ArticlePlant biotechnology journal2022
Genome-wide analyses of PAM-relaxed Cas9 genome editors reveal substantial off-target effects by ABE8e in rice.
Article in Plant biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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37 citing papers in PubMed, 51 citations in OpenAlex.
- Enhancing CRISPR-Cas12a base editing in plants with LbCas12a variants and introns.Journal of integrative plant biology · 2026Article
- Enhanced exonuclease-Cas9 systems promote multiple nucleotide deletions with higher efficiency and broader targeting scope in plants.Journal of integrative plant biology · 2026Article
- The future of pediatric gene therapy: CRISPR-Cas9, AI, and personalized medicine.Pediatric research · 2026Review
- PCdb: A comprehensive plant genome-editing database integrating sgRNA efficiency, off-target predictions, and epigenomic landscapes.Plant communications · 2026Article
- Cas9-Embedding Hyperactive TadA8e Confers Efficient and Highly Specific A-To-G Base Editing in Rice.Plant biotechnology journal · 2026Article
- Functional correction and genome integrity with duplex base editing of β-thalassemic hematopoietic stem cells.Genome biology · 2026Article
- Review
- Engineering Adenine Deaminase TadA for Precise and PAM-Flexible Point Mutagenesis and Gradient-Tuning Endogenous Protein Design.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- CRISPR/Cas genome editing in soybean: challenges and new insights to overcome existing bottlenecks.Journal of advanced research · 2025Review
- Article
- Cas9-Rep fusion tethers donor DNA in vivo and boosts the efficiency of HDR-mediated genome editing.Plant biotechnology journal · 2025Article
- A universal and wide-range cytosine base editor via domain-inlaid and fidelity-optimized CRISPR-FrCas9.Nature communications · 2025Article
- Versatile plant genome engineering using anti-CRISPR-Cas12a systems.Science China. Life sciences · 2024Article
- PhieDBEs: a DBD-containing, PAM-flexible, high-efficiency dual base editor toolbox with wide targeting scope for use in plants.Plant biotechnology journal · 2024Article
- Comprehensive evaluation and prediction of editing outcomes for near-PAMless adenine and cytosine base editors.Communications biology · 2024Article
- High-fidelity PAMless base editing of hematopoietic stem cells to treat chronic granulomatous disease.Science translational medicine · 2024Article
- Expanding plant genome editing scope and profiles with CRISPR-FrCas9 systems targeting palindromic TA sites.Plant biotechnology journal · 2024Article
- Base editing correction of OCRL in Lowe syndrome: ABE-mediated functional rescue in patient-derived fibroblasts.Human molecular genetics · 2024Article
- High performance TadA-8e derived cytosine and dual base editors with undetectable off-target effects in plants.Nature communications · 2024Article
- Boosting genome editing in plants with single transcript unit surrogate reporter systems.Plant communications · 2024Article
Corrections and comments
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Authors and funding
16 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
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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