Genome-wide analyses of PAM-relaxed Cas9 genome editors reveal substantial off-target effects by ABE8e in rice
Open accessPublished version of a preprint
Abstract
PAM-relaxed Cas9 nucleases, cytosine base editors and adenine base editors are promising tools for precise genome editing in plants. However, their genome-wide off-target effects are largely unexplored. Here, we conduct whole-genome sequencing (WGS) analyses of transgenic plants edited by xCas9, Cas9-NGv1, Cas9-NG, SpRY, nCas9-NG-PmCDA1, nSpRY-PmCDA1 and nSpRY-ABE8e in rice. Our results reveal that Cas9 nuclease and base editors, when coupled with the same guide RNA (gRNA), prefer distinct gRNA-dependent off-target sites. De novo generated gRNAs by SpRY editors lead to additional, but insubstantial, off-target mutations. Strikingly, ABE8e results in ~500 genome-wide A-to-G off-target mutations at TA motif sites per transgenic plant. ABE8e's preference for the TA motif is also observed at the target sites. Finally, we investigate the timeline and mechanism of somaclonal variation due to tissue culture, which chiefly contributes to the background mutations. This study provides a comprehensive understanding on the scale and mechanisms of off-target and background mutations occurring during PAM-relaxed genome editing in plants.
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Plasmid transfection for Cas9/sgRNA delivery in cell culture may cause accumulation of off-target mutations.
“| Delivery methods improvement | Application in cell culture [89–94] | Plasmid transfection | May cause accumulation of off-target mutations |”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as [94]
The Abstract and Results report off-target mutations from Cas9-based editing in rice plants, including substantial effects from ABE8e. But the Discussion describes Agrobacterium-mediated transformation and plant tissue culture, not plasmid transfection for Cas9/sgRNA delivery in cell culture. The paper therefore supports the off-target-mutation concern, but not the claimed delivery-method context. (LLM, conf=0.82)
Experimental — accuracy not yet measuredViral transduction for Cas9/sgRNA delivery in cell culture may cause accumulation of off-target mutations.
“| Delivery methods improvement | Application in cell culture [89–94] | Viral transduction | May cause accumulation of off-target mutations |”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as [94]
The Results section on Cas9-NG editors reports gRNA-dependent off-target mutations in edited rice plants. The Experimental procedures describe Agrobacterium-mediated transformation of rice calli, not viral transduction in cell culture, so the claimed delivery method and setting are not supported. Page numbers are unavailable in our copy. (LLM, conf=0.82)
Experimental — accuracy not yet measuredRNP electroporation for Cas9/sgRNA delivery in cell culture eliminates off-target effects.
“| Delivery methods improvement | Application in cell culture [89–94] | RNP electroporation: Rapid transfection and turnover | Eliminate off-target effects |”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as [94]
The Experimental procedures section describes Agrobacterium-mediated transformation of rice calli, not RNP electroporation in cell culture. The Results report off-target mutations from the rice editors studied, but do not test whether RNP electroporation eliminates them. Searches for RNP delivery and electroporation found no passage addressing that claim. (LLM, conf=0.77)
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Off-target effects in CRISPR/Cas9 gene editing
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“ABE catalyzes the editing from adenine to guanine and CBE converts cytosine to thymine (Komor et al., 2016; Gaudelli et al., 2017; Wu et al., 2022).”
Background
- Authors
- Wu, Y., Ren, Q., Zhong, Z., Liu, G., Han, Y., Bao, Y., Liu, L., Xiang, S., Liu, S., Tang, X., Zhou, J., Zheng, X., Sretenovic, S., Zhang, T., Qi, Y., & Zhang, Y.
- Affiliations
- Yangzhou University (CN)
- University of Electronic Science and Technology of China (CN)
- University of Maryland, College Park (US)
- Institute for Bioscience and Biotechnology Research (US)
- Corresponding author
- Zhang, Tao
- Qi, Yiping
- Zhang, Yong
- ORCID
- Venue
- Plant Biotechnology Journal
- Publisher
- Wiley
- Published
- 2022-05-23
- Volume
- 20
- Issue
- 9
- Pages
- 1670-1682
- ISSN
- 1467-7644 (ISSN-L)
- 1467-7652
- PMC
- PMC9398351
- OpenAlex
- W4229012751
- Cited by
- 56
- References
- 72
- Citations by year
- 2026: 12 · 2025: 11 · 2024: 16 · 2023: 13 · 2022: 4
- FWCI
- 3.59
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Plant Biotechnology Journal (publishedVersion, cc-by-nc)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- National Natural Science Foundation of China (32101205, 32072045, 31960423)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Genetically Modified Organisms Research
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Genetic and Mutation Studies
- Keywords
- ABE8e, rice, base editing, SpRY, somaclonal variation, background mutations, transgenic plants, genome editing
- MeSH terms
- Gene Editing, RNA, Guide, CRISPR-Cas Systems, Endonucleases, Oryza, RNA, Guide, Kinetoplastida, Plants, Genetically Modified, 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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