Journal
GENOMICS
Volume 111, Issue 4, Pages 560-566Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ygeno.2018.03.011
Keywords
CRISPRs; Cas9; sgRNA; Protospacer adjacent motif; Genome engineering
Funding
- Senior Research Fellowship (SRF) from CSIR, Govt. of India
- DuPont Young Professor Award
- Lady Tata Memorial Trust (Mumbai)
- Department of Biotechnology (DBT) under the Bioscience Award Scheme
- DBT, Govt. of India
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The ability to direct the CRISPR/Cas9 nuclease to a unique target site within a genome would have broad use in targeted genome engineering. However, CRISPR RNA is reported to bind to other genomic locations that differ from the intended target site by a few nucleotides, demonstrating significant off-target activity. We have developed the CRISPcut tool that screens the off-targets using various parameters and predicts the ideal genomic target for -guide RNAs in human cell lines. sgRNAs for four different types of Cas9 nucleases can be designed with an option for the user to work with different PAM sequences. Direct experimental measurement of genome-wide DNA accessibility is incorporated that effectively restricts the prediction of CRISPR targets to open chromatin. An option to predict target sites for paired CRISPR nickases is also provided. The tool has been validated using a dataset of experimentally used sgRNA and their identified off-targets.
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