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Genome-wide profiling of adenine base editor specificity by EndoV-seq

Published on Dec 1, 2019in Nature Communications11.88
· DOI :10.1038/s41467-018-07988-z
Puping Liang8
Estimated H-index: 8
(SYSU: Sun Yat-sen University),
Xiaowei Xie7
Estimated H-index: 7
(SYSU: Sun Yat-sen University)
+ 9 AuthorsZhou Songyang45
Estimated H-index: 45
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Abstract
The adenine base editor (ABE), capable of catalyzing A•T to G•C conversions, is an important gene editing toolbox. Here, we systematically evaluate genome-wide off-target deamination by ABEs using the EndoV-seq platform we developed. EndoV-seq utilizes Endonuclease V to nick the inosine-containing DNA strand of genomic DNA deaminated by ABE in vitro. The treated DNA is then whole-genome sequenced to identify off-target sites. Of the eight gRNAs we tested with ABE, 2–19 (with an average of 8.0) off-target sites are found, significantly fewer than those found for canonical Cas9 nuclease (7–320, 160.7 on average). In vivo off-target deamination is further validated through target site deep sequencing. Moreover, we demonstrated that six different ABE-gRNA complexes could be examined in a single EndoV-seq assay. Our study presents the first detection method to evaluate genome-wide off-target effects of ABE, and reveals possible similarities and differences between ABE and canonical Cas9 nuclease. Adenine base editors are an important contribution to the genome editing toolbox. Here the authors present EndoV-seq, an endonuclease-based assay for evaluating genomewide off-target effects of base editing.
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