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Programmable DNA pyrimidine base editing via engineered uracil-DNA glycosylase

Author

Listed:
  • Zongyi Yi

    (Peking University)

  • Xiaoxue Zhang

    (Changping Laboratory)

  • Xiaoxu Wei

    (Peking University
    Peking University)

  • Jiayi Li

    (Peking University
    Peking University)

  • Jiwu Ren

    (Changping Laboratory
    Peking University)

  • Xue Zhang

    (Changping Laboratory)

  • Yike Zhang

    (Peking University
    Peking University)

  • Huixian Tang

    (Peking University
    Peking University)

  • Xiwen Chang

    (Changping Laboratory
    Peking University)

  • Ying Yu

    (Peking University)

  • Wensheng Wei

    (Peking University
    Changping Laboratory
    Peking University)

Abstract

DNA base editing technologies predominantly utilize engineered deaminases, limiting their ability to edit thymine and guanine directly. In this study, we successfully achieve base editing of both cytidine and thymine by leveraging the translesion DNA synthesis pathway through the engineering of uracil-DNA glycosylase (UNG). Employing structure-based rational design, exploration of homologous proteins, and mutation screening, we identify a Deinococcus radiodurans UNG mutant capable of effectively editing thymine. When fused with the nickase Cas9, the engineered DrUNG protein facilitates efficient thymine base editing at endogenous sites, achieving editing efficiencies up to 55% without enrichment and exhibiting minimal cellular toxicity. This thymine base editor (TBE) exhibits high editing specificity and significantly restores IDUA enzyme activity in cells derived from patients with Hurler syndrome. TBEs represent efficient, specific, and low-toxicity approaches to base editing with potential applications in treating relevant diseases.

Suggested Citation

  • Zongyi Yi & Xiaoxue Zhang & Xiaoxu Wei & Jiayi Li & Jiwu Ren & Xue Zhang & Yike Zhang & Huixian Tang & Xiwen Chang & Ying Yu & Wensheng Wei, 2024. "Programmable DNA pyrimidine base editing via engineered uracil-DNA glycosylase," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-50012-w
    DOI: 10.1038/s41467-024-50012-w
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    References listed on IDEAS

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    1. 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.
    2. Grace N. Hibshman & Jack P. K. Bravo & Matthew M. Hooper & Tyler L. Dangerfield & Hongshan Zhang & Ilya J. Finkelstein & Kenneth A. Johnson & David W. Taylor, 2024. "Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
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