Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization  

作　　者：Sijie Zhou Yi Wu Yu Zhao Zhen Zhang Limin Jiang Lin Liu Yan Zhang Jijun Tang Ying-Jin Yuan 

机构地区：[1]Frontiers Science Center for Synthetic Biology(Ministry of Education),Tianjin University,Tianjin 300072,China [2]Key Laboratory of Systems Bioengineering(Ministry of Education),School of Chemical Engineering and Technology,Tianjin University,Tianjin 300072,China [3]Institute for Systems Genetics,NYU Langone Health,NewYork,NY10016,USA [4]School of Computer Science and Technology,College of Intelligence and Computing,Tianjin University,Tianjin 300350,China [5]Department of Computer Science,University of South Carolina,Columbia,SC29208,USA [6]Epigenetic Group,Frasergen Bioinformatics Co.,Ltd.,Wuhan 430000 China

出　　处：《National Science Review》2023年第5期234-244,共11页国家科学评论（英文版）

基　　金：supported by the National Key Research and Development Program of China(2021YFC2100800);the National Natural Science Foundation of China(21621004,31861143017 and 31971351);is part of the Synthetic Yeast Genome Project(http://syntheticyeast.org/sc2-0/)。

摘　　要：Synthetic genome evolution provides a dynamic approach for systematically and straightforwardly exploring evolutionary processes.Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution(SCRaMbLE)is an evolutionary system intrinsic to the synthetic yeast genome that can rapidly drive structural variations.Here,we detect over 260000 rearrangement events after the SCRaMbLEing of a yeast strain harboring 5.5 synthetic yeast chromosomes(synⅡ,synⅢ,synⅤ,circular synⅥ,synⅨR and synⅩ).Remarkably,we find that the rearrangement events exhibit a specific landscape of frequency.We further reveal that the landscape is shaped by the combined effects of chromatin accessibili and spatial contact probability.The rearrangements tend to occur in 3D spatially proximal and chromatin-accessible regions.The enormous numbers of rearrangements mediated by SCRaMbLE provide a driving force to potentiate directed genome evolution,and the investigation of the rearrangement landscape offers mechanistic insights into the dynamics of genome evolution.

关 键 词：synthetic biology genome rearrangement hierarchical chromatin organization synthetic yeast genome SCRAMBLE Saccharomyces cerevisiae 

分 类 号：Q343.2[生物学—遗传学]