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Systematic dissection of key factors governing recombination outcomes by GCE-SCRaMbLE

Author

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  • Huiming Zhang

    (University of Chinese Academy of Sciences
    BGI Research-Shenzhen, BGI
    Guangdong Provincial Key Laboratory of Genome Read and Write)

  • Xian Fu

    (BGI Research-Shenzhen, BGI
    Guangdong Provincial Key Laboratory of Genome Read and Write
    BGI Research-Changzhou, BGI)

  • Xuemei Gong

    (University of Chinese Academy of Sciences
    BGI Research-Shenzhen, BGI
    Guangdong Provincial Key Laboratory of Genome Read and Write)

  • Yun Wang

    (BGI Research-Shenzhen, BGI
    Guangdong Provincial Key Laboratory of Genome Read and Write
    BGI Research-Changzhou, BGI)

  • Haolin Zhang

    (BGI Research-Shenzhen, BGI
    Guangdong Provincial Key Laboratory of Genome Read and Write)

  • Yu Zhao

    (NYU Langone Health)

  • Yue Shen

    (BGI Research-Shenzhen, BGI
    Guangdong Provincial Key Laboratory of Genome Read and Write
    BGI Research-Changzhou, BGI
    Chinese Academy of Sciences)

Abstract

With the completion of Sc2.0 chromosomes, synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE) becomes more critical for in-depth investigation of fundamental biological questions and screening of industrially valuable characteristics. Further applications, however, are hindered due to the lack of facile and tight regulation of the SCRaMbLE process, and limited understanding of key factors that may affect the rearrangement outcomes. Here we propose an approach to precisely regulate SCRaMbLE recombination in a dose-dependent manner using genetic code expansion (GCE) technology with low basal activity. By systematically analyzing 1380 derived strains and six yeast pools subjected to GCE-SCRaMbLE, we find that Cre enzyme abundance, genome ploidy and chromosome conformation play key roles in recombination frequencies and determine the SCRaMbLE outcomes. With these insights, the GCE-SCRaMbLE system will serve as a powerful tool in the future exploitation and optimization of the Sc2.0-related technologies.

Suggested Citation

  • Huiming Zhang & Xian Fu & Xuemei Gong & Yun Wang & Haolin Zhang & Yu Zhao & Yue Shen, 2022. "Systematic dissection of key factors governing recombination outcomes by GCE-SCRaMbLE," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-33606-0
    DOI: 10.1038/s41467-022-33606-0
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    References listed on IDEAS

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    1. Jessica S. Dymond & Sarah M. Richardson & Candice E. Coombes & Timothy Babatz & Héloïse Muller & Narayana Annaluru & William J. Blake & Joy W. Schwerzmann & Junbiao Dai & Derek L. Lindstrom & Annabel , 2011. "Synthetic chromosome arms function in yeast and generate phenotypic diversity by design," Nature, Nature, vol. 477(7365), pages 471-476, September.
    2. Feng Guo & Deshmukh N. Gopaul & Gregory D. Van Duyne, 1997. "Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse," Nature, Nature, vol. 389(6646), pages 40-46, September.
    3. Juan Wang & Ze-Xiong Xie & Yuan Ma & Xiang-Rong Chen & Yao-Qing Huang & Bo He & Jia & Bing-Zhi Li & Ying-Jin Yuan, 2018. "Ring synthetic chromosome V SCRaMbLE," Nature Communications, Nature, vol. 9(1), pages 1-9, December.
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    1. Tiantian Chang & Weichao Ding & Shirui Yan & Yun Wang & Haoling Zhang & Yu Zhang & Zhi Ping & Huiming Zhang & Yijian Huang & Jiahui Zhang & Dan Wang & Wenwei Zhang & Xun Xu & Yue Shen & Xian Fu, 2023. "A robust yeast biocontainment system with two-layered regulation switch dependent on unnatural amino acid," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    2. Charlotte Cautereels & Jolien Smets & Jonas De Saeger & Lloyd Cool & Yanmei Zhu & Anna Zimmermann & Jan Steensels & Anton Gorkovskiy & Thomas B. Jacobs & Kevin J. Verstrepen, 2024. "Orthogonal LoxPsym sites allow multiplexed site-specific recombination in prokaryotic and eukaryotic hosts," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    3. Li Cheng & Shijun Zhao & Tianyi Li & Sha Hou & Zhouqing Luo & Jinsheng Xu & Wenfei Yu & Shuangying Jiang & Marco Monti & Daniel Schindler & Weimin Zhang & Chunhui Hou & Yingxin Ma & Yizhi Cai & Jef D., 2024. "Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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