Genome-wide profiling of adenine base editor specificity by EndoV-seq
Open accessAbstract
The adenine base editor (ABE), capable of catalyzing A•T to G•C conversions, is an important gene editing toolbox. Here, we systematically evaluate genome-wide off-target deamination by ABEs using the EndoV-seq platform we developed. EndoV-seq utilizes Endonuclease V to nick the inosine-containing DNA strand of genomic DNA deaminated by ABE in vitro. The treated DNA is then whole-genome sequenced to identify off-target sites. Of the eight gRNAs we tested with ABE, 2-19 (with an average of 8.0) off-target sites are found, significantly fewer than those found for canonical Cas9 nuclease (7-320, 160.7 on average). In vivo off-target deamination is further validated through target site deep sequencing. Moreover, we demonstrated that six different ABE-gRNA complexes could be examined in a single EndoV-seq assay. Our study presents the first detection method to evaluate genome-wide off-target effects of ABE, and reveals possible similarities and differences between ABE and canonical Cas9 nuclease.
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EndoV-seq and Detect-seq have greatly facilitated detection of off-target effects of ABE and CBE on genomic DNA.
“The recent development of EndoV-seq and Detect-seq have greatly facilitated the detection of off-target effects of ABE and CBE on genomic DNA.”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Liang et al., 2019
The Results section reports that EndoV-seq effectively and sensitively detects genome-wide ABE off-target sites. The paper does not report Detect-seq as a method for detecting CBE off-target effects, so that part of the sentence is not supported by this source. (LLM, conf=0.90)
Experimental — accuracy not yet measuredSuch DNA cuts can be detected by sequencing using an experimental platform similar to Digenome-seq.
“Such DNA cuts can be detected by sequencing using an experimental platform similar to Digenome-seq”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Liang et al., 2019
EndoV-seq leverages endonuclease V to specifically cut inosine in DNA.
“EndoV-seq leverages the endonuclease V (EndoV) to specifically cut inosine in DNA”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Liang et al., 2019
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“Such DNA cuts can be detected by sequencing using an experimental platform similar to Digenome-seq (Liang et al., 2019).”
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- Authors
- Liang, P., Xie, X., Zhi, S., Sun, H., Zhang, X., Chen, Y., Chen, Y., Xiong, Y., Ma, W., Liu, D., Huang, J., & Songyang, Z.
- Affiliations
- Sun Yat-sen University (CN)
- Baylor College of Medicine (US)
- Corresponding author
- Huang, Junjiu
- Songyang, Zhou
- ORCID
- Venue
- Nature Communications
- Published
- 2019-01-08
- Volume
- 10
- Issue
- 1
- Pages
- 67-67
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC6325126
- OpenAlex
- W2909752178
- Cited by
- 148
- References
- 62
- Citations by year
- 2026: 15 · 2025: 15 · 2024: 21 · 2023: 14 · 2022: 18 · 2021: 24 · 2020: 26 · 2019: 15
- FWCI
- 6.87
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Natural Science Foundation of Guangdong Province (201707010085, 2016A030310206, 2014A030312011, 2017YFA0102801)
- 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 › DNA and Nucleic Acid Chemistry
- Keywords
- adenine base editors, off-target effects, endonuclease V
- MeSH terms
- Gene Editing, Whole Genome Sequencing, RNA, Guide, CRISPR-Cas Systems, Adenine, Animals, Bacterial Proteins, Base Sequence, Deamination, DNA, Fibroblasts, Humans, Inosine, Sensitivity and Specificity, Genome, Human, Deoxyribonuclease (Pyrimidine Dimer), Mice, HEK293 Cells, High-Throughput Nucleotide Sequencing, Multiplex Polymerase Chain Reaction, CRISPR-Associated Proteins
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