationally identified across the genome using a new DNA cleavage scoring system. We found that many false-positive, bulge-type off-target sites were cleaved by sgRNAs transcribed from an oligonucleotide duplex but not by those transcribed from a plasmid template. Multiplex Digenome-seq captured many bona fide off-target sites, missed by other genome-wide methods, at which indels were induced at frequencies <0.1%. After analyzing 964 sites cleaved in vitro by these sgRNAs and measuring indel frequencies at hundreds of off-target sites in cells, we propose a guideline for the choice of target sites for minimizing CRISPR-Cas9 off-target effects in the human genome.
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