@article{120745b2829e41e5bb37305d265b6a9f,
title = "3D organization of synthetic and scrambled chromosomes",
abstract = "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.",
author = "Guillaume Mercy and Julien Mozziconacci and Scolari, {Vittore F.} and Kun Yang and Guanghou Zhao and Agn{\`e}s Thierry and Yisha Luo and Mitchell, {Leslie A.} and Michael Shen and Yue Shen and Roy Walker and Weimin Zhang and Yi Wu and Xie, {Ze Xiong} and Zhouqing Luo and Yizhi Cai and Junbiao Dai and Huanming Yang and Yuan, {Ying Jin} and Boeke, {Jef D.} and Bader, {Joel S.} and H{\'e}lo{\"i}se Muller and Romain Koszul",
note = "Funding Information: We thank A. Cournac, M. Marbouty, and L. Lazar-Stefanita for fruitful discussions and advice. This research was supported by funding to R.K. from the European Research Council (ERC) under the 7th Framework Program (FP7/2007-2013, ERC grant agreement 260822), Agence Nationale pour la Recherche (ANR) (MeioRec ANR-13-BSV6-0012-02), and ERASynBio and ANR (IESY ANR-14-SYNB-0001-03). H.M. and V.F.S are partly supported by Pasteur-Roux Fellowships. J.D. was funded by the National Science Foundation of China (31471254), Tsinghua University Initiative Scientific Research Program (2011Z02296), Ph.D. Programs Foundation of Ministry of Education of China (20110002120055), and the Chinese Ministry of Science and Technology (2012CB725201). Y.-J.Y. was supported by the Natural Science Foundation of China (21621004 and 21390203). Y.C. was funded by a Chancellor's Fellowship from the University of Edinburgh, a startup fund from the Scottish Universities Life Sciences Alliance, and grants from the U.K. Biotechnology and Biological Sciences Research Council (BB/M005690/1, BB/M025640/1, and BB/M00029X/1). Y.S. was supported by a research grant from the Shenzhen Engineering Laboratory for Clinical Molecular Diagnostic Promotion [JZF no. (2016)884]. This work was supported in part by funding from the U.S. National Science Foundation (grants MCB-0718846 and MCB-1026068 to J.D.B. and J.S.B. and MCB-0546446 and MCB-1445545 to J.S.B.). J.D.B. and J.S.B. are founders and directors of Neochromosome. J.D.B. serves as a scientific advisor to Recombinetics and Sample6. These arrangements are reviewed and managed by the committees on conflict of interest at the New York University Langone Medical Center (J.D.B.) and Johns Hopkins University (J.S.B.). FASTQ files of the reads have been deposited in the Sequence Read Archive database under accession number SRP070421. Publisher Copyright: {\textcopyright} 2017, American Association for the Advancement of Science. All rights reserved.",
year = "2017",
month = mar,
day = "10",
doi = "10.1126/science.aaf4597",
language = "English (US)",
volume = "355",
journal = "Science",
issn = "0036-8075",
publisher = "American Association for the Advancement of Science",
number = "6329",
}