title: Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae.
abstract: DNA-binding proteins are central regulators of chromosome organization; however, in genome-reduced bacteria their diversity is largely diminished. Whether the chromosomes of such bacteria adopt defined three-dimensional structures remains unexplored. Here we combine Hi-C and super-resolution microscopy to determine the structure of the Mycoplasma pneumoniae chromosome at a 10 kb resolution. We find a defined structure, with a global symmetry between two arms that connect opposite poles, one bearing the chromosomal Ori and the other the midpoint. Analysis of local structures at a 3 kb resolution indicates that the chromosome is organized into domains ranging from 15 to 33 kb. We provide evidence that genes within the same domain tend to be co-regulated, suggesting that chromosome organization influences transcriptional regulation, and that supercoiling regulates local organization. This study extends the current understanding of bacterial genome organization and demonstrates that a defined chromosomal structure is a universal feature of living systems.
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.|Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
authors.forename: Marie
authors.identifier: 0000-0002-7258-7272
authors.initials: M
authors.lastname: Trussart
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.|Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
authors.forename: Eva
authors.identifier: 0000-0002-5992-9186
authors.initials: E
authors.lastname: Yus
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.
authors.forename: Sira
authors.initials: S
authors.lastname: Martinez
authors.affiliation: Gene Regulation, Stem Cells and Cancer Program. Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.|CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain.
authors.forename: Davide
authors.initials: D
authors.lastname: Baù
authors.affiliation: Department of Biology, Graduate School of Science, Osaka City University, 558-8585 Osaka, Japan.|OCU Advanced Research Institute for Natural Science and Technology (OCARNA), Osaka City University, 558-8585 Osaka, Japan.
authors.forename: Yuhei O
authors.initials: YO
authors.lastname: Tahara
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.|Advanced Light Microscopy Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain.
authors.forename: Thomas
authors.identifier: 0000-0002-9632-918X
authors.initials: T
authors.lastname: Pengo
authors.affiliation: The ithree Institute, The University of Technology Sydney, Sydney, New South Wales 2007, Australia.
authors.forename: Michael
authors.initials: M
authors.lastname: Widjaja
authors.affiliation: Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany.
authors.forename: Simon
authors.initials: S
authors.lastname: Kretschmer
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.|Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
authors.forename: Jim
authors.initials: J
authors.lastname: Swoger
authors.affiliation: The ithree Institute, The University of Technology Sydney, Sydney, New South Wales 2007, Australia.
authors.forename: Steven
authors.initials: S
authors.lastname: Djordjevic
authors.affiliation: The ithree Institute, The University of Technology Sydney, Sydney, New South Wales 2007, Australia.
authors.forename: Lynne
authors.identifier: 0000-0002-9255-9033
authors.initials: L
authors.lastname: Turnbull
authors.affiliation: The ithree Institute, The University of Technology Sydney, Sydney, New South Wales 2007, Australia.
authors.forename: Cynthia
authors.identifier: 0000-0003-2296-3791
authors.initials: C
authors.lastname: Whitchurch
authors.affiliation: Department of Biology, Graduate School of Science, Osaka City University, 558-8585 Osaka, Japan.|OCU Advanced Research Institute for Natural Science and Technology (OCARNA), Osaka City University, 558-8585 Osaka, Japan.
authors.forename: Makoto
authors.identifier: 0000-0002-7478-7390
authors.initials: M
authors.lastname: Miyata
authors.affiliation: Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.|Gene Regulation, Stem Cells and Cancer Program. Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.|CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain.|Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
authors.forename: Marc A
authors.identifier: 0000-0002-0151-4279
authors.initials: MA
authors.lastname: Marti-Renom
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.|Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
authors.forename: Maria
authors.initials: M
authors.lastname: Lluch-Senar
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.|Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.|Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
authors.forename: Luís
authors.initials: L
authors.lastname: Serrano
mesh_terms: D022004:Chromosome Structures; D002876:Chromosomes, Bacterial / Q000648:ultrastructure*; D004269:DNA, Bacterial / Q000648:ultrastructure*; D004278:DNA, Superhelical / Q000648:ultrastructure*; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial / Q000235:genetics*; D008853:Microscopy; D008968:Molecular Conformation; D009177:Mycoplasma pneumoniae / Q000235:genetics* / Q000648:ultrastructure; D009690:Nucleic Acid Conformation
chemical_list: D004269:DNA, Bacterial; D004278:DNA, Superhelical