Prime editor with rational design and AI-driven optimization for reverse editing window and enhanced fidelity
Abstract Prime editing (PE) is a precise tool for introducing genetic mutations in eukaryotes. Extending the efficient editing scope and mitigating undesired byproducts are possible. We introduce reverse PE (rPE), a SpCas9-directed variant that enabled DNA editing at the 3′ direction of HNH-mediated...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-06-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-60495-w |
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| _version_ | 1850225873735647232 |
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| author | Chao Yang Qingxiao Fang Mengyu Li Jin Zhang Rui Li Tianxing Zhou Keshan Wang Jie Deng Xiuchao Wang Chongbiao Huang Yukuan Feng Xiaoping Zhang Lei Shi Changhao Bi Xueli Zhang Jun Yu Jihui Hao |
| author_facet | Chao Yang Qingxiao Fang Mengyu Li Jin Zhang Rui Li Tianxing Zhou Keshan Wang Jie Deng Xiuchao Wang Chongbiao Huang Yukuan Feng Xiaoping Zhang Lei Shi Changhao Bi Xueli Zhang Jun Yu Jihui Hao |
| author_sort | Chao Yang |
| collection | DOAJ |
| description | Abstract Prime editing (PE) is a precise tool for introducing genetic mutations in eukaryotes. Extending the efficient editing scope and mitigating undesired byproducts are possible. We introduce reverse PE (rPE), a SpCas9-directed variant that enabled DNA editing at the 3′ direction of HNH-mediated nick site. The rPE leveraging nCas9-D10A and rPE gRNA targeting the 5′ direction of HNH-mediated nick site inscribes genetic alterations, achieving a reverse editing window and potentially high fidelity. HNH and reverse transcriptase engineered using protein language models in conjunction with La facilitate circular erPEmax and erPE7max, achieving editing efficiency up to 44.41% without nick gRNA or positive selection. Furthermore, our findings underscore the capability of rPE in inserting functionally enhanced variant (PIK3CD E527G) for cell therapy. By expanding the editing scope and enhancing genomic manipulability, rPE represents a meaningful advancement in prime editing, improving its utility for research and therapeutic applications. |
| format | Article |
| id | doaj-art-c7aaa2cd93b34ec086adcc446191f9fc |
| institution | OA Journals |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-c7aaa2cd93b34ec086adcc446191f9fc2025-08-20T02:05:13ZengNature PortfolioNature Communications2041-17232025-06-0116111410.1038/s41467-025-60495-wPrime editor with rational design and AI-driven optimization for reverse editing window and enhanced fidelityChao Yang0Qingxiao Fang1Mengyu Li2Jin Zhang3Rui Li4Tianxing Zhou5Keshan Wang6Jie Deng7Xiuchao Wang8Chongbiao Huang9Yukuan Feng10Xiaoping Zhang11Lei Shi12Changhao Bi13Xueli Zhang14Jun Yu15Jihui Hao16Pancreas Center, Tianjin Medical University Cancer Institute and HospitalPancreas Center, Tianjin Medical University Cancer Institute and HospitalPancreas Center, Tianjin Medical University Cancer Institute and HospitalPancreas Center, Tianjin Medical University Cancer Institute and HospitalCollege of Biotechnology, Tianjin University of Science and TechnologyPancreas Center, Tianjin Medical University Cancer Institute and HospitalDepartment of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologySchool of Chemistry and Chemical Engineering, Huazhong University of Science and TechnologyPancreas Center, Tianjin Medical University Cancer Institute and HospitalPancreas Center, Tianjin Medical University Cancer Institute and HospitalPancreas Center, Tianjin Medical University Cancer Institute and HospitalDepartment of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyState Key Laboratory of Experimental HematologyTianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesPancreas Center, Tianjin Medical University Cancer Institute and HospitalPancreas Center, Tianjin Medical University Cancer Institute and HospitalAbstract Prime editing (PE) is a precise tool for introducing genetic mutations in eukaryotes. Extending the efficient editing scope and mitigating undesired byproducts are possible. We introduce reverse PE (rPE), a SpCas9-directed variant that enabled DNA editing at the 3′ direction of HNH-mediated nick site. The rPE leveraging nCas9-D10A and rPE gRNA targeting the 5′ direction of HNH-mediated nick site inscribes genetic alterations, achieving a reverse editing window and potentially high fidelity. HNH and reverse transcriptase engineered using protein language models in conjunction with La facilitate circular erPEmax and erPE7max, achieving editing efficiency up to 44.41% without nick gRNA or positive selection. Furthermore, our findings underscore the capability of rPE in inserting functionally enhanced variant (PIK3CD E527G) for cell therapy. By expanding the editing scope and enhancing genomic manipulability, rPE represents a meaningful advancement in prime editing, improving its utility for research and therapeutic applications.https://doi.org/10.1038/s41467-025-60495-w |
| spellingShingle | Chao Yang Qingxiao Fang Mengyu Li Jin Zhang Rui Li Tianxing Zhou Keshan Wang Jie Deng Xiuchao Wang Chongbiao Huang Yukuan Feng Xiaoping Zhang Lei Shi Changhao Bi Xueli Zhang Jun Yu Jihui Hao Prime editor with rational design and AI-driven optimization for reverse editing window and enhanced fidelity Nature Communications |
| title | Prime editor with rational design and AI-driven optimization for reverse editing window and enhanced fidelity |
| title_full | Prime editor with rational design and AI-driven optimization for reverse editing window and enhanced fidelity |
| title_fullStr | Prime editor with rational design and AI-driven optimization for reverse editing window and enhanced fidelity |
| title_full_unstemmed | Prime editor with rational design and AI-driven optimization for reverse editing window and enhanced fidelity |
| title_short | Prime editor with rational design and AI-driven optimization for reverse editing window and enhanced fidelity |
| title_sort | prime editor with rational design and ai driven optimization for reverse editing window and enhanced fidelity |
| url | https://doi.org/10.1038/s41467-025-60495-w |
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