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 byloxP-mediated evolution) strains.
authors.affiliation: Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France.|UMR3525, Centre National de la Recherche Scientifique (CNRS), Paris 75015, France.|Sorbonne Universités, Université Pierre et Marie Curie (Université Paris 6), Paris 75005, France.
authors.forename: Guillaume
authors.identifier: 0000-0002-6274-5927
authors.initials: G
authors.lastname: Mercy
authors.affiliation: Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR7600, Université Pierre et Marie Curie (Université Paris 6), Sorbonne Universités, Paris, France.
authors.forename: Julien
authors.initials: J
authors.lastname: Mozziconacci
authors.affiliation: Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France.|UMR3525, Centre National de la Recherche Scientifique (CNRS), Paris 75015, France.
authors.forename: Vittore F
authors.identifier: 0000-0003-3490-0579
authors.initials: VF
authors.lastname: Scolari
authors.affiliation: Department of Biomedical Engineering and High-Throughput Biology Center, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
authors.forename: Kun
authors.identifier: 0000-0002-1060-8082
authors.initials: K
authors.lastname: Yang
authors.affiliation: 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.
authors.forename: Guanghou
authors.initials: G
authors.lastname: Zhao
authors.affiliation: Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France.|UMR3525, Centre National de la Recherche Scientifique (CNRS), Paris 75015, France.
authors.forename: Agnès
authors.initials: A
authors.lastname: Thierry
authors.affiliation: School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
authors.forename: Yisha
authors.identifier: 0000-0002-4228-7527
authors.initials: Y
authors.lastname: Luo
authors.affiliation: Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, Langone Medical Center, New York University, New York, NY 10016, USA.
authors.forename: Leslie A
authors.identifier: 0000-0001-7869-9817
authors.initials: LA
authors.lastname: Mitchell
authors.affiliation: Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, Langone Medical Center, New York University, New York, NY 10016, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Shen
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|BGI-Qingdao, Qingdao 266555, China.|School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
authors.forename: Yue
authors.identifier: 0000-0002-3276-7295
authors.initials: Y
authors.lastname: Shen
authors.affiliation: School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
authors.forename: Roy
authors.identifier: 0000-0003-0960-4591
authors.initials: R
authors.lastname: Walker
authors.affiliation: 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.
authors.forename: Weimin
authors.identifier: 0000-0002-8836-1438
authors.initials: W
authors.lastname: Zhang
authors.affiliation: 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.
authors.forename: Yi
authors.identifier: 0000-0002-2539-9228
authors.initials: Y
authors.lastname: Wu
authors.affiliation: 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.
authors.forename: Ze-Xiong
authors.initials: ZX
authors.lastname: Xie
authors.affiliation: 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.
authors.forename: Zhouqing
authors.identifier: 0000-0001-5426-5176
authors.initials: Z
authors.lastname: Luo
authors.affiliation: School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
authors.forename: Yizhi
authors.identifier: 0000-0003-1663-2865
authors.initials: Y
authors.lastname: Cai
authors.affiliation: 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.
authors.forename: Junbiao
authors.identifier: 0000-0002-5299-4700
authors.initials: J
authors.lastname: Dai
authors.affiliation: James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.|BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Huanming
authors.identifier: 0000-0003-1703-3012
authors.initials: H
authors.lastname: Yang
authors.affiliation: 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.
authors.forename: Ying-Jin
authors.identifier: 0000-0003-0553-0089
authors.initials: YJ
authors.lastname: Yuan
authors.affiliation: Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, Langone Medical Center, New York University, New York, NY 10016, USA.
authors.forename: Jef D
authors.identifier: 0000-0001-5322-4946
authors.initials: JD
authors.lastname: Boeke
authors.affiliation: Department of Biomedical Engineering and High-Throughput Biology Center, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
authors.forename: Joel S
authors.identifier: 0000-0002-6020-4625
authors.initials: JS
authors.lastname: Bader
authors.affiliation: Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France. heloise.muller@curie.fr romain.koszul@pasteur.fr.|UMR3525, Centre National de la Recherche Scientifique (CNRS), Paris 75015, France.
authors.forename: Héloïse
authors.identifier: 0000-0003-0853-822X
authors.initials: H
authors.lastname: Muller
authors.affiliation: Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France. heloise.muller@curie.fr romain.koszul@pasteur.fr.|UMR3525, Centre National de la Recherche Scientifique (CNRS), Paris 75015, France.
authors.forename: Romain
authors.identifier: 0000-0002-3086-1173
authors.initials: R
authors.lastname: Koszul
mesh_terms: D002467:Cell Nucleus / Q000235:genetics / Q000648:ultrastructure; D002503:Centromere / Q000648:ultrastructure; D018244:Chromosomes, Artificial, Yeast / Q000737:chemistry / Q000235:genetics / Q000648:ultrastructure*; D004275:DNA, Ribosomal / Q000235:genetics; D016681:Genome, Fungal; D009690:Nucleic Acid Conformation; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D017384:Sequence Deletion; D058615:Synthetic Biology; D016615:Telomere / Q000648:ultrastructure
chemical_list: D004275:DNA, Ribosomal