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

Huiming Zhang, Xian Fu (), Xuemei Gong, Yun Wang, Haolin Zhang, Yu Zhao and Yue Shen ()
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Huiming Zhang: University of Chinese Academy of Sciences
Xian Fu: BGI Research-Shenzhen, BGI
Xuemei Gong: University of Chinese Academy of Sciences
Yun Wang: BGI Research-Shenzhen, BGI
Haolin Zhang: BGI Research-Shenzhen, BGI
Yu Zhao: NYU Langone Health
Yue Shen: BGI Research-Shenzhen, BGI

Nature Communications, 2022, vol. 13, issue 1, 1-11

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-33606-0

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