3D organization of synthetic and scrambled chromosomes

Guillaume Mercy (1, 2) , Julien Mozziconacci (3) , Vittore F Scolari (2) , Kun Yang (4) , Guanghou Zhao (5, 6) , Agnès Thierry (2) , Yi Luo (7) , Leslie A Mitchell (8) , Michael Shen (8) , Yue Shen (7, 9) , Roy Walker (7) , Weimin Zhang (6, 5) , Yi Wu (10, 6) , Ze-Xiong Xie (6, 10) , Zhouqing Luo (5, 6) , Yizhi Cai (7) , Junbiao Dai (5, 6) , Huanming Yang (9) , Ying-Jin Yuan (6, 10) , Jef D Boeke (8) , Joel S Bader (4) , Héloïse Muller (2) , Romain Koszul (2)

1 UPMC - Université Pierre et Marie Curie - Paris 6
2 Régulation spatiale des Génomes - Spatial Regulation of Genomes
3 LPTMC - Laboratoire de Physique Théorique de la Matière Condensée
4 JHU - Johns Hopkins University
5 THU - Tsinghua University [Beijing]
6 Ministry of Education of China
7 University of Edinburgh
8 NYU Langone Medical Center - New York University Langone Medical Center
9 BGI - Beijing Genomics Institute [Shenzhen]
10 TJU - Tianjin University

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.

Domains: Life Sciences [q-bio]

Guillaume Mercy, Julien Mozziconacci, Vittore F Scolari, Kun Yang, Guanghou Zhao, et al.. 3D organization of synthetic and scrambled chromosomes. Science, 2017, 355 (6329), pp.eaaf4597. ⟨10.1126/science.aaf4597⟩. ⟨pasteur-01523221⟩