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Your search keyword '"ANR-15-CE11-0023,HiResBaCS,Structure des chromosomes bactériens revélée a haute résolution(2015)"' showing total 5 results
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5 results on '"ANR-15-CE11-0023,HiResBaCS,Structure des chromosomes bactériens revélée a haute résolution(2015)"'

1. Transcriptional units form the elementary constraining building blocks of the bacterial chromosome

Author

Amaury Bignaud, Charlotte Cockram, Eric Allemand, Julien Mozziconnacci, Olivier Espeli, Romain Koszul, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Collège Doctoral, Sorbonne Université (SU), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Structure et Instabilité des Génomes (STRING), Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), This research was supported by the European Research Council under the Horizon 2020 Program (ERC grant agreement 771813) to RK, by Agence Nationale de la Recherche(ANR Hiresbac) to RK, JM and OE, and by the QLife program to RK and OE. We thank all our colleagues from the laboratory régulation spatiale des génomes for fruitful discussions., ANR-15-CE11-0023,HiResBaCS,Structure des chromosomes bactériens revélée a haute résolution(2015), and European Project: 771813,ERC-2017-COG,SynarchiC(2018)

Subjects
[SDV]Life Sciences [q-bio]
Abstract

Transcription generates local topological and mechanical constraints along the DNA fiber, driving for instance the generation of supercoiled chromosomal domains in bacteria. However, the global impact of transcription-based regulation of chromosome organization remains elusive. Notably, the scale of genes and operons in bacteria remains well below the resolution of chromosomal contact maps generated using Hi-C (~ 5 – 10 kb), preventing to resolve the impact of transcription on genomic organization at the fine-scale. Here, we combined sub-kb Hi-C contact maps and chromosome engineering to visualize individual transcriptional units (TUs) while turning off transcription across the rest of the genome. We show that each TU forms a discrete, transcription-induced 3D domain (TIDs). These local structures impose mechanical and topological constraints on their neighboring sequences at larger scales, bringing them closer together and restricting their dynamics. These results show that the primary building blocks of bacteria chromosome folding consists of transcriptional domains that together shape the global genome structure.

Published
2022
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2. Chromosome organization by a conserved condensin-ParB system in the actinobacterium Corynebacterium glutamicum

Author

Marc Bramkamp, Romain Koszul, Andreas Schmidt, Kati Boehm, Martial Marbouty, Axel Imhof, Giacomo Giacomelli, Ludwig-Maximilians-Universität München (LMU), Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel (CAU), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), This work was funded by grants to M.B. from the Deutsche Forschungsgemeinschaft (project 326464754 in TRR174 and BR2815/6-2) and the Ministry of Science and Education (BMBF: 031A302 e:Bio-Modul II: 0.6 plus). This research was supported by funding to R.K. from the European Research Council under the Horizon 2020 Program (ERC grant agreement 260822), and from Agence Nationale pour la Recherche (HiResBac ANR-15-CE11-0023-03) and JPI-EC-AMR STARCS ANR-16-JPEC-0003-05 all to R.K., ANR-15-CE11-0023,HiResBaCS,Structure des chromosomes bactériens revélée a haute résolution(2015), ANR-16-JPEC-0003,STARCS,Selection and Transmission of Antimicrobial Resistance in Complex Systems(2016), European Project: 260822,EC:FP7:ERC,ERC-2010-StG_20091118,DICIG(2011), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
DNA, Bacterial, 0301 basic medicine, [SDV]Life Sciences [q-bio], Condensin, Science, Centromere, General Physics and Astronomy, Replication Origin, DNA Primase, macromolecular substances, Article, General Biochemistry, Genetics and Molecular Biology, Corynebacterium glutamicum, Plasmid maintenance, Chromosome segregation, Chromosome conformation capture, 03 medical and health sciences, Condensin complex, 0302 clinical medicine, Bacterial Proteins, Cellular microbiology, lcsh:Science, 030304 developmental biology, Adenosine Triphosphatases, 0303 health sciences, Multidisciplinary, Bacteria, biology, Chemistry, Circular bacterial chromosome, Chromosome, General Chemistry, Chromosomes, Bacterial, Cell biology, DNA-Binding Proteins, Nucleoproteins, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 030104 developmental biology, Chromosome Structures, Multiprotein Complexes, biology.protein, bacteria, lcsh:Q, Nucleoid organization, 030217 neurology & neurosurgery, Bacillus subtilis
Abstract

Higher-order chromosome folding and segregation are tightly regulated in all domains of life. In bacteria, details on nucleoid organization regulatory mechanisms and function remain poorly characterized, especially in non-model species. Here, we investigate the role of DNA-partitioning protein ParB and SMC condensin complexes in the actinobacterium Corynebacterium glutamicum. Chromosome conformation capture reveals SMC-mediated long-range interactions around ten centromere-like parS sites clustered at the replication origin (oriC). At least one oriC-proximal parS site is necessary for reliable chromosome segregation. We use chromatin immunoprecipitation and photoactivated single-molecule localization microscopy to show the formation of distinct, parS-dependent ParB-nucleoprotein subclusters. We further show that SMC/ScpAB complexes, loaded via ParB at parS sites, mediate chromosomal inter-arm contacts (as previously shown in Bacillus subtilis). However, the MukBEF-like SMC complex MksBEFG does not contribute to chromosomal DNA-folding; instead, this complex is involved in plasmid maintenance and interacts with the polar oriC-tethering factor DivIVA. Our results complement current models of ParB-SMC/ScpAB crosstalk and show that some condensin complexes evolved functions that are apparently uncoupled from chromosome folding., The regulation of higher-order chromosome folding and segregation in bacteria is poorly understood. Here, Böhm et al. provide insights into the roles of DNA partitioning protein ParB and SMC condensin complexes in Corynebacterium glutamicum.

Published
2020
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3. Generating High-Resolution Hi-C Contact Maps of Bacteria

Author

Charlotte Cockram, Agnès Thierry, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), This research was supported by funding to Romain Koszul from the Agence Nationale pour la Recherche (HiResBac ANR-15-CE11-0023-03) and from the European Research Council under the Horizon 2020 program (ERC grant agreement: 771813)., We thank Romain Koszul and the members of the RSG lab for insightful discussions regarding the development of this protocol., ANR-15-CE11-0023,HiResBaCS,Structure des chromosomes bactériens revélée a haute résolution(2015), and European Project: 771813,ERC-2017-COG,SynarchiC(2018)

Subjects
Chromosome conformation capture, biology, Bacteria, Computer science, [SDV]Life Sciences [q-bio], Resolution (electron density), High resolution, Computational biology, Bacterial genome size, biology.organism_classification, Genome organization, MESH: Gram-Positive Bacteria, MESH: Bacteria, MESH: Software, Chromosome (genetic algorithm), Hi-C, MESH: Anti-Bacterial Agents, MESH: Gram-Negative Bacteria, MESH: Chromosomes, Prokaryotes, 3C, Genomic organization
Abstract

International audience; During the past decade, Chromosome Conformation Capture (3C/Hi-C)-based methods have been used to probe the 3D structure and organization of bacterial genomes, revealing fundamental aspects of chromosome dynamics. However, the current protocols are expensive, inefficient, and limited in their resolution. Here we present a simple, cost-effective Hi-C approach that is readily applicable to a range of Gram-positive and Gram-negative bacteria.

Published
2021
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4. Genomic contacts reveal the control of sister chromosome decatenation in E. coli

Author

Cockram C, Romain Koszul, Conin B, Ingrid Billault-Chaumartin, Sayyed He, Olivier Espéli, Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Collège Doctoral, Sorbonne Université (SU), Université de Lausanne = University of Lausanne (UNIL), University of Oxford, This research was supported by funding from the European Research Council under the 7th Framework Program (ERC Grant Agreement 771813 to R.K.) and ANR (HiResBac ANR-15-CE11-0023-03 to R.K. and O.E)., ANR-15-CE11-0023,HiResBaCS,Structure des chromosomes bactériens revélée a haute résolution(2015), and European Project: 771813,ERC-2017-COG,SynarchiC(2018)

Subjects
Genetics, 0303 health sciences, biology, Topoisomerase IV, [SDV]Life Sciences [q-bio], 030302 biochemistry & molecular biology, Chromosome, Locus (genetics), Genetic analysis, Genome, Chromosome segregation, 03 medical and health sciences, Catenation, biology.protein, Sister chromatids, 030304 developmental biology
Abstract

In bacteria, chromosome segregation occurs progressively, from the origin to the terminus, a few minutes after the replication of each locus. In-between replication and segregation, sister loci are maintained in an apparent cohesive state by topological links. Whereas topoisomerase IV (Topo IV), the main bacteria decatenase, controls segregation, little is known regarding the influence of the cohesion step on chromosome folding. In this work, we investigated chromosome folding in cells with altered decatenation activities. Within minutes after Topo IV inactivation, a massive chromosome reorganization takes place, associated with increases in trans-contacts between catenated sister chromatids and in long-range cis-contacts between the terminus and distant loci on the genome. A genetic analysis of these signals allowed us to decipher specific roles for Topo IV and Topo III, an accessory decatenase. Moreover we revealed the role of MatP, the terminus macrodomain organizing system and MukB, the E. coli SMC in organizing sister chromatids tied by persistent catenation links. We propose that large-scale conformation changes observed in these conditions reveal a defective decatenation hub located in the terminus area. Altogether, our findings support a model of spatial and temporal partition of the tasks required for sister chromosome segregation.

Published
2021

5. Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins

Author

Frédéric Boccard, Axel Cournac, Virginia S. Lioy, Romain Koszul, Olivier Espéli, Stéphane Duigou, Martial Marbouty, Julien Mozziconacci, Conformation et Ségrégation du chromosome bactérien (OCB), Département Biologie des Génomes (DBG), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), This research was supported by funding from the European Research Council under the 7th Framework Program (FP7/2007-2013, ERC Grant Agreement 260822 to R.K.), by the Agence Nationale pour la Recherche (HiResBac ANR-15-CE11-0023-03 to R.K., O.E., and J.M.), by the Fondation pour la Recherche Médicale (to V.S.L.), and by the Agence Nationale pour la Recherche (ANR-12-BSV8-0020-01 to F.B.)., ANR-15-CE11-0023,HiResBaCS,Structure des chromosomes bactériens revélée a haute résolution(2015), European Project: 260822,EC:FP7:ERC,ERC-2010-StG_20091118,DICIG(2011), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris)

Subjects
0301 basic medicine, MESH: Chromosomes, Bacterial, MESH: Protein Structure, Quaternary, Chromosomal Proteins, Non-Histone, DBG, Condensin, [SDV]Life Sciences [q-bio], MESH: Escherichia coli Proteins, Bacterial genome size, Origin of replication, Genome, General Biochemistry, Genetics and Molecular Biology, MESH: Escherichia coli K12, 03 medical and health sciences, 0302 clinical medicine, HU, Hi-C, MESH: Chromosomal Proteins, Non-Histone, MESH: Adenosine Triphosphatases, Nucleoid, genome organization, Protein Structure, Quaternary, bacteria, Genetics, Adenosine Triphosphatases, OCB, biology, Escherichia coli K12, SMC, Circular bacterial chromosome, Escherichia coli Proteins, Chromosome, Chromosomes, Bacterial, MESH: Multiprotein Complexes, MatP, DNA-Binding Proteins, Repressor Proteins, 030104 developmental biology, MESH: Repressor Proteins, Multiprotein Complexes, biology.protein, chromatin, Nucleoid organization, 030217 neurology & neurosurgery, MESH: DNA-Binding Proteins
Abstract

International audience; As in eukaryotes, bacterial genomes are not randomly folded. Bacterial genetic information is generally carried on a circular chromosome with a single origin of replication from which two replication forks proceed bidirectionally toward the opposite terminus region. Here, we investigate the higher-order architecture of the Escherichia coli genome, showing its partition into two structurally distinct entities by a complex and intertwined network of contacts: the replication terminus (ter) region and the rest of the chromosome. Outside of ter, the condensin MukBEF and the ubiquitous nucleoid-associated protein (NAP) HU promote DNA contacts in the megabase range. Within ter, the MatP protein prevents MukBEF activity, and contacts are restricted to ∼280 kb, creating a domain with distinct structural properties. We also show how other NAPs contribute to nucleoid organization, such as H-NS, which restricts short-range interactions. Combined, these results reveal the contributions of major evolutionarily conserved proteins in a bacterial chromosome organization.

Published
2018
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