Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease
Abstract
RNA-guided genome editing with the CRISPR-Cas9 system has great potential for basic and clinical research, but the determinants of targeting specificity and the extent of off-target cleavage remain insufficiently understood. Using chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq), we mapped genome-wide binding sites of catalytically inactive Cas9 (dCas9) in HEK293T cells, in combination with 12 different single guide RNAs (sgRNAs). The number of off-target sites bound by dCas9 varied from ∼10 to >1,000 depending on the sgRNA. Analysis of off-target binding sites showed the importance of the PAM-proximal region of the sgRNA guiding sequence and that dCas9 binding sites are enriched in open chromatin regions. When targeted with catalytically active Cas9, some off-target binding sites had indels above background levels in a region around the ChIP-seq peak, but generally at lower rates than the on-target sites. Our results elucidate major determinants of Cas9 targeting, and we show that ChIP-seq allows unbiased detection of Cas9 binding sites genome-wide.
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dCas9 ChIP-Seq with 12 different sgRNAs in HEK293T cells successfully validated DNA cleavage at about 50% of the predicted off-target sites.
“One study reported dCas9 ChIP-Seq with 12 different sgRNAs in HEK293T cells and successfully validated DNA cleavage at about 50% of the predicted off-target sites (Kuscu et al., 2014).”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Kuscu et al., 2014
Epigenome editing suffers from challenges of binding Cas9 to off-target sites and influencing histone and chromatin modifiers, which inadvertently affect transcription of off-target genes.
“It suffers from the challenges of binding Cas9 to off-target sites and influencing histone and chromatin modifiers, which inadvertently affect the transcription of off-target genes (Kuscu et al., 2014).”
From Emerging applications of gene editing technologies for the development of climate-resilient crops (2025) · cites this paper as Kuscu et al., 2014
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- Authors
- Kuscu, C., Arslan, S., Singh, R., Thorpe, J., & Adli, M.
- Affiliations
- University of Virginia (US)
- Corresponding author
- Adli, Mazhar
- Venue
- Nature Biotechnology
- Published
- 2014-05-18
- Volume
- 32
- Issue
- 7
- Pages
- 677-683
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2030994161
- Cited by
- 777
- References
- 36
- Citations by year
- 2026: 29 · 2025: 26 · 2024: 45 · 2023: 36 · 2022: 52 · 2021: 57 · 2020: 77 · 2019: 67 · 2018: 79 · 2017: 76 · 2016: 98 · 2015: 91 · 2014: 43 · 2013: 1
- FWCI
- 42.07
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
- Keywords
- CRISPR/Cas9, off-target binding, dCas9, single guide RNA, targeting specificity, PAM sequence, open chromatin, genome-wide binding sites, indels, HEK293T cells, ChIP-seq
- MeSH terms
- Base Sequence, Binding Sites, Cells, Cultured, Chromosome Mapping, Deoxyribonuclease I, Humans, Models, Genetic, Molecular Sequence Data, Genome, Gene Targeting, Embryonic Stem Cells, HEK293 Cells, CRISPR-Cas Systems
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