3D organization of synthetic and scrambled chromosomes

Guillaume Mercy, Julien Mozziconacci, Vittore F. Scolari, Kun Yang, Guanghou Zhao, Agnès Thierry, Yisha Luo, Leslie A. Mitchell, Michael Shen, Yue Shen, Roy Walker, Weimin Zhang, Yi Wu, Ze-xiong Xie, Zhouqing Luo, Yizhi Cai, Junbiao Dai, Huanming Yang, Ying-Jin Yuan, Jef D. BoekeJoel S. Bader, Héloïse Muller*, Romain Koszul

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

103 Citations (Scopus)


Although the design of the synthetic yeast genome Sc2.0 is highly conservative with respect to gene content, the deletion of several classes of repeated sequences and the introduction of thousands of designer changes may affect genome organization and potentially alter cellular functions. We report here the Hi-C-determined three-dimensional (3D) conformations of Sc2.0 chromosomes. The absence of repeats leads to a smoother contact pattern and more precisely tractable chromosome conformations, and the large-scale genomic organization is globally unaffected by the presence of synthetic chromosome(s). Two exceptions are synIII, which lacks the silent mating-type cassettes, and synXII, specifically when the ribosomal DNA is moved to another chromosome. We also exploit the contact maps to detect rearrangements induced in SCRaMbLE (synthetic chromosome rearrangement and modification by loxP-mediated evolution) strains.

Original languageEnglish
Article numbereaaf4597
Number of pages8
Issue number6329
Publication statusPublished - 10 Mar 2017
Externally publishedYes


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