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Development of deaminase-free T-to-S base editor and C-to-G base editor by engineered human uracil DNA glycosylase

Author

Listed:
  • Huawei Tong

    (Ltd.)

  • Haoqiang Wang

    (Ltd.)

  • Xuchen Wang

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Nana Liu

    (Ltd.)

  • Guoling Li

    (Ltd.)

  • Danni Wu

    (Ltd.)

  • Yun Li

    (Ltd.)

  • Ming Jin

    (Fujian Medical University)

  • Hengbin Li

    (Ltd.)

  • Yinghui Wei

    (Northwest A&F University
    Northwest A&F University)

  • Tong Li

    (Ltd.)

  • Yuan Yuan

    (Ltd.)

  • Linyu Shi

    (Ltd.)

  • Xuan Yao

    (Ltd.)

  • Yingsi Zhou

    (Ltd.)

  • Hui Yang

    (Ltd.
    Chinese Academy of Sciences)

Abstract

DNA base editors enable direct editing of adenine (A), cytosine (C), or guanine (G), but there is no base editor for direct thymine (T) editing currently. Here we develop two deaminase-free glycosylase-based base editors for direct T editing (gTBE) and C editing (gCBE) by fusing Cas9 nickase (nCas9) with engineered human uracil DNA glycosylase (UNG) variants. By several rounds of structure-informed rational mutagenesis on UNG in cultured human cells, we obtain gTBE and gCBE with high activity of T-to-S (i.e., T-to-C or T-to-G) and C-to-G conversions, respectively. Furthermore, we conduct parallel comparison of gTBE/gCBE with those recently developed using other protein engineering strategies, and find gTBE/gCBE show the outperformance. Thus, we provide several base editors, gTBEs and gCBEs, with corresponding engineered UNG variants, broadening the targeting scope of base editors.

Suggested Citation

  • Huawei Tong & Haoqiang Wang & Xuchen Wang & Nana Liu & Guoling Li & Danni Wu & Yun Li & Ming Jin & Hengbin Li & Yinghui Wei & Tong Li & Yuan Yuan & Linyu Shi & Xuan Yao & Yingsi Zhou & Hui Yang, 2024. "Development of deaminase-free T-to-S base editor and C-to-G base editor by engineered human uracil DNA glycosylase," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49343-5
    DOI: 10.1038/s41467-024-49343-5
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    1. Nana Yan & Hu Feng & Yongsen Sun & Ying Xin & Haihang Zhang & Hongjiang Lu & Jitan Zheng & Chenfei He & Zhenrui Zuo & Tanglong Yuan & Nana Li & Long Xie & Wu Wei & Yidi Sun & Erwei Zuo, 2023. "Cytosine base editors induce off-target mutations and adverse phenotypic effects in transgenic mice," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    2. Liwei Chen & Jung Eun Park & Peter Paa & Priscilla D. Rajakumar & Hong-Ting Prekop & Yi Ting Chew & Swathi N. Manivannan & Wei Leong Chew, 2021. "Programmable C:G to G:C genome editing with CRISPR-Cas9-directed base excision repair proteins," Nature Communications, Nature, vol. 12(1), pages 1-7, December.
    3. Minh Thuan Nguyen Tran & Mohd Khairul Nizam Mohd Khalid & Qi Wang & Jacqueline K. R. Walker & Grace E. Lidgerwood & Kimberley L. Dilworth & Leszek Lisowski & Alice Pébay & Alex W. Hewitt, 2020. "Engineering domain-inlaid SaCas9 adenine base editors with reduced RNA off-targets and increased on-target DNA editing," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    4. Shuo Li & Bo Yuan & Jixin Cao & Jingqi Chen & Jinlong Chen & Jiayi Qiu & Xing-Ming Zhao & Xiaolin Wang & Zilong Qiu & Tian-Lin Cheng, 2020. "Docking sites inside Cas9 for adenine base editing diversification and RNA off-target elimination," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    5. Tanglong Yuan & Nana Yan & Tianyi Fei & Jitan Zheng & Juan Meng & Nana Li & Jing Liu & Haihang Zhang & Long Xie & Wenqin Ying & Di Li & Lei Shi & Yongsen Sun & Yongyao Li & Yixue Li & Yidi Sun & Erwei, 2021. "Optimization of C-to-G base editors with sequence context preference predictable by machine learning methods," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    6. Alexis C. Komor & Yongjoo B. Kim & Michael S. Packer & John A. Zuris & David R. Liu, 2016. "Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage," Nature, Nature, vol. 533(7603), pages 420-424, May.
    7. Oecd, 2023. "Case Law," Nuclear Law Bulletin, OECD Publishing, vol. 2022(1).
    8. Zhixin Lei & Haowei Meng & Lulu Liu & Huanan Zhao & Xichen Rao & Yongchang Yan & Hao Wu & Min Liu & Aibin He & Chengqi Yi, 2022. "Mitochondrial base editor induces substantial nuclear off-target mutations," Nature, Nature, vol. 606(7915), pages 804-811, June.
    9. Yajing Liu & Changyang Zhou & Shisheng Huang & Lu Dang & Yu Wei & Jun He & Yingsi Zhou & Shaoshuai Mao & Wanyu Tao & Yu Zhang & Hui Yang & Xingxu Huang & Tian Chi, 2020. "A Cas-embedding strategy for minimizing off-target effects of DNA base editors," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
    10. Beverly Y. Mok & Marcos H. de Moraes & Jun Zeng & Dustin E. Bosch & Anna V. Kotrys & Aditya Raguram & FoSheng Hsu & Matthew C. Radey & S. Brook Peterson & Vamsi K. Mootha & Joseph D. Mougous & David R, 2020. "A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing," Nature, Nature, vol. 583(7817), pages 631-637, July.
    11. Andrew V. Anzalone & Peyton B. Randolph & Jessie R. Davis & Alexander A. Sousa & Luke W. Koblan & Jonathan M. Levy & Peter J. Chen & Christopher Wilson & Gregory A. Newby & Aditya Raguram & David R. L, 2019. "Search-and-replace genome editing without double-strand breaks or donor DNA," Nature, Nature, vol. 576(7785), pages 149-157, December.
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