Journal
NUCLEIC ACIDS RESEARCH
Volume 48, Issue 18, Pages 10576-10589Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkaa764
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Funding
- KRIBB Research Initiative Program [KG-20200023]
- Ministry of Science and ICT [NRF2016M3A9B6903343]
- National Research Council of Science Technology [CAP-15-03-KRIBB]
- Institute for Basic Science [IBS-R021-D1]
- National Research Council of Science Technology [CAP-15-03-KRIBB]
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Prime editors (PEs) enable targeted precise editing, including the generation of substitutions, insertions and deletions, in eukaryotic genomes. However, their genome-wide specificity has not been explored. Here, we developed Nickase-based Digenome-seq (nDigenome-seq), an in vitro assay that uses whole-genome sequencing to identify single-strand breaks induced by CRISPR (clustered regularly interspaced short palindromic repeats)Cas9 (CRISPR-associated protein 9) nickase. We used nDigenome-seq to screen for potential genome-wide off-target sites of Cas9 H840A nickase, a PE component, targeted to nine human genomic sites. Then, using targeted amplicon sequencing of off-target candidates identified by nDigenome-seq, we showed that only five off-target sites showed detectable PE-induced modifications in cells, at frequencies ranging from 0.1 to 1.9%, suggesting that PEs provide a highly specific method of precise genome editing. We also found that PE specificity in human cells could be further improved by incorporating mutations from engineered Cas9 variants, particularly eSpCas9 and Sniper Cas9, into PE.
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