Manipulating the 3D organization of the largest synthetic yeast chromosome
Author:
Zhang Weimin, Lazar-Stefanita Luciana, Yamashita Hitoyoshi, Shen Michael J., Mitchell Leslie A., Kurasawa Hikaru, Haase Max A. B., Sun Xiaoji, Jiang Qingwen, Lauer Stephanie L., McCulloch Laura H., Zhao Yu, Ichikawa David, Easo Nicole, Lin S. Jiaming, Fanfani ViolaORCID, Camellato Brendan R., Zhu Yinan, Cai Jitong, Xu Zhuwei, Sacasa Maya, Accardo Ryan, Ahn Ju Young, Annadanam Surekha, Brammer Basta Leighanne A., Bello Nicholas R., Cai Lousanna, Cerritos Stephanie, Cornwell MacIntosh, D’Amato Anthony, Hacker Maria, Hersey Kenneth, Kennedy Emma, Kianercy Ardeshir, Kim Dohee, Lim Hong Seo, McCutcheon Griffin, McGirr Kimiko, Meaney Nora, Meyer Lauren, Moyer Ally, Nimer Maisa, Sabbatini Carla, Scheifele Lisa, Shores Lucas S., Silvestrone Cassandra, Snee Arden, Spina Antonio, Staiti Anthony, Stuver Matt, Tian Elli, Whearty Danielle, Zhao Calvin, Zheng Tony, Zhou Vivian, Zeller Karen, Bader Joel S.ORCID, Stracquadanio GiovanniORCID, Deutsch Samuel, Dai Junbiao, Aizawa Yasunori, Boeke Jef D.
Abstract
SummaryWhether synthetic genomes can power life has attracted broad interest in the synthetic biology field, especially when the synthetic genomes are extensively modified with thousands of designer features. Here we report de novo synthesis of the largest eukaryotic chromosome thus far, synIV, a 1,454,621-bp Saccharomyces cerevisiae chromosome resulting from extensive genome streamlining and modification. During the construction of synIV, we developed a megachunk assembly method, combined with a hierarchical integration strategy. This strategy significantly increased the accuracy and flexibility of synthetic chromosome construction and facilitated chromosome debugging. In addition to the drastic sequence changes made to synIV by rewriting it, we further manipulated the three-dimensional structure of synIV in the yeast nucleus to explore spatial gene regulation within the nuclear space. Surprisingly, we found few gene expression changes, suggesting that positioning inside the yeast nucleoplasm plays a minor role in gene regulation. Therefore, our manipulation of the spatial structure of the largest synthetic yeast chromosome shed light on higher-order architectural design of the synthetic genomes.
Publisher
Cold Spring Harbor Laboratory
Cited by
2 articles.
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