Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice

Shuai Jin, Yuan Zong, Qiang Gao, Zixu Zhu, Yanpeng Wang, Peng Qin, Chengzhi Liang, Daowen Wang, Jin Long Qiu, Feng Zhang, Caixia Gao

Research output: Contribution to journalArticlepeer-review

455 Scopus citations


Cytosine and adenine base editors (CBEs and ABEs) are promising new tools for achieving the precise genetic changes required for disease treatment and trait improvement. However, genome-wide and unbiased analyses of their off-target effects in vivo are still lacking. Our whole-genome sequencing analysis of rice plants treated with the third-generation base editor (BE3), high-fidelity BE3 (HF1-BE3), or ABE revealed that BE3 and HF1-BE3, but not ABE, induce substantial genome-wide off-target mutations, which are mostly the C→T type of single-nucleotide variants (SNVs) and appear to be enriched in genic regions. Notably, treatment of rice with BE3 or HF1-BE3 in the absence of single-guide RNA also results in the rise of genome-wide SNVs. Thus, the base-editing unit of BE3 or HF1-BE3 needs to be optimized in order to attain high fidelity.

Original languageEnglish (US)
Pages (from-to)292-295
Number of pages4
Issue number6437
StatePublished - 2019

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© 2019 American Association for the Advancement of Science. All rights reserved.


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