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SpG and SpRY variants expand the CRISPR toolbox for genome editing in zebrafish

Author

Listed:
  • Fang Liang

    (South China Normal University
    South China Normal University)

  • Yu Zhang

    (South China Normal University)

  • Lin Li

    (South China Normal University)

  • Yexin Yang

    (South China Normal University)

  • Ji-Feng Fei

    (Guangdong Academy of Medical Sciences)

  • Yanmei Liu

    (South China Normal University)

  • Wei Qin

    (South China Normal University)

Abstract

Precise genetic modifications in model organisms are essential for biomedical research. The recent development of PAM-less base editors makes it possible to assess the functional impact and pathogenicity of nucleotide mutations in animals. Here we first optimize SpG and SpRY systems in zebrafish by purifying protein combined with synthetically modified gRNA. SpG shows high editing efficiency at NGN PAM sites, whereas SpRY efficiently edit PAM-less sites in the zebrafish genome. Then, we generate the SpRY-mediated cytosine base editor SpRY-CBE4max and SpRY-mediated adenine base editor zSpRY-ABE8e. Both target relaxed PAM with up to 96% editing efficiency and high product purity. With these tools, some previously inaccessible disease-relevant genetic variants are generated in zebrafish, supporting the utility of high-resolution targeting across genome-editing applications. Our study significantly improves CRISPR-Cas targeting in the genomic landscape of zebrafish, promoting the application of this model organism in revealing gene function, physiological mechanisms, and disease pathogenesis.

Suggested Citation

  • Fang Liang & Yu Zhang & Lin Li & Yexin Yang & Ji-Feng Fei & Yanmei Liu & Wei Qin, 2022. "SpG and SpRY variants expand the CRISPR toolbox for genome editing in zebrafish," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31034-8
    DOI: 10.1038/s41467-022-31034-8
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    References listed on IDEAS

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    1. Yu Zhang & Yang Liu & Wei Qin & Shaohui Zheng & Jiawang Xiao & Xinxin Xia & Xuanyao Yuan & Jingjing Zeng & Yu Shi & Yan Zhang & Hui Ma & Gaurav K. Varshney & Ji-Feng Fei & Yanmei Liu, 2024. "Cytosine base editors with increased PAM and deaminase motif flexibility for gene editing in zebrafish," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    2. Wei Qin & Fang Liang & Sheng-Jia Lin & Cassidy Petree & Kevin Huang & Yu Zhang & Lin Li & Pratishtha Varshney & Philippe Mourrain & Yanmei Liu & Gaurav K. Varshney, 2024. "ABE-ultramax for high-efficiency biallelic adenine base editing in zebrafish," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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