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Science. 2017 Mar 10;355(6329). pii: eaaf4597. doi: 10.1126/science.aaf4597.

3D organization of synthetic and scrambled chromosomes.

Author information

1
Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France.
2
UMR3525, Centre National de la Recherche Scientifique (CNRS), Paris 75015, France.
3
Sorbonne Universités, Université Pierre et Marie Curie (Université Paris 6), Paris 75005, France.
4
Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR7600, Université Pierre et Marie Curie (Université Paris 6), Sorbonne Universités, Paris, France.
5
Department of Biomedical Engineering and High-Throughput Biology Center, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
6
Key Laboratory for Industrial Biocatalysis (Ministry of Education), Key Laboratory of Bioinformatics (Ministry of Education), Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
7
School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
8
Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, Langone Medical Center, New York University, New York, NY 10016, USA.
9
BGI-Shenzhen, Shenzhen 518083, China.
10
BGI-Qingdao, Qingdao 266555, China.
11
Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
12
James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.
13
Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France. heloise.muller@curie.fr romain.koszul@pasteur.fr.

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.

PMID:
28280150
PMCID:
PMC5679085
DOI:
10.1126/science.aaf4597
[Indexed for MEDLINE]
Free PMC Article

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