韩国延世大学医学院Hyongbum Henry Kim小组对Cas9变体的序列特异性切割活性进行了大规模预测。这一研究成果于2020年6月8日在线发表在国际学术期刊《自然—生物技术》上。
Title: Prediction of the sequence-specific cleavage activity of Cas9 variants
Author: Nahye Kim, Hui Kwon Kim, Sungtae Lee, Jung Hwa Seo, Jae Woo Choi, Jinman Park, Seonwoo Min, Sungroh Yoon, Sung-Rae Cho, Hyongbum Henry Kim
Abstract: Several Streptococcus pyogenes Cas9 (SpCas9) variants have been developed to improve an enzyme’s specificity or to alter or broaden its protospacer-adjacent motif (PAM) compatibility, but selecting the optimal variant for a given target sequence and application remains difficult. To build computational models to predict the sequence-specific activity of 13 SpCas9 variants, we first assessed their cleavage efficiency at 26,891 target sequences. We found that, of the 256 possible four-nucleotide NNNN sequences, 156 can be used as a PAM by at least one of the SpCas9 variants. For the high-fidelity variants, overall activity could be ranked as SpCas9≥Sniper-Cas9>eSpCas9(1.1) > SpCas9-HF1>HypaCas9≈xCas9 >> evoCas9, whereas their overall specificities could be ranked as evoCas9 >> HypaCas9≥SpCas9-HF1≈eSpCas9(1.1) > xCas9>Sniper-Cas9>SpCas9. Using these data, we developed 16 deep-learning-based computational models that accurately predict the activity of these variants at any target sequence.