Prediction of the sequence-specific cleavage activity of Cas9 variants.

Nature Biotechnology
Nahye KimHyongbum 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.

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Citations

Sep 18, 2020·Nucleic Acids Research·Do Yon KimDaesik Kim
Jun 24, 2020·Nature Biotechnology·Andrew V AnzaloneDavid R Liu
Sep 23, 2020·Nature Biotechnology·Hui Kwon KimHyongbum Henry Kim
Feb 23, 2021·The CRISPR Journal·Aashutosh Boob, Huimin Zhao
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Apr 4, 2021·International Journal of Molecular Sciences·Monika HalatRafal Baranski
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Apr 17, 2021·Nature Biotechnology·Shuai JinCaixia Gao
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Jun 17, 2021·Nucleic Acids Research·Weiwei ZhangJiazhi Hu
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Sep 25, 2021·Nature Communications·Myungjae SongHyongbum Henry Kim
Jan 28, 2022·Yonsei Medical Journal·Jung Min Lim, Hyongbum Henry Kim

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Methods Mentioned

BETA
transfection
PCR
electrophoresis
Illumina sequencing
Protein Assay
feature extraction

Software Mentioned

GN
sgRNA
Python
Python scripts
GenScript
house
SPSS Statistics
DeepSpCas9variants
ImageQuant
XGBoost

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