Journal
BRIEFINGS IN BIOINFORMATICS
Volume 23, Issue 5, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bib/bbac183
Keywords
Seq2seq-attention; CRISPR system; sgRNA; Off-targets; mismatch
Funding
- National Natural Science Foundation of China [32170616, 82170896, 31970569, 31871264]
- Natural Science Basic Research Program of Shaanxi Province [2021JC-02]
- Innovation Capability Support Program of Shaanxi Province [2022TD-44]
- China Postdoctoral Science Foundation [2021T140546, 2020M683454]
- Natural Science Foundation of Zhejiang Province [LWY20H060001]
- Fundamental Research Funds for the Central Universities
- High-Performance Computing Platform and Instrument Analysis Center of Xi'an Jiaotong University
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Research shows that designing sgRNAs with on-target mismatches can improve binding activity and reduce off-target effects. A web tool named ExsgRNA is provided for optimizing sgRNA design.
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing technology has been widely used to facilitate efficient genome editing. Current popular sgRNA design tools only consider the sgRNA perfectly matched to the target site and provide the results without any on-target mismatch. We suppose taking on-target gRNA-DNA mismatches into consideration might provide better sgRNA with similar binding activity and reduced off-target sites. Here, we trained a seq2seq-attention model with feedback-loop architecture, to automatically generate sgRNAs with on-target mismatches. Dual-luciferase reporter experiment showed that multiple sgRNAs with three mismatches could achieve the 80% of the relative activity of the perfect matched sgRNA. Meanwhile, it could reduce the number of off-target sites using sgRNAs with on-target mismatches. Finally, we provided a freely accessible web server sgRNA design tool named ExsgRNA. Users could submit their target sequence to this server and get optimal sgRNAs with less off-targets and similar on-target activity compared with the perfect-matched sgRNA.
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