Circular RNA-mediated inverse prime editing in human cells

Ronghong Liang, Shan Wang, Yibo Cai, Zhenyu Li, Ka Ming Li, Jingjing Wei, Chao Sun, Haocheng Zhu, Kunling Chen and Caixia Gao ()
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Ronghong Liang: Chinese Academy of Sciences
Shan Wang: Chinese Academy of Sciences
Yibo Cai: Chinese Academy of Sciences
Zhenyu Li: Chinese Academy of Sciences
Ka Ming Li: University of Chinese Academy of Sciences
Jingjing Wei: Chinese Academy of Sciences
Chao Sun: Chinese Academy of Sciences
Haocheng Zhu: Chinese Academy of Sciences
Kunling Chen: Chinese Academy of Sciences
Caixia Gao: Chinese Academy of Sciences

Nature Communications, 2025, vol. 16, issue 1, 1-11

Abstract: Abstract Prime editors are restricted to performing precise edits downstream of cleavage sites, thereby limiting their editing scope. Therefore, we develop inverse prime editors (iPEs) that act upstream of the nickase cleavage site by replacing nCas9-H840A with nCas9-D10A, but the editing efficiencies are limited. To address this limitation, we develop circular RNA-mediated iPEs (ciPEs), achieving editing efficiencies ranging from 0.1% to 24.7%. Further optimization using Rep-X helicase increases editing efficiencies to a range of 2.7%–55.4%. The Rep-X-assisted ciPE system thus expands the scope of editing and improves efficiencies at genomic sites that are previously difficult to target. The Rep-X-assisted ciPE system will complement canonical PE system in enabling more extensive and efficient editing across a wider range of the human genome.

Date: 2025
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DOI: 10.1038/s41467-025-59120-7

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