Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos
Open accessAbstract
Spotting off-targets from gene editing: Unintended genomic modifications limit the potential therapeutic use of gene-editing tools. Available methods to find off-targets generally do not work in vivo or detect single-nucleotide changes. Three papers in this issue report new methods for monitoring gene-editing tools in vivo (see the Perspective by Kempton and Qi). Wienert et al. followed the recruitment of a DNA repair protein to DNA breaks induced by CRISPR-Cas9, enabling unbiased detection of off-target editing in cellular and animal models. Zuo et al. identified off-targets without the interference of natural genetic heterogeneity by injecting base editors into one blastomere of a two-cell mouse embryo and leaving the other genetically identical blastomere unedited. Jin et al. performed whole-genome sequencing on individual, genome-edited rice plants to identify unintended mutations. Cytosine, but not adenine, base editors induced numerous single-nucleotide variants in both mouse and rice. Science , this issue p. 286 , p. 289 , p. 292 ; see also p. 234
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These reports and early-stage patient data highlight the gap between animal studies and applications in humans and underscore the need for improved methods for in situ delivery.
“Although promising, these reports, as well as early-stage data from patients treated with in vivo gene editing using ZFNs, highlight the gap between animal studies and applications in humans 51-53 and underscore the need for improved methods for in situ delivery, as discussed in the next section.”
From The promise and challenge of therapeutic genome editing (2020) · cites this paper as [51]
The paper’s Abstract (page not provided) reports substantial off-target variants from cytosine base editing in mouse embryos and says their frequency requires a solution to address editing fidelity. That supports a concern about applying this approach therapeutically, but the paper does not assess the gap between animal studies and human applications, report patient data, or identify in situ delivery as the needed improvement. (LLM, conf=0.77)
Experimental — accuracy not yet measuredAAV delivery in vivo may cause accumulation of off-target mutations.
“| Delivery methods improvement | Application in vivo [95–105] | AAV: Last for years in terminally differentiated cell types | May cause accumulation of off-target mutations |”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as [104]
The paper reports substantial off-target single-nucleotide variants after BE3 editing in mouse embryos (Abstract; page unavailable). It delivered the editors by injection into embryonic cells, not by AAV, and does not examine whether mutations accumulate during long-term AAV expression. Thus it supports the off-target-mutation concern, but not the AAV-specific claim. (LLM, conf=0.86)
Experimental — accuracy not yet measuredPreviously it has been shown that cytidine but not adenine base editors result in significant, genome-wide, off-target effects.
“Previously it has been shown that cytidine but not adenine base editors result in significant, genome-wide, off-target effects57,69.”
From One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids (2023) · cites this paper as [69]
The Abstract reports genome-wide sequencing of mouse embryos and finds substantially more off-target SNVs after cytosine base editing than after adenine base editing. The comparison was between BE3 and ABE7.10 in mouse embryos; it does not establish the same result for all cytidine and adenine base editors or settings. (LLM, conf=0.85)
Experimental — accuracy not yet measuredLNP delivery in vivo eliminates off-target effects.
“| Delivery methods improvement | Application in vivo [95–105] | LNP: Can be quickly degraded in vivo | Eliminate off-target effects |”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as [104]
The Abstract (page not supplied) describes injection into mouse embryo blastomeres and reports substantial off-target variants after cytosine base editing. Searches for LNP delivery, degradation, and elimination of off-target effects found no passage testing or addressing the LNP-specific claim. (LLM, conf=0.76)
Experimental — accuracy not yet measuredAAV delivery in vivo lasts for years in terminally differentiated cell types.
“| Delivery methods improvement | Application in vivo [95–105] | AAV: Last for years in terminally differentiated cell types | May cause accumulation of off-target mutations |”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as [104]
The paper’s Abstract describes base-editor injection into two-cell mouse embryos and off-target variants measured at embryonic day 14.5. Searches for AAV delivery, years-long persistence, and terminally differentiated cells found no passage addressing the attributed claim. (LLM, conf=0.76)
Experimental — accuracy not yet measured
LNP delivery in vivo can be quickly degraded.
“| Delivery methods improvement | Application in vivo [95–105] | LNP: Can be quickly degraded in vivo | Eliminate off-target effects |”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as [104]
The study description (section labeled Abstract; page unavailable) says the editors were injected into mouse embryos and reports off-target mutations, not lipid nanoparticle delivery or degradation. Searches for LNP delivery and rapid degradation in vivo found no passage addressing the claim. (LLM, conf=0.74)
Experimental — accuracy not yet measured
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- Authors
- Zuo, E., Sun, Y., Wei, W., Yuan, T., Ying, W., Sun, H., Yuan, L., Steinmetz, L. M., Li, Y., & Yang, H.
- Affiliations
- Chinese Academy of Sciences (CN)
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
- Agricultural Genomics Institute at Shenzhen (CN)
- University of California San Diego (US)
- Shanghai Institutes for Biological Sciences (CN)
- European Molecular Biology Laboratory (DE)
- Fudan University (CN)
- Corresponding author
- Zuo, Erwei
- Sun, Yidi
- Yuan, Tanglong
- Steinmetz, Lars M.
- Li, Yixue
- Yang, Hui
- ORCID
- Venue
- Science
- Published
- 2019-04-19
- Volume
- 364
- Issue
- 6437
- Pages
- 289-292
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC7301308
- OpenAlex
- W2916364858
- Cited by
- 782
- References
- 35
- Citations by year
- 2026: 69 · 2025: 70 · 2024: 88 · 2023: 105 · 2022: 90 · 2021: 113 · 2020: 150 · 2019: 96
- FWCI
- 37.24
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Human Genome Research Institute (P01HG000205)
- 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 › Genetics › Animal Genetics and Reproduction
- Keywords
- cytosine base editors, off-target effects, single nucleotide variants, CRISPR/Cas9, mouse embryo, genome editing, DNA repair, whole genome sequencing
- MeSH terms
- Gene Editing, CRISPR-Associated Protein 9, Animals, Blastomeres, Cytosine, DNA Mutational Analysis, Embryo, Mammalian, Female, Male, Mice, Inbred C57BL, Mutation, Polymorphism, Single Nucleotide, Mice, Genome-Wide Association Study, CRISPR-Cas Systems
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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