Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization

被引：20

作者：

Zhou, Sijie ^{[1
,2
]}

Wu, Yi ^{[1
,2
]}

Zhao, Yu ^{[3
]}

Zhang, Zhen ^{[1
,2
]}

Jiang, Limin ^{[4
]}

Liu, Lin ^{[5
]}

Zhang, Yan ^{[1
]}

Tang, Jijun ^{[4
,6
]}

Yuan, Ying-Jin ^{[1
,2
]}

机构：

[1] Tianjin Univ, Minist Educ, Frontiers Sci Ctr Synthet Biol, Tianjin 300072, Peoples R China

[2] Tianjin Univ, Sch Chem Engn & Technol, Minist Educ, Key Lab Syst Bioengn, Tianjin 300072, Peoples R China

[3] NYU Langone Hlth, Inst Syst Genet, New York, NY 10016 USA

[4] Tianjin Univ, Coll Intelligence & Comp, Sch Comp Sci & Technol, Tianjin 300350, Peoples R China

[5] Univ South Carolina, Dept Comp Sci, Columbia, SC 29208 USA

[6] Frasergen Bioinformat Co Ltd, Epigenet Grp, Wuhan 430000, Peoples R China

来源：

NATIONAL SCIENCE REVIEW | 2023年 / 10卷 / 05期

基金：

中国国家自然科学基金;

关键词：

synthetic biology; genome rearrangement; hierarchical chromatin organization; synthetic yeast genome; SCRaMbLE; Saccharomyces cerevisiae; GENOME; DIVERSITY; ARCHITECTURE; DIVERGENCE; LANDSCAPE; VIEW;

D O I：

10.1093/nsr/nwad073

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

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 260 000 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 accessibility 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. A specific landscape of over 260,000 rearrangements in SCRaMbLEd yeast harboring 5.5 synthetic chromosomes was uncovered and found to be a result of combinatorial effects of chromatin accessibility and 3D spatial contact probability.

引用

页数：11

共 56 条

[1] Gene Duplication and Environmental Adaptation within Yeast Populations [J].

Ames, Ryan M. ;

Rash, Bharat M. ;

Hentges, Kathryn E. ;

Robertson, David L. ;

Delneri, Daniela ;

Lovell, Simon C. .

GENOME BIOLOGY AND EVOLUTION, 2010, 2 :591-601

[2] Total Synthesis of a Functional Designer Eukaryotic Chromosome [J].

Annaluru, Narayana ;

Muller, Heloise ;

Mitchell, Leslie A. ;

Ramalingam, Sivaprakash ;

Stracquadanio, Giovanni ;

Richardson, Sarah M. ;

Dymond, Jessica S. ;

Kuang, Zheng ;

Scheifele, Lisa Z. ;

Cooper, Eric M. ;

Cai, Yizhi ;

Zeller, Karen ;

Agmon, Neta ;

Han, Jeffrey S. ;

Hadjithomas, Michalis ;

Tullman, Jennifer ;

Caravelli, Katrina ;

Cirelli, Kimberly ;

Guo, Zheyuan ;

London, Viktoriya ;

Yeluru, Apurva ;

Murugan, Sindurathy ;

Kandavelou, Karthikeyan ;

Agier, Nicolas ;

Fischer, Gilles ;

Yang, Kun ;

Martin, J. Andrew ;

Bilgel, Murat ;

Bohutski, Pavlo ;

Boulier, Kristin M. ;

Capaldo, Brian J. ;

Chang, Joy ;

Charoen, Kristie ;

Choi, Woo Jin ;

Deng, Peter ;

DiCarlo, James E. ;

Doong, Judy ;

Dunn, Jessilyn ;

Feinberg, Jason I. ;

Fernandez, Christopher ;

Floria, Charlotte E. ;

Gladowski, David ;

Hadidi, Pasha ;

Ishizuka, Isabel ;

Jabbari, Javaneh ;

Lau, Calvin Y. L. ;

Lee, Pablo A. ;

Li, Sean ;

Lin, Denise ;

Linder, Matthias E. .

SCIENCE, 2014, 344 (6179) :55-58

[3] High-resolution lineage tracking reveals travelling wave of adaptation in laboratory yeast [J].

Ba, Alex N. Nguyen ;

Cvijovic, Ivana ;

Echenique, Jose I. Rojas ;

Lawrence, Katherine R. ;

Rego-Costa, Artur ;

Liu, Xianan ;

Levy, Sasha F. ;

Desai, Michael M. .

NATURE, 2019, 575 (7783) :494-+

[4] A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes [J].

Bergstroem, Anders ;

Simpson, Jared T. ;

Salinas, Francisco ;

Barre, Benjamin ;

Parts, Leopold ;

Zia, Amin ;

Nguyen Ba, Alex N. ;

Moses, Alan M. ;

Louis, Edward J. ;

Mustonen, Ville ;

Warringer, Jonas ;

Durbin, Richard ;

Liti, Gianni .

MOLECULAR BIOLOGY AND EVOLUTION, 2014, 31 (04) :872-888

[5] The landscape of somatic copy-number alteration across human cancers [J].

Beroukhim, Rameen ;

Mermel, Craig H. ;

Porter, Dale ;

Wei, Guo ;

Raychaudhuri, Soumya ;

Donovan, Jerry ;

Barretina, Jordi ;

Boehm, Jesse S. ;

Dobson, Jennifer ;

Urashima, Mitsuyoshi ;

Mc Henry, Kevin T. ;

Pinchback, Reid M. ;

Ligon, Azra H. ;

Cho, Yoon-Jae ;

Haery, Leila ;

Greulich, Heidi ;

Reich, Michael ;

Winckler, Wendy ;

Lawrence, Michael S. ;

Weir, Barbara A. ;

Tanaka, Kumiko E. ;

Chiang, Derek Y. ;

Bass, Adam J. ;

Loo, Alice ;

Hoffman, Carter ;

Prensner, John ;

Liefeld, Ted ;

Gao, Qing ;

Yecies, Derek ;

Signoretti, Sabina ;

Maher, Elizabeth ;

Kaye, Frederic J. ;

Sasaki, Hidefumi ;

Tepper, Joel E. ;

Fletcher, Jonathan A. ;

Tabernero, Josep ;

Baselga, Jose ;

Tsao, Ming-Sound ;

Demichelis, Francesca ;

Rubin, Mark A. ;

Janne, Pasi A. ;

Daly, Mark J. ;

Nucera, Carmelo ;

Levine, Ross L. ;

Ebert, Benjamin L. ;

Gabriel, Stacey ;

Rustgi, Anil K. ;

Antonescu, Cristina R. ;

Ladanyi, Marc ;

Letai, Anthony .

NATURE, 2010, 463 (7283) :899-905

[6] Rapid host strain improvement by in vivo rearrangement of a synthetic yeast chromosome [J].

Blount, B. A. ;

Gowers, G-O. F. ;

Ho, J. C. H. ;

Ledesma-Amaro, R. ;

Jovicevic, D. ;

McKiernan, R. M. ;

Xie, Z. X. ;

Li, B. Z. ;

Yuan, Y. J. ;

Ellis, T. .

NATURE COMMUNICATIONS, 2018, 9

[7] Yeast: An Experimental Organism for 21st Century Biology [J].

Botstein, David ;

Fink, Gerald R. .

GENETICS, 2011, 189 (03) :695-704

[8] Rapid Expansion and Functional Divergence of Subtelomeric Gene Families in Yeasts [J].

Brown, Chris A. ;

Murray, Andrew W. ;

Verstrepen, Kevin J. .

CURRENT BIOLOGY, 2010, 20 (10) :895-903

[9] An artificial chromosome for data storage [J].

Chen, Weigang ;

Han, Mingzhe ;

Zhou, Jianting ;

Ge, Qi ;

Wang, Panpan ;

Zhang, Xinchen ;

Zhu, Siyu ;

Song, Lifu ;

Yuan, Yingjin .

NATIONAL SCIENCE REVIEW, 2021, 8 (05)

[10] A three-dimensional model of the yeast genome [J].

Duan, Zhijun ;

Andronescu, Mirela ;

Schutz, Kevin ;

McIlwain, Sean ;

Kim, Yoo Jung ;

Lee, Choli ;

Shendure, Jay ;

Fields, Stanley ;

Blau, C. Anthony ;

Noble, William S. .

NATURE, 2010, 465 (7296) :363-367

← 1 2 3 4 5 6 →