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Programmable C:G to G:C genome editing with CRISPR-Cas9-directed base excision repair proteins

Author

Listed:
  • Liwei Chen

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Jung Eun Park

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Peter Paa

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Priscilla D. Rajakumar

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Hong-Ting Prekop

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Yi Ting Chew

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Swathi N. Manivannan

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Wei Leong Chew

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

Abstract

Many genetic diseases are caused by single-nucleotide polymorphisms. Base editors can correct these mutations at single-nucleotide resolution, but until recently, only allowed for transition edits, addressing four out of twelve possible DNA base substitutions. Here, we develop a class of C:G to G:C Base Editors to create single-base genomic transversions in human cells. Our C:G to G:C Base Editors consist of a nickase-Cas9 fused to a cytidine deaminase and base excision repair proteins. Characterization of >30 base editor candidates reveal that they predominantly perform C:G to G:C editing (up to 90% purity), with rAPOBEC-nCas9-rXRCC1 being the most efficient (mean 15.4% and up to 37% without selection). C:G to G:C Base Editors target cytidine in WCW, ACC or GCT sequence contexts and within a precise three-nucleotide window of the target protospacer. We further target genes linked to dyslipidemia, hypertrophic cardiomyopathy, and deafness, showing the therapeutic potential of these base editors in interrogating and correcting human genetic diseases.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-21559-9
    DOI: 10.1038/s41467-021-21559-9
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    Cited by:

    1. I. F. Schene & I. P. Joore & J. H. L. Baijens & R. Stevelink & G. Kok & S. Shehata & E. F. Ilcken & E. C. M. Nieuwenhuis & D. P. Bolhuis & R. C. M. Rees & S. A. Spelier & H. P. J. Doef & J. M. Beekman, 2022. "Mutation-specific reporter for optimization and enrichment of prime editing," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    2. Jianli Tao & Daniel E. Bauer & Roberto Chiarle, 2023. "Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    3. Annabel K. Sangree & Audrey L. Griffith & Zsofia M. Szegletes & Priyanka Roy & Peter C. DeWeirdt & Mudra Hegde & Abby V. McGee & Ruth E. Hanna & John G. Doench, 2022. "Benchmarking of SpCas9 variants enables deeper base editor screens of BRCA1 and BCL2," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    4. Chao Yang & Zhenzhen Ma & Keshan Wang & Xingxiao Dong & Meiyu Huang & Yaqiu Li & Xiagu Zhu & Ju Li & Zhihui Cheng & Changhao Bi & Xueli Zhang, 2023. "HMGN1 enhances CRISPR-directed dual-function A-to-G and C-to-G base editing," Nature Communications, Nature, vol. 14(1), pages 1-12, December.

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