Evaluation and minimization of Cas9-independent off-target DNA editing by cytosine base editors
Open accessAbstract
Cytosine base editors (CBEs) enable targeted C•G-to-T•A conversions in genomic DNA. Recent studies report that BE3, the original CBE, induces a low frequency of genome-wide Cas9-independent off-target C•G-to-T•A mutation in mouse embryos and in rice. Here we develop multiple rapid, cost-effective methods to screen the propensity of different CBEs to induce Cas9-independent deamination in Escherichia coli and in human cells. We use these assays to identify CBEs with reduced Cas9-independent deamination and validate via whole-genome sequencing that YE1, a narrowed-window CBE variant, displays background levels of Cas9-independent off-target editing. We engineered YE1 variants that retain the substrate-targeting scope of high-activity CBEs while maintaining minimal Cas9-independent off-target editing. The suite of CBEs characterized and engineered in this study collectively offer ~10-100-fold lower average Cas9-independent off-target DNA editing while maintaining robust on-target editing at most positions targetable by canonical CBEs, and thus are especially promising for applications in which off-target editing must be minimized.
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The primer base editors CBE and ABE have been improved through several modifications with increased specificity and reduced deaminase-induced off-target activity.
“The primer base editors CBE and ABE have been improved a lot through several modifications with increased specificity and reduced deaminase—induced off-target activity (Doman et al., 2020).”
From Emerging applications of gene editing technologies for the development of climate-resilient crops (2025) · cites this paper as Doman et al., 2020
The Results (Human cell orthogonal R-loop assay) and Discussion report modified CBE variants with substantially reduced Cas9-independent off-target deamination. The Results (Comparison of adenine and cytosine base editors) report low off-target activity for the canonical ABE, but do not show that modifications improved ABE specificity or reduced its deaminase-induced off-target activity. (LLM, conf=0.88)
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“The primer base editors CBE and ABE have been improved a lot through several modi fi cations with increased speci fi city and reduced deaminase — induced off-target activity (Doman et al., 2020).”
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- Authors
- Doman, J. L., Raguram, A., Newby, G. A., & Liu, D. R.
- Affiliations
- Broad Institute (US)
- Corresponding author
- Liu, David R.
- Venue
- Nature Biotechnology
- Published
- 2020-02-10
- Volume
- 38
- Issue
- 5
- Pages
- 620-628
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC7335424
- OpenAlex
- W3004494456
- Cited by
- 473
- References
- 59
- Citations by year
- 2026: 68 · 2025: 70 · 2024: 64 · 2023: 82 · 2022: 70 · 2021: 71 · 2020: 47
- FWCI
- 21.90
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion)
- Funders
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases (U01 AI142756)
- U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (RM1 HG009490)
- U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (R35 GM118062)
- Howard Hughes Medical Institute (Liu investigatorship)
- 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 › Epigenetics and DNA Methylation
- Keywords
- cytosine base editors, BE3, genome editing safety, Escherichia coli, human cells
- MeSH terms
- Gene Editing, Whole Genome Sequencing, CRISPR-Associated Protein 9, Cytosine, Escherichia coli, Humans, Mutation, HEK293 Cells
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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