Base Editing

Base Editing


Base editing technology induces precise base substitutions to achieve genome editing through combining two moieties, "effector" and "locator".


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CRISPR-mediated Gene Editing and Base Editing


More than 75,000 genetic mutations are corelated with human diseases and around half of these diseases are caused by point mutations, which are hard to be fixed by traditional gene editing tools. Base editing technology can realize single base pair change in human genome in a precise and permanent manner. Thus, base editing technology provides great potential for the cure of hereditary diseases and the immunotherapy of cancer.


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Our Technology

Our Base Editing Systems


Our scientific founders have developed five series base editing systems, including enhanced Base Editor (eBE), dCpf1 Base Editor (dCpf1-BE), human APOBEC3A Base Editor (hA3A-BE), BEACON, transformer Base Editor (tBE).

transformer Base Editor (tBE) with Ultra-high Editing Precision


tBE was developed with ultra-high editing precision to eliminate both gRNA-dependent and gRNA-independent off-target mutations (tBE, Nature Cell Biology, 2021). Through a cleavable “lock”, tBE becomes active only at on-target sites to induce highly efficient editing. When binding at off-target sites, tBE was “locked” to avoid triggering off-target mutations. Like a “Transformer”, tBE has great flexibility to suit for different kinds of deliver methods such as AAV and mRNA/LNP. Furthermore, tBE can simultaneously edit multiple target sites with high efficiency. These characters greatly expand the scope of tBE’s clinical application. 


图片关键词


▲ transformer Base Editor (tBE) of Correctseq

（Han et al., Nature Protocols, 2023）


Gene Therapy

Base Editing Therapy


With traditional transgene therapy, the original mutations still exist, which makes it hard to be applied to treat the hereditary diseases caused by dominant-negative mutations. Also, the lifelong effect of transgene therapy is yet to be validated. Comparing with transgene therapy, base editing therapy which can be applied in vivo and ex vivo fixes the mutations directly and can cure various genetic diseases for a lifelong effect. Compared with Cas Nuclease gene editing therapy, tBE exhibits undetected off-target mutations, higher editing efficiency and better therapeutic effect, and lower cytotoxicity.



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Scientific Publications

  Research Articles
  Reviews, Comments, Interviews

1. Guangye Li#, Guo Chen#, Guo-Hua Yuan#, Jia Wei#, Qingyang Ni, Jing Wu, Bei Yang, Li Yang*, Jia Chen*. Specific and efficient RNA A-to-I editing through cleavage of an ADAR inhibitor. Nat Biotechnol, 2025, doi: 10.1038/s41587-025-02591-2.

 

2. Yuhang Fan#, Wenchao Xu#, Bao-Qing Gao#, Huichao Qin, Xiaoyi Wu, Jia Wei, Qingyang Ni, Lina Zhou, Jiangchao Xiang, Jing Wu, Bei Yang, Li Yang, Jia Chen*. Leveraging base excision repair for efficient adenine base editing of mitochondrial DNA. Nat Biotechnol, 2025, doi: 10.1038/s41587-025-02608-w.

 

3. Qimingxing Chen#, Yan Chang#, Xiaoyan He, Yan Ding, Runyuan Wang, Ran Luo, Jialu Yuan, Jiabei Chen, Guisheng Zhong, Huiying Yang, Jia Chen*, Jianfeng Li*. Targeted delivery of mRNA with polymer–lipid nanoparticles for in vivo base editing. ACS NANO, Feb 2025, 19(8): 7835–7850.

 

4. Wenyan Han#, Hou-Yuan Qiu#, Shangwu Sun#, Zhi-Can Fu#, Guo-Quan Wang#, Xiaowen Qian#, Lijie Wang, Xiaowen Zhai, Jia Wei, Yichuan Wang, Yi-Lin Guo, Guo-Hua Cao, Rui-Jin Ji, Yi-Zhou Zhang, Hongxia Ma, Hongsheng Wang, Mingli Zhao, Jing Wu, Lili Bi, Qiu-Bing Chen, Zifeng Li, Ling Yu, Xiaodun Mou, Hao Yin, Li Yang*, Jia Chen*, Bei Yang*, Ying Zhang*. Therapeutic base editing of the HBG promoter reactivates γ-globin expression with no detectable off-target mutations in beta-thalassemia HSCs. Cell Stem Cell, 2023, 30(12): 1624-1639.e8.

 

5. Wenyan Han#, Baoqing Gao#, Junjie Zhu#, Zongxing He#, Jianfeng Li*, Li Yang*, Jia Chen*. Design and application of the transformer base editor in mammalian cells and mice. Nat Protoc, 2023, 18(11): 3194-3228.

 

6. Wenwen Zhao#, Jifang Li#, Xiao Wang#, Wei Xu#, Baoqing Gao#, Jiangchao Xiang, Yaofeng Hou, Wei Liu, Jing Wu, Qilian Qi, Jia Wei, Xiaoyu Yang, Lu Lu*, Li Yang*, Jia Chen*, Bei Yang*. Prime editor-mediated functional reshaping of ACE2 prevents the entry of multiple human coronaviruses, including SARS-CoV-2variants. MedComm, 2023, 4: e356.

 

7. Xiaosa Li#*, Lina Zhou#, Bao-Qing Gao#, Guangye Li, Xiao Wang, Ying Wang, Jia Wei, Wenyan Han, Zixian Wang, Jifang Li, Runze Gao, Junjie Zhu, Wenchao Xu, Jing Wu, Bei Yang, Xiaodong Sun*, Li Yang*, Jia Chen*. Highly efficient prime editing by introducing same-sense mutations in pegRNA or stabilizing its structure. Nat Commun, 2022, 13: 1669


8. Runze Gao#, Zhi-Can Fu#, Xiangyang Li#, Ying Wang#, Jia Wei, Guangye Li, Lijie Wang, Jing Wu, Xingxu Huang*, Li Yang*, and Jia Chen*. Genomic and transcriptomic analyses of prime editing guide RNA-independent off-target effects by prime editors. CRISPR J, 2022, 5(2): 276-293.


9. Jinlin Wang#, Zhou He#, Guoquan Wang#, Ruiwen Zhang#, Junyi Duan, Pan Gao, Xinlin Lei, Houyuan Qiu, Chuanping Zhang, Ying Zhang & Hao Yin*. Efficient targeted insertion of large DNA fragments without DNA donors. Nat Methods, 2022, 19(3): 331-340.

 

10. Xiang Gao#, Xu-Kai Ma#, Xiang Li, Guo-Wei Li, Chu-Xiao Liu, Jun Zhang, Ying Wang, Jia Wei, Jia Chen, Ling-Ling Chen & Li Yang*. Knockout of circRNAs by base editing back-splice sites of circularized exons. Genome Biol, 2022, 23: 16.

 

11. Lijie Wang#, Wei Xue#, Hongxia Zhang#, Runze Gao#, Houyuan Qiu#, Jia Wei, Lina Zhou, Yun-Ni Lei, Xiaocheng Wu, Xiao Li, Chengfang Liu, Jing Wu, Qiubing Chen, Hanhui Ma, Xingxu Huang, Cheguo Cai, Ying Zhang, Bei Yang*, Hao Yin*, Li Yang* & Jia Chen*. Eliminating base-editor-induced genome-wide and transcriptome-wide off-target mutations. Nat Cell Biol, 2021, 23(5): 552-563.

 

12. Xiao Wang#, Chengfeng Ding#, Wenxia Yu#, Ying Wang#, Siting He#, Bei Yang#, Yi-Chun Xiong, Jia Wei, Jifang Li, Jiayi Liang, Zongyang Lu, Wei Zhu, Jing Wu, Zhi Zhou, Xingxu Huang, Zhen Liu*, Li Yang* & Jia Chen*. Cas12a Base editors induce efficient and specific editing with low DNA damage response. Cell Rep, 2020, 31(9): 107723.

 

13. Chun-Qing Song#, Tingting Jiang#, Michelle Richter, Luke H Rhym, Luke W Koblan, Maria Paz Zafra, Emma M Schatoff, Jordan L Doman, Yueying Cao, Lukas E Dow, Lihua Julie Zhu, Daniel G Anderson, David R Liu*, Hao Yin*, Wen Xue*. Adenine base editing in an adult mouse model of tyrosinaemia. Nat Biomed Eng, 2020, 4: 125-130.

 

14. Ying Wang#, Runze Gao#, Jing Wu#, Yi-Chun Xiong, Jia Wei, Sipin Zhang, Bei Yang, Jia Chen* and Li Yang*. Comparison of cytosine base editors and development of the BEable-GPS database for targeting pathogenic SNVs. Genome Biol, 2019, 20(1): 218.

 

15. Xiao Wang#, Jianan Li#, Ying Wang#, Bei Yang#, Jia Wei#, Jing Wu, Ruixuan Wang, Xingxu Huang*, Jia Chen* and Li Yang*. Efficient base editing in methylated regions with a human APOBEC3A-Cas9 fusion. Nat Biotechnol, 2018, 36(10): 946-949.

 

16. Xiaosa Li#, Ying Wang#, Yajing Liu#, Bei Yang#, Xiao Wang, Jia Wei, Zongyang Lu, Yuxi Zhang, Jing Wu, Xingxu Huang*, Li Yang* and Jia Chen*. Base editing with a Cpf1-cytidine deaminase fusion. Nat Biotechnol, 2018, 36(4): 324-327.

 

17. Jian-Feng Xiang#, Qin Yang#, Chu-Xiao Liu#, Man Wu, Ling-Ling Chen*, Li Yang*. N(6)-Methyladenosines Modulate A-to-I RNA Editing. Mol Cell, 2018, 69(1): 126-135 e126.

 

18. Liqun Lei#, Hongquan Chen#, Wei Xue#, Bei Yang#, Bian Hu#, Jia Wei, Lijie Wang, Yiqiang Cui, Wei Li, Jianying Wang, Lei Yan, Wanjing Shang, Jimin Gao, Jiahao Sha, Min Zhuang, Xingxu Huang, Bin Shen*, Li Yang* and Jia Chen*. APOBEC3 induces mutations during repair of CRISPR-Cas9-generated DNA breaks. Nat Struct Mol Biol, 2018, 25(1): 45-52.

 

19. Hao Yin#, Chun-Qing Song#, Sneha Suresh, Suet-Yan Kwan, Qiongqiong Wu, Stephen Walsh, Junmei Ding, Roman L Bogorad, Lihua Julie Zhu, Scot A Wolfe, Victor Koteliansky, Wen Xue*, Robert Langer* & Daniel G Anderson*. Partial DNA-guided Cas9 enables genome editing with reduced off-target activity. Nat Chem Biol, 2018, 14(3): 311-316.

 

20. Lijie Wang#, Wei Xue#, Lei Yan#, Xiaosa Li, Jia Wei, Miaomiao Chen, Jing Wu, Bei Yang*, Li Yang* and Jia Chen*. Enhanced base editing by co-expression of free uracil DNA glycosylase inhibitor. Cell Res, 2017, 27(10): 1289-1292.

 

21. Hao Yin, Chun-Qing Song, Sneha Suresh, Qiongqiong Wu, Stephen Walsh, Luke Hyunsik Rhym, Esther Mintzer, Mehmet Fatih Bolukbasi, Lihua Julie Zhu, Kevin Kauffman, Haiwei Mou, Alicia Oberholzer, Junmei Ding, Suet-Yan Kwan, Roman L Bogorad, Timofei Zatsepin, Victor Koteliansky, Scot A Wolfe, Wen Xue, Robert Langer & Daniel G Anderson*. Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing. Nat Biotechnol, 2017, 35(12): 1179-1187.

 

22. Hao Yin, Chun-Qing Song, Joseph R Dorkin, Lihua J Zhu, Yingxiang Li, Qiongqiong Wu, Angela Park, Junghoon Yang, Sneha Suresh, Aizhan Bizhanova, Ankit Gupta, Mehmet F Bolukbasi, Stephen Walsh, Roman L Bogorad, Guangping Gao, Zhiping Weng, Yizhou Dong, Victor Koteliansky, Scot A Wolfe, Robert Langer, Wen Xue* & Daniel G Anderson*. Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo. Nat Biotechnol, 2016, 34(3): 328-33.

 

23. Xiao-Ou Zhang#, Hai-Bin Wang#, Yang Zhang, Xuhua Lu, Ling-Ling Chen*, and Li Yang*. Complementary sequence-mediated exon circularization. Cell, 2014, 159(1): 134-147.

 

24. Hao Yin#, Wen Xue#, Sidi Chen, Roman L Bogorad, Eric Benedetti, Markus Grompe, Victor Koteliansky, Phillip A Sharp, Tyler Jacks & Daniel G Anderson*. Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype. Nat Biotechnol, 2014, 32(6): 551-553.

 

25. Wen Xue#, Sidi Chen#, Hao Yin#, Tuomas Tammela, Thales Papagiannakopoulos, Nikhil S. Joshi, Wenxin Cai, Gillian Yang, Roderick Bronson, Denise G. Crowley, Feng Zhang, Daniel G. Anderson, Phillip A. Sharp & Tyler Jacks*. CRISPR-mediated direct mutation of cancer genes in the mouse liver. Nature, 2014, 514(7522): 380-384.

 

26. Jia Chen, Brendan F. Miller and Anthony V. Furano*. Repair of naturally occurring mismatches can induce mutations in flanking DNA. Elife, 2014, 3: e02001.


(#: co-first author, *: corresponding author)

1. Chengfang Liu#, Sifan Cheng#, Junjie Zhu, Lina Zhou, Jia Chen*. A quick guide to evaluating prime editing efficiency in mammalian cells. Methods in Enzymology, 2025, 712: 419-436

 

2. Jiangchao Xiang#, Wenchao Xu#, Jing Wu#, Yaxin Luo, Bei Yang*, Jia Chen*. Nucleoside deaminases: the key players in base editing toolkit. Biophys Rep, 2023, 9(6): 325-337.

 

3. Jin-Soo Kim*, Jia Chen*. Base editing of organellar DNA with programmable deaminases. Nat Rev Mol Cell Biol, 2024, 25(1): 34-45.

 

4. Li Yang*, Jia Chen*. Expanding genome editing scopes with artificial intelligence. Sci Bull, 2023, 68(23): 2881-2883.

 

5. Caixia Gao* & Jia Chen*. CRISPR adventures in China. CRISPR J, 2021, 4: 304-306

 

6. Qiubing Chen, Ying Zhang* and Hao Yin*. Recent advances in chemical modifications of guide RNA, mRNA and donor template for CRISPR-mediated genome editing. Adv Drug Deliv Rev, 2021, 168: 246-258.

 

7. Li Yang* & Jia Chen*. A tale of two moieties: rapidly evolving CRISPR/Cas-based genome editing. Trends Biochem Sci, 2020, 45: 874-888

 

8. Li Yang*, Bei Yang* and Jia Chen*. One prime for all editing. Cell, 2019, 179: 1448-1450

 

9. Jia Chen*, Bei Yang* and Li Yang*. To BE or not to BE, that is the question. Nat Biotechnol, 2019, 37: 520-522

 

10. Bei Yang*, Li Yang* and Jia Chen*. Development and application of base editors. CRISPR J, 2019, 2: 91-104

 

11. Hong-Xia Zhang, Ying Zhang* and Hao Yin*. Genome editing with mRNA encoding ZFN, TALEN, and Cas9. Mol Ther, 2019, 27(4): 735-746.

 

12. Hao Yin*, Wen Xue* and Daniel G. Anderson*. CRISPR-Cas: a tool for cancer research and therapeutics. Nat Rev Clin Oncol, 2019, 16(5): 281-295.

 

13. Jia Chen, Weizhi Ji, Prashant Mali and April Pawluk. The future of genome editing. Cell, 2018, 173: 1311-1313

 

14. Bei Yang*, Xiaosa Li, Liqun Lei and Jia Chen*. APOBEC: from mutator to editor. J Genet Genomics, 2017, 44: 423-437


15. Hao Yin, Kevin J. Kauffman and Daniel G. Anderson*. Delivery technologies for genome editing. Nat Rev Drug Discov, 2017, 16(6): 387-399.

 

16. Hao Yin, Rosemary L Kanasty, Ahmed A Eltoukhy, Arturo J Vegas, J Robert Dorkin and Daniel G Anderson*. Non-viral vectors for gene-based therapy. Nat Rev Genet, 2014, 15(8): 541-555.

 

(#: co-first author, *: corresponding author)

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