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1. Chromosome folding and prophage activation reveal specific genomic architecture for intestinal bacteria

Author: Lamy-Besnier, Quentin, Bignaud, Amaury, Garneau, Julian, Titecat, Marie, Conti, Devon, von Strempel, Alexandra, Monot, Marc, Stecher, Bärbel, Koszul, Romain, Debarbieux, Laurent, Marbouty, Martial, Bactériophage, bactérie, hôte - Bacteriophage, bacterium, host, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-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)-Université Paris Cité (UPCité), Collège Doctoral, Sorbonne Université (SU), Biomics (plateforme technologique), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Institute for Translational Research in Inflammation - U 1286 (INFINITE (Ex-Liric)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), CHU Lille, Max Von Pettenkofer Institute (MVP), Ludwig-Maximilians-Universität München (LMU), German Center for Infection Research, Partnersite Munich (DZIF), This research was supported by funding to BS from DFG-STE-1971/11–1 (PhaStGut project), to BS from the European Research Council under the Horizon 2020 Program (ERC grant agreement 865615), to LD and MMa from PRCI ANR-20-CE92-0048 (PhaStGut project), and to RK from the European Research Council under the Horizon 2020 Program (ERC grant agreement 771813) and from JPI-EC-AMR STARCS ANR-16-JPEC-0003–05. QLB received funding from École Doctorale FIRE-Program Bettencourt. AB is supported by an ENS fellowship from the French Ministry of Higher Education, Research and Innovation. MMo and JRG were supported by JCJC ANR-18-CE35-0011 (project CDPhages). MT received funding from DigestScience. Biomics Platform, C2RT, Institut Pasteur, Paris, France, was supported by France Génomique (ANR-10-INBS-09) and IBISA. AB and DC belong to Ecole Doctorale Complexité du vivant ED515 of Sorbonne Université., ANR-20-CE92-0048,PhaStGut,Etude des mécanismes de la coexistence stable entre bactériophages et bactéries et de ses conséquences sur la fonction du microbiote intestinal(2020), ANR-16-JPEC-0003,STARCS,Selection and Transmission of Antimicrobial Resistance in Complex Systems(2016), ANR-18-CE35-0011,CDPhages,Le role des bactériophages dans l'évolution de la virulence chez Clostridium difficile(2018), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), and European Project: 771813,ERC-2017-COG,SynarchiC(2018)
Subjects: Microbiology (medical), MESH: Humans, Virome, MESH: Genomics, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, OMM12, Phages Gut HiC Virome OMM12 3D signatures, Microbiology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Bacteria, MESH: Prophages, 3D signatures, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Phages, Gut, MESH: Animals, MESH: Ecosystem, MESH: Chromosomes, MESH: Bacteriophages, HiC, MESH: Mice
Abstract: Background Bacteria and their viruses, bacteriophages, are the most abundant entities of the gut microbiota, a complex community of microorganisms associated with human health and disease. In this ecosystem, the interactions between these two key components are still largely unknown. In particular, the impact of the gut environment on bacteria and their associated prophages is yet to be deciphered. Results To gain insight into the activity of lysogenic bacteriophages within the context of their host genomes, we performed proximity ligation-based sequencing (Hi-C) in both in vitro and in vivo conditions on the 12 bacterial strains of the OMM12 synthetic bacterial community stably associated within mice gut (gnotobiotic mouse line OMM12). High-resolution contact maps of the chromosome 3D organization of the bacterial genomes revealed a wide diversity of architectures, differences between environments, and an overall stability over time in the gut of mice. The DNA contacts pointed at 3D signatures of prophages leading to 16 of them being predicted as functional. We also identified circularization signals and observed different 3D patterns between in vitro and in vivo conditions. Concurrent virome analysis showed that 11 of these prophages produced viral particles and that OMM12 mice do not carry other intestinal viruses. Conclusions The precise identification by Hi-C of functional and active prophages within bacterial communities will unlock the study of interactions between bacteriophages and bacteria across conditions (healthy vs disease).
Published: 2023

2. The slow evolving genome of the xenacoelomorph worm Xenoturbella bocki

Author: Philipp H. Schiffer, Paschalis Natsidis, Daniel J. Leite, Helen E. Robertson, François Lapraz, Ferdinand Marlétaz, Bastian Fromm, Liam Baudry, Fraser Simpson, Eirik Høye, Anne-C. Zakrzewski, Paschalia Kapli, Katharina J. Hoff, Steven Mueller, Martial Marbouty, Heather Marlow, Richard R. Copley, Romain Koszul, Peter Sarkies, Maximilian J. Telford, University College of London [London] (UCL), Institut de Biologie Valrose (IBV), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), The Arctic University of Norway [Tromsø, Norway] (UiT), Collège Doctoral, Sorbonne Université (SU), Norwegian Radium Hospital, University of Oslo (UiO), Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde [Berlin], Universität Greifswald - University of Greifswald, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), University of Chicago, Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Department of Biochemistry [Oxford], and University of Oxford
Subjects: [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy
Abstract: The evolutionary origins of Bilateria remain enigmatic. One of the more enduring proposals highlights similarities between a cnidarian-like planula larva and simple acoel-like flatworms. This idea is based in part on the view of the Xenacoelomorpha as an outgroup to all other bilaterians which are themselves designated the Nephrozoa (protostomes and deuterostomes). Genome data, which can help to elucidate phylogenetic relationships and provide important comparative data, remain sparse for early branching bilaterians. Here we assemble and analyse the genome of the simple, marine xenacoelomorphXenoturbella bocki, a key species for our understanding of early bilaterian and deuterostome evolution. Our highly contiguous genome assembly ofX. bockihas a size of ∼110 Mbp in 18 chromosome like scaffolds, with repeat content, and intron, exon and intergenic space comparable to other bilaterian invertebrates. We findX. bockito have a similar number of genes to other bilaterians and to have retained ancestral metazoan synteny. Key bilaterian signalling pathways are also largely complete and most bilaterian miRNAs are present. We conclude thatX. bockihas a complex genome typical of bilaterians, in contrast to the apparent simplicity of its body plan. Overall, our data do not provide evidence supporting the idea that Xenacoelomorpha are a primitively simple outgroup to other bilaterians and gene presence/absence data support a relationship with Ambulacraria.
Published: 2022

3. Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection–related chromatin reorganization

Author: Cyril Matthey-Doret, Morgan J. Colp, Pedro Escoll, Agnès Thierry, Pierrick Moreau, Bruce Curtis, Tobias Sahr, Matt Sarrasin, Michael W. Gray, B. Franz Lang, John M. Archibald, Carmen Buchrieser, 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), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada, Dalhousie University [Halifax], Biologie des Bactéries intracellulaires - Biology of Intracellular Bacteria, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Département de Biochimie et Centre Robert-Cedergren en Bioinformatique et Génomique, C.M.-D. is supported by the Pasteur—Paris University (PPU) International PhD Program. This research was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 to R.K. (ERC grant agreement 771813). The C.B. laboratory is financed by the Fondation pour la Recherche Médicale (FRM) grant no. EQU201903007847 and the Agence Nationale de la Recherche (ANR) grant no. ANR-10-LABX-62-IBEID. Research in the Archibald laboratory was supported by a grant from the Gordon and Betty Moore Foundation (GBMF5782). M.J.C. is supported by graduate student scholarships from the Natural Sciences and Engineering Research Council of Canada (NSERC) and Dalhousie University. B.F.L. and M.S. were supported by the NSERC (RGPIN-2017-05411) and by the 'Fonds de Recherche Nature et Technologie,' Quebec., We thank Axel Cournac, Laura Gomez Valero, Christophe Rusniok, and Lyam Baudry for their comments on the bioinformatics analysis, Charlotte Cockram for her help with Oxford Nanopore sequencing, Olivier Espeli, and all members of the Koszul laboratory and Buchrieser laboratory for stimulating discussions., Author contributions: Conceptualization was done by C.M.-D., M.J.C., C.B., J.M.A., and R.K. Methodology was done by C.M.-D., M.J.C., C.B., J.M.A., and R.K. Investigation was done by M.J.C., C.M.-D., P.E., T.S., and A.T. Formal analysis was done by C.M.-D. and M.J.C. Data curation was done by C.M.-D., M.J.C., B.C., M.S., M.W.G., and B.F.L. Visualization was done by C.M.-D. and M.J.C. Writing of the original draft was done by C.M.-D., M.J.C., J.M.A., and R.K. Writing of the other drafts and editing were done by all authors. Supervision was done by J.M.A., C.B., and R.K. Funding acquisition was done by J.M.A., C.B., and R.K., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), and European Project: 771813,ERC-2017-COG,SynarchiC(2018)
Subjects: [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Genetics (clinical)
Abstract: The unicellular amoeba Acanthamoeba castellanii is ubiquitous in aquatic environments, where it preys on bacteria. The organism also hosts bacterial endosymbionts, some of which are parasitic, including human pathogens such as Chlamydia and Legionella spp. Here we report complete, high-quality genome sequences for two extensively studied A. castellanii strains, Neff and C3. Combining long- and short-read data with Hi-C, we generated near chromosome-level assemblies for both strains with 90% of the genome contained in 29 scaffolds for the Neff strain and 31 for the C3 strain. Comparative genomics revealed strain-specific functional enrichment, most notably genes related to signal transduction in the C3 strain and to viral replication in Neff. Furthermore, we characterized the spatial organization of the A. castellanii genome and showed that it is reorganized during infection by Legionella pneumophila. Infection-dependent chromatin loops were found to be enriched in genes for signal transduction and phosphorylation processes. In genomic regions where chromatin organization changed during Legionella infection, we found functional enrichment for genes associated with metabolism, organelle assembly, and cytoskeleton organization. Given Legionella infection is known to alter its host's cell cycle, to exploit the host's organelles, and to modulate the host's metabolism in its favor, these changes in chromatin organization may partly be related to mechanisms of host control during Legionella infection.
Published: 2022

4. 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

5. Normalization of Chromosome Contact Maps: Matrix Balancing and Visualization

Author: Romain Koszul, Pierrick Moreau, Axel Cournac, Shogofa Mortaza, Lyam Baudry, Cyril Matthey-Doret, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Collège Doctoral, Sorbonne Université (SU), Laboratoire Cogitamus, and Silvio Bicciato, Francesco Ferrari
Subjects: Normalization (statistics), Computer science, Proximity ligation, Chromatin folding, Computational biology, Python (programming language), computer.software_genre, Genome, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Chromatin, Visualization, Matrix (mathematics), normalization, Scripting language, Hi-C, Genome architecture, Chromosome organization, Transcription (software), 3C, computer, computer.programming_language
Abstract: International audience; Over the last decade, genomic proximity ligation approaches have reshaped our vision of chromosomes 3D organizations, from bacteria nucleoids to larger eukaryotic genomes. The different protocols (3Cseq, Hi-C, TCC, MicroC [XL], Hi-CO, etc.) rely on common steps (chemical fixation digestion, ligation…) to detect pairs of genomic positions in close proximity. The most common way to represent these data is a matrix, or contact map, which allows visualizing the different chromatin structures (compartments, loops, etc.) that can be associated to other signals such as transcription, protein occupancy, etc. as well as, in some instances, to biological functions.In this chapter we present and discuss the filtering of the events recovered in proximity ligation experiments as well as the application of the balancing normalization procedure on the resulting contact map. We also describe a computational tool for visualizing normalized contact data dubbed Scalogram.The different processes described here are illustrated and supported by the laboratory custom-made scripts pooled into "hicstuff," an open-access python package accessible on github ( https://github.com/koszullab/hicstuff ).
Published: 2022

6. 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

7. Chromosomal assembly of the flat oyster (Ostrea edulis L.) genome as a new genetic resource for aquaculture

Author: Isabelle Boutet, Homère J. Alves Monteiro, Lyam Baudry, Takeshi Takeuchi, Eric Bonnivard, Bernard Billoud, Sarah Farhat, Ricardo Gonzales‐Araya, Benoit Salaun, Ann C. Andersen, Jean‐Yves Toullec, François H. Lallier, Jean‐François Flot, Nadège Guiglielmoni, Ximing Guo, Cui Li, Bassem Allam, Emmanuelle Pales‐Espinosa, Jakob Hemmer‐Hansen, Pierrick Moreau, Martial Marbouty, Romain Koszul, Arnaud Tanguy, Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Collège Doctoral, Sorbonne Université (SU), Okinawa Institute of Science and Technology Graduate University (OIST), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), School of Marine and Atmospheric Sciences [Stony Brook] (SoMAS), Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY), Adaptation et Biologie des Invertébrés en Conditions Extrêmes (ABICE), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Haskin Shellfish Research Laboratory (HSRL), Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers)-Rutgers University System (Rutgers), Marine Sciences Research Center, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Centre Régional de la Conchyliculture Bretagne Nord, Université libre de Bruxelles (ULB), Chinese Academy of Sciences [Beijing] (CAS), and This study was funded by the Roscoff_O.edulis-V1 Fonds Européen pour les Affaires Maritimes et la Pêche (FEAMP) (grant code: PFEA470017FA1000016).
Subjects: Genome, aquaculture, [SDV]Life Sciences [q-bio], Genetics, Flat oyster, Aquaculture, transposable elements, General Agricultural and Biological Sciences, Martelia, Transposable elements, genome, Ecology, Evolution, Behavior and Systematics, flat oyster
Abstract: The European flat oyster (Ostrea edulis L.) is a native bivalve of the European coasts. Harvest of this species has declined during the last decades because of the appearance of two parasites that have led to the collapse of the stocks and the loss of the natural oyster beds. O. edulis has been the subject of numerous studies in population genetics and on the detection of the parasites Bonamia ostreae and Marteilia refringens. These studies investigated immune responses to these parasites at the molecular and cellular levels. Several genetic improvement programs have been initiated especially for parasite resistance. Within the framework of a European project (PERLE 2) that aims to produce genetic lines of O. edulis with hardiness traits (growth, survival, resistance) for the purpose of repopulating natural oyster beds in Brittany and reviving the culture of this species in the foreshore, obtaining a reference genome becomes essential as done recently in many bivalve species of aquaculture interest. Here, we present a chromosome-level genome assembly and annotation for the European flat oyster, generated by combining PacBio, Illumina, 10X linked, and Hi-C sequencing. The finished assembly is 887.2 Mb with a scaffold-N50 of 97.1 Mb scaffolded on the expected 10 pseudochromosomes. Annotation of the genome revealed the presence of 35,962 protein-coding genes. We analyzed in detail the transposable element (TE) diversity in the flat oyster genome, highlighted some specificities in tRNA and miRNA composition, and provided the first insight into the molecular response of O. edulis to M. refringens. This genome provides a reference for genomic studies on O. edulis to better understand its basic physiology and as a useful resource for genetic breeding in support of aquaculture and natural reef restoration.
Published: 2022

8. Diagnosis accuracy of muscule MRI for autoimmune myopathies: Multicentricprospective study (DARWIM)

Author: Allenbach, Yves, Mercy, Guillaume, Deux, Jean-Francois, Foissac, Frantz, Shoindre, Yoland, Leonard-Louis, Sarah, Maisonobe, Thierry, Seilhean, Danielle, Charuel, Jean-Luc, Ghillani-Dablin, Pascale, Gorochov, Guy, Lucidarme, Olivier, Cornec, Divi, Brihaye, Benoit, Bienvenu, Boris, Benveniste, Olivier, Allenbach, Yves, Service de Département de médecine interne et immunologie clinique [CHU Pitié-Salpêtrière] (DMIIC), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Centre de recherche en Myologie – U974 SU-INSERM, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Evaluation thérapeutique et pharmacologie périnatale et pédiatrique (EA_7323), Université Paris Descartes - Paris 5 (UPD5), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service de Neuropathologie [CHU Pitié Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Centre d'Immunologie et des Maladies Infectieuses (CIMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Service d'Immunologie [CHU Pitié-Salpétrière], Centre d'Immunologie et de Maladies Infectieuses (CIMI), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Imagerie Biomédicale (LIB), CHRU Brest - Service de Rhumatologie (CHU - BREST - Rhumato), Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Immunologie et Pathologie (EA2216), and Université de Brest (UBO)-IFR148
Subjects: [SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio]
Abstract: International audience
Published: 2022

9. Kinetics of the Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Response and Serological Estimation of Time Since Infection

Author: Pelleau, Stéphane, Woudenberg, Tom, Rosado, Jason, Donnadieu, Françoise, Garcia, Laura, Obadia, Thomas, Gardais, Soazic, Elgharbawy, Yasmine, Velay, Aurelie, Gonzalez, Maria, Nizou, Jacques Yves, Khelil, Nizar, Zannis, Konstantinos, Cockram, Charlotte, Merkling, Sarah Hélène, Meola, Annalisa, Kerneis, Solen, Terrier, Benjamin, de Seze, Jerome, Planas, Delphine, Schwartz, Olivier, Dejardin, François, Petres, Stéphane, von Platen, Cassandre, Pellerin, Sandrine Fernandes, Arowas, Laurence, de Facci, Louise Perrin, Duffy, Darragh, Cheallaigh, Clíona Ní, Dunne, Jean, Conlon, Niall, Townsend, Liam, Duong, Veasna, Auerswald, Heidi, Pinaud, Laurie, Tondeur, Laura, Backovic, Marija, Hoen, Bruno, Fontanet, Arnaud, Mueller, Ivo, Fafi-Kremer, Samira, Bruel, Timothée, White, Michael, Epidémiologie et Analyse des Maladies Infectieuses - Infectious Disease Epidemiology and Analytics, Institut Pasteur [Paris] (IP), Malaria : parasites et hôtes - Malaria : parasites and hosts, Santé publique : épidémiologie & sciences de l'information biomédicale (ED 393), Sorbonne Université (SU), Département de Biologie Computationnelle - Department of Computational Biology, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Immuno-Rhumatologie Moléculaire, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Strasbourg, Institut Mutualiste de Montsouris (IMM), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Interactions Virus-Insectes - Insect-Virus Interactions (IVI), Virologie Structurale - Structural Virology, Epidémiologie et modélisation de la résistance aux antimicrobiens - Epidemiology and modelling of bacterial escape to antimicrobials (EMAE), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, Assistance Publique Hôpitaux de Paris-Centre (APHP-CUP), Université de Paris, Paris, France, Paris-Centre de Recherche Cardiovasculaire (PARCC (UMR_S 970/ U970)), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), CIC Strasbourg (Centre d’Investigation Clinique Plurithématique (CIC - P) ), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Nouvel Hôpital Civil de Strasbourg-Hôpital de Hautepierre [Strasbourg], Virus et Immunité - Virus and immunity (CNRS-UMR3569), Plateforme technologique Production et purification de protéines recombinantes – Production and Purification of Recombinant Proteins Technological Platform (PPR), Centre de Recherche Translationnelle - Center for Translational Science (CRT), Investigation Clinique et d’Accès aux Ressources Biologiques (Plate-forme) - Clinical Investigation and Access to BioResources (ICAReB), Immunologie Translationnelle - Translational Immunology lab, St James's University Hospital, Leeds Teaching Hospitals NHS Trust, Trinity College Dublin, Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Direction de la recherche médicale de l'Institut Pasteur, Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), The Walter and Eliza Hall Institute of Medical Research (WEHI), University of Melbourne, Vaccine Research Institute [Créteil, France] (VRI), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), This work was supported by the European Research Council (MultiSeroSurv ERC Starting Grant 852373, MW), l’Agence Nationale de la Recherche and Fondation pour la Recherche Médicale (CorPopImm, MW), and the Institut Pasteur International Network (CoronaSeroSurv, MW). JR was supported by the Pasteur Paris University (PPU) International PhD Program. CC was supported by the European Research Council 771813. MB, AL and HA were supported by the « URGENCE COVID-19 » fundraising campaign of Institut Pasteur. HA is supported by Centre for International Migration and Development. NC and CNC are part-funded by a Science Foundation Ireland (SFI) grant, Grant Code 20/SPP/3685. LT has been awarded the Irish ClinicalAcademic Training (ICAT) Programme, supported by the Wellcome Trust and the Health Research Board (Grant Number 203930/B/16/Z), the Health Service Executive, National Doctors Training and Planning and the Health and Social Care, Research and Development Division, Northern Ireland (https://icatprogramme.org/). MB and AM were supported by Institut Pasteur TaskForce funding (TooLab project). IM is supported by a NHMRC Principal Research Fellowship. SFK lab is funded by Strasbourg University Hospitals (SeroCoV-HUS, PRI 7782), the Agence Nationale de la Recherche (ANR-18-CE17-0028), Laboratoire d'Excellence TRANSPLANTEX (ANR-11-LABX-0070_TRANSPLANTEX), and Institut National de la Santé et de la Recherche Médicale (UMR_S1109)., ANR-20-COVI-0052,CorPopImm,Évaluer l'immunité contre SARS-CoV-2 à l'échelle de la population grâce aux tests sérologiques(2020), ANR-18-CE17-0028,HuMABK,Les anticorps monoclonaux humains : une Nouvelle approche thérapeutique contre l'infection par le virus BK et les maladies associées(2018), ANR-11-LABX-0070,TRANSPLANTEX,Nouveaux loci d'histocompatibilité/biomarqueurs en transplantation humaine: de la découverte à l'app(2011), European Project: 852373,ERC-2019-STG,MultiSeroSurv(2020), European Project: 771813,ERC-2017-COG,SynarchiC(2018), Institut Pasteur [Paris], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPC), Virus et Immunité - Virus and immunity, Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université (HESAM)-HESAM Université (HESAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université (HESAM)-HESAM Université (HESAM), HESAM Université (HESAM), Vaccine Research Institute (VRI), and HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)
Subjects: Male, Aucun, Antibodies, Viral, time since infection, MESH: Aged, 80 and over, Antibody Specificity, Seroepidemiologic Studies, MESH: COVID-19, Aged, 80 and over, MESH: Immunoglobulin G, MESH: Aged, MESH: Middle Aged, seroprevalence, MESH: Kinetics, Middle Aged, MESH: Antibody Formation, AcademicSubjects/MED00290, MESH: Young Adult, surveillance, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, France, Adult, antibody kinetics, Adolescent, SARS-SoV-2, Sensitivity and Specificity, Young Adult, Major Article, Humans, Serologic Tests, MESH: SARS-CoV-2, MESH: Antibody Specificity, Aged, MESH: Adolescent, MESH: Humans, MESH: Seroepidemiologic Studies, SARS-CoV-2, MESH: Serologic Tests, COVID-19, MESH: Adult, MESH: Male, MESH: Sensitivity and Specificity, MESH: France, Kinetics, sero-prevalence, Immunoglobulin G, Antibody Formation, MESH: Female, MESH: Antibodies, Viral
Abstract: Background Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces a complex antibody response that varies by orders of magnitude between individuals and over time. Methods We developed a multiplex serological test for measuring antibodies to 5 SARS-CoV-2 antigens and the spike proteins of seasonal coronaviruses. We measured antibody responses in cohorts of hospitalized patients and healthcare workers followed for up to 11 months after symptoms. A mathematical model of antibody kinetics was used to quantify the duration of antibody responses. Antibody response data were used to train algorithms for estimating time since infection. Results One year after symptoms, we estimate that 36% (95% range, 11%–94%) of anti-Spike immunoglobulin G (IgG) remains, 31% (95% range, 9%–89%) anti-RBD IgG remains, and 7% (1%–31%) of anti-nucleocapsid IgG remains. The multiplex assay classified previous infections into time intervals of 0–3 months, 3–6 months, and 6–12 months. This method was validated using data from a seroprevalence survey in France, demonstrating that historical SARS-CoV-2 transmission can be reconstructed using samples from a single survey. Conclusions In addition to diagnosing previous SARS-CoV-2 infection, multiplex serological assays can estimate the time since infection, which can be used to reconstruct past epidemics., Longitudinal follow-up of individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reveals differences in the duration of antibodies to multiple antigens. Mathematical models of antibody waning and statistical algorithms can estimate an individual’s time since SARS-CoV-2 infection, and previous transmission waves in a population.
Published: 2021

10. Cohesin regulates homology search during recombinational DNA repair

Author: Jérôme Savocco, Fabien Girard, Romain Koszul, Agnès Dumont, Hélène Bordelet, Agnès Thierry, Aurèle Piazza, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Laboratoire de biologie et modélisation de la cellule (LBMC UMR 5239), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), This research was supported by the CNRS as part of its Momentum programme to A.P., and the European Research Council (ERC) under the European Union’s Horizon 2020 programme to A.P. and R.K. (ERC grants nos. 851006 and 771813, respectively)., European Project: 771813,ERC-2017-COG,SynarchiC(2018), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), European Project: 771813,SynarchiC, This research was supported by the CNRS as part of its Momentum programme to A.P., and the European Research Council (ERC) under the European Union’s Horizon 2020 to A.P. and R.K. (ERC grant agreement 851006 and 771813, respectively)., and We thank Axel Cournac, Cyril Matthey-Doret, Vittore Scolari, Jacques Serizay and Théo Foutel-Rodier for their help with bioinformatics analysis and sharing unpublished scripts and programs, Christophe Chapard for his help with cell synchronization, ChIP and test datasets, as well as members of the Koszul lab and of the Parisian Yeast club for stimulating discussions. We are grateful to Nancy Kleckner, Wolf-Dietrich Heyer and David Leach for helpful comments on the manuscript.
Subjects: DNA repair, RAD52, Saccharomyces cerevisiae, genetic processes, RAD51, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], 030304 developmental biology, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, biology, Cohesin, Chemistry, fungi, Chromosome, Cell Biology, G2-M DNA damage checkpoint, biology.organism_classification, Chromatin, Cell biology, Establishment of sister chromatid cohesion, enzymes and coenzymes (carbohydrates), health occupations, biological phenomena, cell phenomena, and immunity, Homologous recombination, 030217 neurology & neurosurgery, DNA
Abstract: SummaryHomologous recombination (HR) is a ubiquitous DNA double-strand break (DSB) repair mechanism that promotes cell survival. It entails a potentially genome-wide homology search step, carried out along a conserved RecA/Rad51-ssDNA nucleoprotein filament (NPF) assembled on each DSB ends1–3. This search is subdued to NPF-dsDNA collision probability, dictated in part by chromatin conformation2,4. In contrast to the extensive knowledge about chromatin composition and mobility changes elicited by the DNA damage checkpoint (DDC)5–7, whether, how, and to which extent a DSB impacts spatial chromatin organization, and whether this organization in turns influences the homology search process, remains ill-defined8,9. Here we characterize two layers of spatial chromatin reorganization following DSB formation inS. cerevisiae.While cohesin folds chromosomes into cohesive arrays of 10-20 kb long chromatin loops as cells arrest in G2/M10,11, the DSB-flanking regions locally interact in a resection- and 9-1-1 clamp-dependent manner, independently of cohesin and HR proteins. This local structure blocks cohesin progression, constraining the extending NPF at loop base. Functionally this organization promotes side-specificcisDSB-dsDNA interactions that scales with loop expansion span, and provides a kinetic advantage for identification of intra- over inter-chromosomal homologies. We propose that cohesins regulate homology search by promotingcisdsDNA over-sampling, both upon loop expansion-coupled unidimensional dsDNA scanning, NPF trapping, and chromosome individualization, largely independent of their role in sister chromatid cohesion.
Published: 2021

11. Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga

Author: Karine Van Doninck, Richard Cordaux, Thomas Lenormand, Clément Gilbert, Karine Labadie, Lyam Baudry, Julie Virgo, Boris Hespeels, Djampa K. L. Kozlowski, Jitendra Narayan, Alessandro Derzelle, Marie Cariou, Antoine Limasset, Florence Gaudray, Bernard Hallet, Martial Marbouty, Etienne Danchin, Antoine Houtain, Rohan Arora, Matthieu Terwagne, Corinne Cruaud, Nadège Guiglielmoni, Jean-François Flot, Romain Koszul, Paul Simion, Emilien Nicolas, Marc Llirós, Université de Namur [Namur] (UNamur), 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), Université libre de Bruxelles (ULB), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta - Girona Biomedical Research Institute (IDIBGI), Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Louvain Institute of Biomolecular Science and Technology (LIBST), Université Catholique de Louvain = Catholic University of Louvain (UCL), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Interuniversity Institute of Bioinformatics in Brussels (IB2), Université libre de Bruxelles (ULB)-Vrije Universiteit Brussel (VUB), This project received funding from the Horizon 2020 research and innovation program under European Research Council (ERC) grant agreement 725998 (RHEA) and from BELSPO PRODEX for the ESA selected ILSRA-2014-0106 Project to K.V.D., from the Fédération Wallonie-Bruxelles via an 'Action de Recherche Concertée' (ARC) grant to K.V.D. and B.Ha., from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement 764840 to J.-F.F. (ITN IGNITE), from the Fédération Wallonie-Bruxelles via an Action de Recherche Concertée (ARC) grant to J.-F.F., from the European Research Council under the Horizon 2020 Program (ERC grant agreement 260822) and JPI-EC-AMR STARCS ANR-16-JPEC-0003-05 grant to R.K., and through funding by the French Government 'Investissement d’Avenir' program FRANCE GENOMIQUE (ANR-10-INBS-09). E.N. obtained an FSR UNamur fund. A.H., A.D., and R.A. are Research Fellows of the Fonds de la Recherche Scientifique—FNRS., ANR-16-JPEC-0003,STARCS,Selection and Transmission of Antimicrobial Resistance in Complex Systems(2016), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), European Project: 764840,IGNITE, European Project: 260822,EC:FP7:ERC,ERC-2010-StG_20091118,DICIG(2011), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Collège doctoral [Sorbonne universités], Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Sequence assembly, Rotifer, Evolution des espèces, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Homologous chromosome, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Océanographie biologique, Clade, 030304 developmental biology, Genetics, 0303 health sciences, Multidisciplinary, Biologie moléculaire, Chromosome, Adineta vaga, Genome, LOH, Adineta vaga, bdelloid rotifer, biology.organism_classification, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, chemistry, Génétique, cytogénétique, Systématique des espèces [zoologie], DNA, Recombination
Abstract: Bdelloid rotifers are notorious as a speciose ancient clade comprising only asexual lineages. Thanks to their ability to repair highly fragmented DNA, most bdelloid species also withstand complete desiccation and ionizing radiation. Producing a well-assembled reference genome is a critical step to developing an understanding of the effects of long-term asexuality and DNA breakage on genome evolution. To this end, we present the first high-quality chromosome-level genome assemblies for the bdelloid Adineta vaga, composed of six pairs of homologous (diploid) chromosomes with a footprint of paleotetraploidy. The observed large-scale losses of heterozygosity are signatures of recombination between homologous chromosomes, either during mitotic DNA double-strand break repair or when resolving programmed DNA breaks during a modified meiosis. Dynamic subtelomeric regions harbor more structural diversity (e.g. chromosome rearrangements, transposable elements, and haplotypic divergence). Our results trigger the reappraisal of potential meiotic processes in bdelloid rotifers and help unravel the factors underlying their long-term asexual evolutionary success., SCOPUS: ar.j, info:eu-repo/semantics/published
Published: 2021

12. High-throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome

Author: Garneau, Julian, Legrand, Véronique, Marbouty, Martial, Press, Maximilian, Vik, Dean, Fortier, Louis-Charles, Sullivan, Matthew, Bikard, David, Monot, Marc, Biomics (plateforme technologique), Institut Pasteur [Paris], Infrastructure et Ingénierie scientifique (plateforme), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Phase Genomics [Seattle], Ohio State University [Columbus] (OSU), Université de Sherbrooke (UdeS), Biologie de Synthèse - Synthetic biology, This work was supported by the French Government’s program Investissement d’Avenir program, Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ [ANR-10-LABX-62-IBEID] and the Natural Sciences and Engineering Research Council of Canada (NSERC #341450-2010). Biomics Platform, C2RT, Institut Pasteur, Paris, France, is supported by France Génomique (ANR-10-INBS-09-09) and the Infrastructures de recherche en biologie, santé et agronomie (IBISA)., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), and Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Science, [SDV]Life Sciences [q-bio], viruses, Phage biology, Genome, Viral, Genome informatics, Microbiology, Article, Workflow, Virology, Databases, Genetic, Sequencing, Bacteriophages, Virome, High-throughput screening, Computational Biology, High-Throughput Nucleotide Sequencing, Genomics, Viral Packaging Sequence, Computational biology and bioinformatics, Data processing, Medicine, Metagenomics, Algorithms, Software
Abstract: International audience; Viruses that infect bacteria (phages) are increasingly recognized for their importance in diverse ecosystems but identifying and annotating them in large-scale sequence datasets is still challenging. Although efficient scalable virus identification tools are emerging, defining the exact ends (termini) of phage genomes is still particularly difficult. The proper identification of termini is crucial, as it helps in characterizing the packaging mechanism of bacteriophages and provides information on various aspects of phage biology. Here, we introduce PhageTermVirome (PTV) as a tool for the easy and rapid high-throughput determination of phage termini and packaging mechanisms using modern large-scale metagenomics datasets. We successfully tested the PTV algorithm on a mock virome dataset and then used it on two real virome datasets to achieve the rapid identification of more than 100 phage termini and packaging mechanisms, with just a few hours of computing time. Because PTV allows the identification of free fully formed viral particles (by recognition of termini present only in encapsidated DNA), it can also complement other virus identification softwares to predict the true viral origin of contigs in viral metagenomics datasets. PTV is a novel and unique tool for high-throughput characterization of phage genomes, including phage termini identification and characterization of genome packaging mechanisms. This software should help researchers better visualize, map and study the virosphere. PTV is freely available for downloading and installation at https://gitlab.pasteur.fr/vlegrand/ptv .
Published: 2021

13. 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

14. Metagenomes Binning Using Proximity-Ligation Data

Author: Romain Koszul, Martial Marbouty, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This research was supported by funding to R.K. from the European Research Council under the Horizon 2020 Program (ERC grant agreement 771813) and Agence Nationale pour la Recherche JPI-EC-AMR STARCS (ANR-16-JPEC-0003-05)., ANR-16-JPEC-0003,STARCS,Selection and Transmission of Antimicrobial Resistance in Complex Systems(2016), European Project: 771813,SynarchiC, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), and European Project: 771813,ERC-2017-COG,SynarchiC(2018)
Subjects: Metagenomic Hi-C, Chromosome conformation capture, 0303 health sciences, Contig, [SDV]Life Sciences [q-bio], Metagenomes assemble genomes, Binning, Computational biology, Biology, Genome, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, chemistry, Hi-C, Metagenomics, Extrachromosomal DNA, metaHiC, 030217 neurology & neurosurgery, DNA, Meta3C, 030304 developmental biology
Abstract: International audience; Microbial communities are key components of all ecosystems, but characterization of their complete genomic structure remains challenging. Typical analysis tends to elude the complexity of the mixes in terms of species, strains, as well as extrachromosomal DNA molecules. Recently, approaches have been developed that bins DNA contigs into individual genomes and episomes according to their 3D contact frequencies. Those contacts are quantified by chromosome conformation capture experiments (3C, Hi-C), also known as proximity-ligation approaches, applied to metagenomics samples. Here, we present a simple computational pipeline that allows to recover high-quality Metagenomics Assemble Genomes (MAGs) starting from metagenomic 3C or Hi-C datasets and a metagenome assembly.
Published: 2021

15. Kinetics of the SARS-CoV-2 antibody response and serological estimation of time since infection

Author: Pelleau, Stéphane, Woudenberg, Tom, Rosado, Jason, Donnadieu, Françoise, Garcia, Laura, Obadia, Thomas, Gardais, Soazic, Elgharbawy, Yasmine, Velay, Aurelie, Gonzalez, Maria, Nizou, Jacques Yves, Khelil, Nizar, Zannis, Konstantinos, Cockram, Charlotte, Merkling, Sarah Hélène, Meola, Annalisa, Kerneis, Solen, Terrier, Benjamin, de Seze, Jerome, Planas, Delphine, schwartz, olivier, Dejardin, François, Petres, Stéphane, von Platen, Cassandre, Pellerin, Sandrine Fernandes, Arowas, Laurence, de Facci, Louise Perrin, Duffy, Darragh, Cheallaigh, Clíona Ní, Dunne, Jean, Conlon, Niall, Townsend, Liam, Duong, Veasna, Auerswald, Heidi, Pinaud, Laurie, Tondeur, Laura, Backovic, Marija, Hoen, Bruno, Fontanet, Arnaud, Mueller, Ivo, Fafi-Kremer, Samira, Bruel, Timothée, White, Michael, Epidémiologie et Analyse des Maladies Infectieuses - Infectious Disease Epidemiology and Analytics, Institut Pasteur [Paris], Malaria : parasites et hôtes - Malaria : parasites and hosts, Santé publique : épidémiologie & sciences de l'information biomédicale (ED 393), Sorbonne Université (SU), Département de Biologie Computationnelle - Department of Computational Biology, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Immuno-Rhumatologie Moléculaire, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Strasbourg, Institut Mutualiste de Montsouris (IMM), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Interactions Virus-Insectes - Insect-Virus Interactions (IVI), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Virologie Structurale - Structural Virology, Epidémiologie et modélisation de la résistance aux antimicrobiens - Epidemiology and modelling of bacterial escape to antimicrobials (EMAE), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, Assistance Publique Hôpitaux de Paris-Centre (APHP-CUP), Université de Paris, Paris, France, Paris-Centre de Recherche Cardiovasculaire (PARCC (UMR_S 970/ U970)), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), CIC Strasbourg (Centre d’Investigation Clinique Plurithématique (CIC - P) ), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Strasbourg (UNISTRA)-Hôpital de Hautepierre [Strasbourg]-Nouvel Hôpital Civil de Strasbourg, Virus et Immunité - Virus and immunity, Plateforme technologique Production et purification de protéines recombinantes – Production and Purification of Recombinant Proteins Technological Platform (PPR), Centre de Recherche Translationnelle - Center for Translational Science (CRT), Investigation Clinique et d’Accès aux Ressources Biologiques (Plate-forme) - Clinical Investigation and Access to BioResources (ICAReB), Immunologie Translationnelle - Translational Immunology lab, St James's University Hospital, Leeds Teaching Hospitals NHS Trust, Trinity College Dublin, Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Direction de la recherche médicale de l'Institut Pasteur, Conservatoire National des Arts et Métiers [CNAM] (CNAM), The Walter and Eliza Hall Institute of Medical Research (WEHI), University of Melbourne, Vaccine Research Institute (VRI), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), This work was supported by the European Research Council (MultiSeroSurv ERC Starting Grant 852373, MW), l’Agence Nationale de la Recherche and Fondation pour la Recherche Médicale (CorPopImm, MW), and the Institut Pasteur International Network (CoronaSeroSurv, MW). JR was supported by the Pasteur Paris University (PPU) International PhD Program. CC was supported by the European Research Council 771813. MB, AL and HA were supported by the « URGENCE COVID-19 » fundraising campaign of Institut Pasteur. HA is supported by Centre for International Migration and Development. NC and CNC are part-funded by a Science Foundation Ireland (SFI) grant, Grant Code 20/SPP/3685. LT has been awarded the Irish ClinicalAcademic Training (ICAT) Programme, supported by the Wellcome Trust and the Health Research Board (Grant Number 203930/B/16/Z), the Health Service Executive, National Doctors Training and Planning and the Health and Social Care, Research and Development Division, Northern Ireland (https://icatprogramme.org/). MB and AM were supported by Institut Pasteur TaskForce funding (TooLab project). IM is supported by a NHMRC Principal Research Fellowship. SFK lab is funded by Strasbourg University Hospitals (SeroCoV-HUS, PRI 7782), the Agence Nationale de la Recherche (ANR-18-CE17-0028), Laboratoire d'Excellence TRANSPLANTEX (ANR-11-LABX-0070_TRANSPLANTEX), and Institut National de la Santé et de la Recherche Médicale (UMR_S1109)., ANR-20-COVI-0052,CorPopImm,Évaluer l'immunité contre SARS-CoV-2 à l'échelle de la population grâce aux tests sérologiques(2020), ANR-18-CE17-0028,HuMABK,Les anticorps monoclonaux humains : une Nouvelle approche thérapeutique contre l'infection par le virus BK et les maladies associées(2018), ANR-11-LABX-0070,TRANSPLANTEX,Nouveaux loci d'histocompatibilité/biomarqueurs en transplantation humaine: de la découverte à l'app(2011), European Project: 852373,ERC-2019-STG,MultiSeroSurv(2020), European Project: 771813,SynarchiC, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPC), HESAM Université (HESAM)-HESAM Université (HESAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université (HESAM)-HESAM Université (HESAM)-Institut Pasteur [Paris], and HESAM Université (HESAM)
Subjects: antibody kinetics, time since infection, sero-prevalence, surveillance, [SDV.IMM]Life Sciences [q-bio]/Immunology, SARS-SoV-2
Abstract: All data and code used for reproducing the results is freely available on GitHub: https://github.com/MWhite-InstitutPasteur/SARSCoV2_AB_kinetics.; International audience; Background Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces a complex antibody response that varies by orders of magnitude between individuals and over time. Methods We developed a multiplex serological test for measuring antibodies to five SARS-CoV-2 antigens and the Spike proteins of seasonal coronaviruses. We measured antibody responses in cohorts of hospitalized patients and healthcare workers followed for up to eleven months after symptoms. A mathematical model of antibody kinetics was used to quantify the duration of antibody responses. Antibody response data were used to train algorithms for estimating time since infection. Results One year after symptoms, we estimate that 36% (95% range: 11%, 94%) of anti-Spike IgG remains, 31% (9%, 89%) anti-RBD IgG remains, and 7% (1%, 31%) anti-Nucleocapsid IgG remains. The multiplex assay classified previous infections into time intervals of 0–3 months, 3–6 months, and 6–12 months. This method was validated using data from a sero-prevalence survey in France, demonstrating that historical SARS-CoV-2 transmission can be reconstructed using samples from a single survey. Conclusions In addition to diagnosing previous SARS-CoV-2 infection, multiplex serological assays can estimate the time since infection which can be used to reconstruct past epidemics.
Published: 2021

16. 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

17. Closed and high quality bacterial genomes of the Oligo Mouse Microbiota community

Author: Lamy-Besnier, Quentin, Koszul, Romain, Debarbieux, Laurent, Marbouty, Martial, Bactériophage, bactérie, hôte - Bacteriophage, bacterium, host, Institut Pasteur [Paris], Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5), This research was supported by funding to L.D. and M.M. from ANR-20-CE92-0048 and to R.K. from the European Research Council under the Horizon 2020 Program (ERC grant agreement 771813) and from JPI-EC-AMR STARCS ANR-16-JPEC-0003-05. Q.L.-B. is funded by École Doctorale FIRE-Program Bettencourt., ANR-20-CE92-0048,PhaStGut,Etude des mécanismes de la coexistence stable entre bactériophages et bactéries et de ses conséquences sur la fonction du microbiote intestinal(2020), ANR-16-JPEC-0003,STARCS,Selection and Transmission of Antimicrobial Resistance in Complex Systems(2016), European Project: 771813,SynarchiC, Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and European Project: 771813,ERC-2017-COG,SynarchiC(2018)
Subjects: [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV]Life Sciences [q-bio], Genome Sequences
Abstract: The Oligo-Mouse-Microbiota (OMM12) gnotobiotic murine model is an increasingly popular model in microbiota studies. However, following Illumina and PacBio sequencing, the genomes of the 12 strains could not be closed. Here, we used genomic chromosome conformation capture (Hi-C) data to reorganize, close, and improve the quality of these 12 genomes.
Published: 2021

18. Smc3 acetylation, Pds5 and Scc2 control the translocase activity that establishes cohesin dependent chromatin loops

Author: Olivier Gadal, C. Chapard, Lise Dauban, Romain Koszul, Frédéric Beckouët, N. Bastie, Unité de biologie moléculaire, cellulaire et du développement (MCD), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-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), the Fondation ARC pour la Recherche sur le Cancer (ARCPJA22020060002067 to FB) and the Comité de l’Occitanie de la Ligue Nationale contre le Cancer (to FB). Nathalie Bastié and LD were supported by the Ministère de l’Enseignement Supérieur et de la Recherche. Christophe Chapard was supported by Pasteur-Roux-Cantarini fellowship., European Project: 771813,SynarchiC, Unité de biologie moléculaire, cellulaire et du développement - UMR5077 (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), European Project: 771813,ERC-2017-COG,SynarchiC(2018), and Institut Pasteur [Paris]
Subjects: Cohesin, 0303 health sciences, biology, Chemistry, DNA repair, DNA loop extrusion, Cell biology, Chromatin, DNA loop borders, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Acetylation, calibrated ChIP-seq, biology.protein, Translocase, Hi-C metaphase yeast, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Chromatin Loop, biological phenomena, cell phenomena, and immunity, 030217 neurology & neurosurgery, DNA, 030304 developmental biology, Cohesin ATPase activity
Abstract: Chromosome spatial organization and dynamics influence DNA-related metabolic processes. SMC complexes like cohesin are essential instruments of chromosome folding. Cohesin-dependent chromatin loops bring together distal loci to regulate gene transcription, DNA repair and V(D)J recombination processes. Here we characterize further the roles of members of the cohesin holocomplex in regulating chromatin loop expansion, showing that Scc2, which stimulates cohesin ATPase activity, is essential for the translocation process required to extend DNA loop length. Eco1-dependent acetylation of Smc3 during S phase counteracts this activity through the stabilization of Pds5, to finely tune loop sizes and stability during G2. Inhibiting Pds5 in G2 leads to a strong enlargement of pre-established, stable DNA loops, in a Scc2-dependent manner. Altogether, the study strongly supports a Scc2-mediated translocation process driving expansion of DNA loops in living cells.
Published: 2021

19. Sir3 mediates long-range chromosome interactions in budding yeast

Author: Romain Koszul, Angela Taddei, Luciana Lazar-Stefanita, Antoine Hocher, Myriam Ruault, Vittore F. Scolari, Isabelle Loïodice, Dynamique du noyau [Institut Curie], Institut Curie [Paris]-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Collège doctoral [Sorbonne universités], Sorbonne Université (SU), Laboratoire Cogitamus, A.T. team was financially supported by funding from the Labex DEEP (ANR-11-LABEX-0044 DEEP and ANR-10-IDEX-0001-02 PSL), from the ANR DNA-Life (ANR-15-CE12-0007), Fondation pour la Recherche Médicale (DEP20151234398), and CNRS grant 80prime PhONeS.The authors greatly acknowledge the PICT-IBiSA@Pasteur Imaging Facility of the Institut Curie, member of the France Bioimaging National Infrastructure (ANR-10-INBS-04).V.F.S. is the recipient of a Roux-Cantarini Pasteur fellowship. L.L.S. was supported in part by a fellowship from the Fondation pour la Recherche Médicale. This research was supported by funding to R.K. from the European Research Council under the Horizon 2020 Program (ERC grant agreement 771813)., ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), ANR-15-CE12-0007,DNA-Life,Impact de l'achitecture nucléaire sur la longévité(2015), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), European Project: 771813,SynarchiC, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Collège Doctoral, European Project: 771813,ERC-2017-COG,SynarchiC(2018), HAL-SU, Gestionnaire, Initiative d'excellence - Paris Sciences et Lettres - - PSL2010 - ANR-10-IDEX-0001 - IDEX - VALID, Impact de l'achitecture nucléaire sur la longévité - - DNA-Life2015 - ANR-15-CE12-0007 - AAPG2015 - VALID, Développment d'une infrastructure française distribuée coordonnée - - France-BioImaging2010 - ANR-10-INBS-0004 - INBS - VALID, Investigating the functional architecture of microbial genomes with synthetic approaches - SynarchiC - - ERC-2017-COG2018-04-01 - 2023-09-30 - 771813 - VALID, Laboratoire Physico-Chimie Curie [Institut Curie] (PCC), and Institut Curie [Paris]-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Heterochromatin, nuclear organization, Context (language use), Saccharomyces cerevisiae, Biology, yeast, Genome, DNA, Ribosomal, 03 medical and health sciences, 0302 clinical medicine, Sirtuin 2, Hi-C, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, nucleolus, Genetics (clinical), Silent Information Regulator Proteins, Saccharomyces cerevisiae, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, 030304 developmental biology, 0303 health sciences, Research, heterochromatin, Chromosome, Telomere, Subtelomere, telomeres, [SDV.MP.MYC] Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Rap1, Chromosomes, Fungal, 030217 neurology & neurosurgery, Function (biology)
Abstract: Physical contacts between distant loci contribute to regulate genome function. However, the molecular mechanisms responsible for settling and maintaining such interactions remain poorly understood. Here, we investigate the well-conserved interactions between heterochromatin loci. In budding yeast, the 32 telomeres cluster in 3–5 foci in exponentially growing cells. This clustering is functionally linked to the formation of heterochromatin in subtelomeric regions through the recruitment of the silencing SIR complex composed of Sir2/3/4. Combining microscopy and Hi-C on strains expressing different alleles of SIR3, we show that the binding of Sir3 directly promotes long-range contacts between distant regions, including the rDNA, telomeres, and internal Sir3-bound sites. Furthermore, we unveil a new property of Sir3 in promoting rDNA compaction. Finally, using a synthetic approach, we demonstrate that Sir3 can bond loci belonging to different chromosomes together, when targeted to these loci, independently of its interaction with its known partners (Rap1, Sir4), Sir2 activity, or chromosome context. Altogether, these data suggest that Sir3 acts as a molecular bridge that stabilizes long-range interactions.
Published: 2021

20. Euryarchaeal genomes are folded into SMC-dependent loops and domains, but lack transcription-mediated compartmentalization

Author: Romain Koszul, Charlotte Cockram, Agnès Thierry, Aurore Gorlas, Roxane Lestini, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-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), Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), This research was supported by funding to R.K. from the European Research Council under the Horizon 2020 Program (ERC grant agreement 771813)., European Project: 771813,SynarchiC, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), European Project: 771813,ERC-2017-COG,SynarchiC(2018), CCSD, Accord Elsevier, and Investigating the functional architecture of microbial genomes with synthetic approaches - SynarchiC - - ERC-2017-COG2018-04-01 - 2023-09-30 - 771813 - VALID
Subjects: Halobacterium salinarum, Transcription, Genetic, Operon, Chromosomes, Archaeal, archaea, euryarchaeota, Computational biology, [SDV.GEN] Life Sciences [q-bio]/Genetics, Biology, high-resolution, Genome, DNA loops, 03 medical and health sciences, 0302 clinical medicine, Crenarchaeota, Genome, Archaeal, Hi-C, Nucleotide Motifs, bacteria, Molecular Biology, Gene, Haloferax volcanii, Phylogeny, 030304 developmental biology, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, SMC, Chromosome, Cell Biology, biology.organism_classification, Chromatin Assembly and Disassembly, Chromatin, Cell Compartmentation, chromosome organization, Thermococcus, DNA, Archaeal, compartments, Euryarchaeota, Gene Expression Regulation, Archaeal, transcription, 030217 neurology & neurosurgery, Archaea
Abstract: International audience; Hi-C has become a routine method for probing the 3D organization of genomes. However, when applied to prokaryotes and archaea, the current protocols are expensive and limited in their resolution. We develop a cost-effective Hi-C protocol to explore chromosome conformations of these two kingdoms at the gene or operon level. We first validate it on E. coli and V. cholera, generating sub-kilobase-resolution contact maps, and then apply it to the euryarchaeota H. volcanii, Hbt. salinarum, and T. kodakaraensis. With a resolution of up to 1 kb, we explore the diversity of chromosome folding in this phylum. In contrast to crenarchaeota, these euryarchaeota lack (active/inactive) compartment-like structures. Instead, their genomes are composed of self-interacting domains and chromatin loops. In H. volcanii, these structures are regulated by transcription and the archaeal structural maintenance of chromosomes (SMC) protein, further supporting the ubiquitous role of these processes in shaping the higher-order organization of genomes.
Published: 2021

21. Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization

Author: Myriam Harry, Bernard Duvic, Anthony Bretaudeau, Hélène Boulain, Jetske G. de Boer, Jean-Marc Aury, Claire Capdevielle-Dulac, Annie Bézier, Diane Bigot, Natacha Kremer, Laure Kaiser, Lyam Baudry, Joke J.F.A. van Vugt, Jean-Michel Drezen, Georges Periquet, Stéphane Dupas, Romain Koszul, Aurélie Hua-Van, Jérémy Gauthier, Fabrice Legeai, Emma Persyn, Mahnaz Sabeti-Azad, Fernando Luis Cônsoli, Valérie Barbe, Joelle Amselem, Karine Labadie, Benjamin Noel, Frédérique Hilliou, Martine Maïbèche, Géraldine Dubreuil, Isabelle Luyten, Karine Musset, Martial Marbouty, Christophe Bressac, Isabelle Boulogne, Louise E. M. Vet, Thibaut Josse, Philippe Gayral, Hans M. Smid, Emmanuelle Jacquin-Joly, David Siaussat, James B. Whitfield, Elisabeth A. Herniou, Mohamed Amine Chebbi, Thomas Chertemps, Nicolas Montagné, Sébastien J. M. Moreau, Elisabeth Huguet, Bruna Laís Merlin, Gaëlle Le Goff, Sven Warris, Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours-Centre National de la Recherche Scientifique (CNRS), Natural History Museum [Geneva], Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Collège doctoral [Sorbonne universités], Sorbonne Université (SU), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Wageningen University and Research [Wageningen] (WUR), Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Recherche Génomique Info (URGI), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), Universidade de São Paulo (USP), Department of Entomology [Urbana], University of Illinois System, Department of Terrestrial Ecology [Wageningen], Netherlands Institute of Ecology (NIOO-KNAW), ANR-12-ADAP-0001, Agence Nationale de la Recherche, Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Collège Doctoral, Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Universidade de São Paulo = University of São Paulo (USP), ANR-12-ADAP-0001,ABC - PaPoGen,Adaptation en lutte biologique - Génomique des populations de parasitoïdes(2012), Evolutionary Genetics, Development & Behaviour, Terrestrial Ecology (TE), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique)
Subjects: Genome evolution, food.ingredient, QH301-705.5, Bioinformatics, [SDV]Life Sciences [q-bio], Medicine (miscellaneous), macromolecular substances, Biology, Genome, Article, Evolutionary genetics, General Biochemistry, Genetics and Molecular Biology, Plan_S-Compliant-OA, Parasitoid wasp, 03 medical and health sciences, BIOS Applied Bioinformatics, 0302 clinical medicine, food, Bioinformatica, Life Science, Cotesia congregata, VÍRUS DE DNA, Biology (General), Laboratory of Entomology, Gene, 030304 developmental biology, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, Human evolutionary genetics, Chromosome, biology.organism_classification, PE&RC, Laboratorium voor Entomologie, Evolutionary biology, international, EPS, General Agricultural and Biological Sciences, Bracovirus, Entomology, 030217 neurology & neurosurgery
Abstract: Endogenous viruses form an important proportion of eukaryote genomes and a source of novel functions. How large DNA viruses integrated into a genome evolve when they confer a benefit to their host, however, remains unknown. Bracoviruses are essential for the parasitism success of parasitoid wasps, into whose genomes they integrated ~103 million years ago. Here we show, from the assembly of a parasitoid wasp genome at a chromosomal scale, that bracovirus genes colonized all ten chromosomes of Cotesia congregata. Most form clusters of genes involved in particle production or parasitism success. Genomic comparison with another wasp, Microplitis demolitor, revealed that these clusters were already established ~53 mya and thus belong to remarkably stable genomic structures, the architectures of which are evolutionary constrained. Transcriptomic analyses highlight temporal synchronization of viral gene expression without resulting in immune gene induction, suggesting that no conflicts remain between ancient symbiotic partners when benefits to them converge., Jeremy Gauthier et al. present the chromosome scale assembly of the genome of the parasitic wasp C. congregata and show that bracovirus genes have colonized all ten chromosomes. Comparison with genome scaffolds of another wasp reveals a striking stability of these regions over ~53 million years, suggesting strong evolutionary constraints.
Published: 2021

22. Gene level resolution of bacteria and archaea genome folding

Author: Cockram, Charlotte, Thierry, Agnès, Lestini, Roxane, Koszul, Romain, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Koszul, Romain, and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV] Life Sciences [q-bio], [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV]Life Sciences [q-bio], [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.GEN] Life Sciences [q-bio]/Genetics, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Published: 2021

23. Nucleosome Positioning on Large Tandem DNA Repeats of the ‘601’ Sequence Engineered in Saccharomyces cerevisiae

Author: Agnès Thierry, Astrid Lancrey, Marta Sigarteu, Saurabh Raj, Evelyne Duvernois-Berthet, Etienne Routhier, Loïc Ponger, Vincent Croquette, Julien Mozziconacci, Jean-Baptiste Boulé, Alexandra Joubert, 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), Physiologie moléculaire et adaptation (PhyMA), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Laboratoire de physique de l'ENS - ENS Paris (LPENS), Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Sorbonne Université (SU)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL), This work was supported by a grant from the national research agency (MuSeq, ANR-15-CE12-0015) and by core funding from CNRS, INSERM and MNHN to the Structure and Genome instability unit. French Museum of National History to the Genome Structure and Instability unit. AL was supported by a doctoral fellowship from the National Museum of Natural History. Work in the group of VC is part of 'Institut Pierre-Gilles de Gennes' ('Investissements d’Avenir' program ANR-10-IDEX-0001-02 PSL and ANR-10-LABX-31) and the Qlife Institute of Convergence (PSL Université)., The authors thank the members of the Genome Structure and Instability unit for discussions and Dr Romain Koszul for providing assistance with sequencing., ANR-15-CE12-0015,Museq,Séquençage multi-échelle d'ADN génomique répété G/C riche par manipulation en molecule unique en pinces magnétiques(2015), ANR-10-LABX-0031,IPGG_LABEX,Pierre-Gilles de Gennes Institute for microfluidics(2010), Laboratoire de physique de l'ENS - ENS Paris (LPENS (UMR_8023)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPC), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Département de Physique de l'ENS-PSL, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), ABCD : Biophysique des Biomolécules, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Département de Physique de l'ENS-PSL, Boulé, Jean-Baptiste, Séquençage multi-échelle d'ADN génomique répété G/C riche par manipulation en molecule unique en pinces magnétiques - - Museq2015 - ANR-15-CE12-0015 - AAPG2015 - VALID, and Pierre-Gilles de Gennes Institute for microfluidics - - IPGG_LABEX2010 - ANR-10-LABX-0031 - LABX - VALID
Subjects: Base pair, [SDV]Life Sciences [q-bio], Context (language use), Computational biology, Saccharomyces cerevisiae, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, DNA sequencing, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Tandem repeat, Structural Biology, Nucleosome, A-DNA, DNA, Fungal, Molecular Biology, 030304 developmental biology, Sequence (medicine), 0303 health sciences, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Chemistry, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Chromatin Assembly and Disassembly, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Nucleosomes, [SDV] Life Sciences [q-bio], Tandem Repeat Sequences, Genetic Engineering, 030217 neurology & neurosurgery, DNA
Abstract: The so-called 601 DNA sequence is often used to constrain the position of nucleosomes on a DNA molecule in vitro. Although the ability of the 147 base pair sequence to precisely position a nucleosome in vitro is well documented, in vivo application of this property has been explored only in a few studies and yielded contradictory conclusions. Our goal in the present study was to test the ability of the 601 sequence to dictate nucleosome positioning in Saccharomyces cerevisiae in the context of a long tandem repeat array inserted in a yeast chromosome. We engineered such arrays with three different repeat size, namely 167, 197 and 237 base pairs. Although our arrays are able to position nucleosomes in vitro as expected, analysis of nucleosome occupancy on these arrays in vivo revealed that nucleosomes are not preferentially positioned as expected on the 601-core sequence along the repeats and that the measured nucleosome repeat length does not correspond to the one expected by design. Altogether our results demonstrate that the rules defining nucleosome positions on this DNA sequence in vitro are not valid in vivo, at least in this chromosomal context, questioning the relevance of using the 601 sequence in vivo to achieve precise nucleosome positioning on designer synthetic DNA sequences.
Published: 2022

24. Computer vision for pattern detection in chromosome contact maps

Author: Axel Breuer, Axel Cournac, Antoine Vigouroux, Etienne Jean, Adrien Meot, Edgar Oriol, Romain Koszul, Laurent Politis, Arnaud Campeas, Nadège Guiglielmoni, Cyril Matthey-Doret, Lyam Baudry, Vittore F. Scolari, Philippe Henri Chanut, Pierrick Moreau, Rémi Montagne, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Collège doctoral [Sorbonne universités], Sorbonne Université (SU), ENGIE, Biologie de Synthèse - Synthetic biology, Institut Pasteur [Paris], Département de Biologie Computationnelle - Department of Computational Biology, This work used the computational and storage services (TARS cluster) provided by the IT department at Institut Pasteur, Paris. C.M.-D. was supported by the Pasteur—Paris University (PPU) International PhD Program. A.B. works within the framework of a 'Mécénat Compétence' contract of the company ENGIE. V.S. is the recipient of a Roux-Cantarini Pasteur fellowship. This research was supported by funding to R.K. from the European Research Council under the Horizon 2020 Program (ERC grant agreement 771813) and by ANR JCJC 2019, 'Apollo' allocated to A.C., This work was initiated during a Hackathon between Institut Pasteur scientists and ENGIE engineers. We would like to thank all the people that allow the organisation of this event especially Anne-Gaelle Coutris, Romain Tchertchian and Olivier Gascuel. Julien Mozziconacci, Frédéric Beckouët and all the members of Spatial Regulation of Genomes unit are thanked for stimulating discussions and feedback., ANR-19-CE45-0003,Apollo,Intelligence Artificielle pour atteindre la face cachée des chromosomes(2019), European Project: 771813,SynarchiC, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Collège Doctoral, Institut Pasteur [Paris] (IP), and European Project: 771813,ERC-2017-COG,SynarchiC(2018)
Subjects: 0301 basic medicine, Computer science, [SDV]Life Sciences [q-bio], General Physics and Astronomy, Genome informatics, Genome, Pattern Recognition, Automated, Workflow, Chromosome conformation capture, chemistry.chemical_compound, 0302 clinical medicine, Chromosomes, Human, MESH: Pattern Recognition, Automated, Computer vision, lcsh:Science, 0303 health sciences, Multidisciplinary, Fungal genetics, MESH: Chromosomes, Fungal, MESH: Saccharomyces cerevisiae, Chromatin, Data processing, Simulated data, MESH: Genome, Fungal, Pattern recognition (psychology), Chromosomes, Fungal, Genome, Fungal, Algorithms, MESH: Computers, Bioinformatics, Science, MESH: Algorithms, Saccharomyces cerevisiae, MESH: Chromosomes, Human, Chromosomes, Article, General Biochemistry, Genetics and Molecular Biology, MESH: Workflow, 03 medical and health sciences, Pattern detection, Code (cryptography), Humans, 030304 developmental biology, Nuclear organization, MESH: Humans, Computers, business.industry, Chromosome, General Chemistry, 030104 developmental biology, chemistry, lcsh:Q, MESH: Chromosomes, Artificial intelligence, business, DNA, 030217 neurology & neurosurgery
Abstract: Chromosomes of all species studied so far display a variety of higher-order organisational features, such as self-interacting domains or loops. These structures, which are often associated to biological functions, form distinct, visible patterns on genome-wide contact maps generated by chromosome conformation capture approaches such as Hi-C. Here we present Chromosight, an algorithm inspired from computer vision that can detect patterns in contact maps. Chromosight has greater sensitivity than existing methods on synthetic simulated data, while being faster and applicable to any type of genomes, including bacteria, viruses, yeasts and mammals. Our method does not require any prior training dataset and works well with default parameters on data generated with various protocols., Chromatin loops bridging distant loci within chromosomes can be detected by a variety of techniques such as Hi-C. Here the authors present Chromosight, an algorithm applied on mammalian, bacterial, viral and yeast genomes, able to detect various types of pattern in chromosome contact maps, including chromosomal loops.
Published: 2020

25. 4-Methylcytosine DNA modification is critical for global epigenetic regulation and virulence in the human pathogen Leptospira interrogans

Author: Céline Lorioux, Robert A. Gaultney, Jean-Yves Coppée, Charlotte Cockram, Odile Sismeiro, Rachel Legendre, Frédéric J. Veyrier, Mathieu Picardeau, Hugo Varet, Antony T. Vincent, Biologie des Spirochètes / Biology of Spirochetes, Institut Pasteur [Paris], Institut Armand Frappier (INRS-IAF), Réseau International des Instituts Pasteur (RIIP)-Institut National de la Recherche Scientifique [Québec] (INRS), Pôle Biomics (C2RT), Centre de Ressources et de Recherche Technologique - Center for Technological Resources and Research (C2RT), Institut Pasteur [Paris]-Institut Pasteur [Paris], Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [PTR 30-2017 to M.P.], ANR 18 CE15 0027 LEPTOMOVE to M.P., Pasteur Foundation Fellowship to R.A.G. (April 2017–June 2020), ERC grant agreement 771813 to R.K., Fellowship from the Natural Sciences and Engineering Research Council of Canada to ATV. FJV is a research scholar of the Fonds de Recherche du Québec-Santé. Funding for open access charge: Institut Pasteur., We thank Drs. Matsunaga and Haake for providing plasmid pRAT724 and Dr. Koszul for feedback on CCMs. We thank Dr. Linda Grillova for aid with bioinformatic analysis and critical reading of the manuscript. We also thank Drs. Simonetta Gribaldo and Nadia Benaroudj for critical reading of the manuscript., ANR-18-CE15-0027,LEPTOMOVE,Mécanismes moléculaires de la motilité chez les spirochètes: le modèle de l'endoflagelle des leptospires(2018), Institut Pasteur [Paris] (IP), Institut National de la Recherche Scientifique [Québec] (INRS)-Réseau International des Instituts Pasteur (RIIP), Institut Pasteur [Paris] (IP)-Institut Pasteur [Paris] (IP), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: DNA, Bacterial, Methyltransferase, Transcription, Genetic, AcademicSubjects/SCI00010, [SDV]Life Sciences [q-bio], Sigma Factor, Biology, Epigenesis, Genetic, 03 medical and health sciences, Cytosine, Bacterial Proteins, Sigma factor, Genetics, Animals, Leptospirosis, Epigenetics, DNA (Cytosine-5-)-Methyltransferases, Promoter Regions, Genetic, Gene, 030304 developmental biology, Regulation of gene expression, 0303 health sciences, Mesocricetus, Virulence, 030306 microbiology, Gene regulation, Chromatin and Epigenetics, Gene Expression Regulation, Bacterial, DNA Methylation, biology.organism_classification, Survival Analysis, Regulon, DNA methylation, Leptospira interrogans, Genome, Bacterial
Abstract: In bacteria, DNA methylation can be facilitated by ‘orphan’ DNA methyltransferases lacking cognate restriction endonucleases, but whether and how these enzymes control key cellular processes are poorly understood. The effects of a specific modification, 4-methylcytosine (4mC), are even less clear, as this epigenetic marker is unique to bacteria and archaea, whereas the bulk of epigenetic research is currently performed on eukaryotes. Here, we characterize a 4mC methyltransferase from the understudied pathogen Leptospira spp. Inactivating this enzyme resulted in complete abrogation of CTAG motif methylation, leading to genome-wide dysregulation of gene expression. Mutants exhibited growth defects, decreased adhesion to host cells, higher susceptibility to LPS-targeting antibiotics, and, importantly, were no longer virulent in an acute infection model. Further investigation resulted in the discovery of at least one gene, that of an ECF sigma factor, whose transcription was altered in the methylase mutant and, subsequently, by mutation of the CTAG motifs in the promoter of the gene. The genes that comprise the regulon of this sigma factor were, accordingly, dysregulated in the methylase mutant and in a strain overexpressing the sigma factor. Our results highlight the importance of 4mC in Leptospira physiology, and suggest the same of other understudied species.
Published: 2020

26. Serological signatures of SARS-CoV-2 infection: Implications for antibody-based diagnostics

Author: François Dejardin, Caroline Demeret, Narimane Nekkab, Charlotte Cockram, Michael T. White, Rhea J. Longley, Annalisa Meola, Marija Backovic, Sarah H. Merkling, Stéphane Petres, Jérôme De Seze, Ivo Mueller, Solen Kernéis, Samira Fafi-Kremer, Benjamin Terrier, Stéphane Pelleau, Jason Rosado, Malaria : parasites et hôtes - Malaria : parasites and hosts, Institut Pasteur [Paris], Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Interactions Virus-Insectes - Insect-Virus Interactions (IVI), Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Virologie Structurale, Equipe mobile d'infectiologie, CHU Necker - Enfants Malades [AP-HP], Epidémiologie et modélisation de la résistance aux antimicrobiens - Epidemiology and modelling of bacterial escape to antimicrobials, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de Référence Maladies auto-immunes Systémiques Rares [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Pitié-Salpêtrière [APHP], Paris-Centre de Recherche Cardiovasculaire (PARCC - UMR-S U970), Hôpital Européen Georges Pompidou [APHP] (HEGP), Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Virologie [Strasbourg], CIC Strasbourg (Centre d’Investigation Clinique Plurithématique (CIC - P) ), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Strasbourg (UNISTRA)-Hôpital de Hautepierre [Strasbourg]-Nouvel Hôpital Civil de Strasbourg, The Walter and Eliza Hall Institute of Medical Research (WEHI), Santé publique : épidémiologie & sciences de l'information biomédicale (ED 393), Sorbonne Université (SU), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Virologie Structurale - Structural Virology, Epidémiologie et modélisation de la résistance aux antimicrobiens - Epidemiology and modelling of bacterial escape to antimicrobials (EMAE), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Melbourne, This work was supported by the European Research Council (MultiSeroSurv ERC Starting Grant, MW), l’Agence Nationale de la Recherche and Fondation pour la Recherche Médicale (CorPopImm, MW), and the Institut Pasteur International Network (CoronaSeroSurv, MW). JR was supported by the Pasteur Paris University (PPU) International PhD Program, Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Nouvel Hôpital Civil de Strasbourg-Hôpital de Hautepierre [Strasbourg], Michael, White, Service de Département de médecine interne et immunologie clinique [CHU Pitié-Salpêtrière] (DMIIC), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), and Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), [SDV]Life Sciences [q-bio], Serology, Peak response, 03 medical and health sciences, 0302 clinical medicine, Antigen, Medicine, Multiplex, 030212 general & internal medicine, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, 030304 developmental biology, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, 0303 health sciences, biology, business.industry, Serum samples, Confidence interval, 3. Good health, [SDV] Life Sciences [q-bio], [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Immunology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, biology.protein, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Antibody, business
Abstract: BackgroundInfection with SARS-CoV-2 induces an antibody response targeting multiple antigens that changes over time. This complexity presents challenges and opportunities for serological diagnostics.MethodsA multiplex serological assay was developed to measure IgG and IgM antibody responses to seven SARS-CoV-2 spike or nucleoprotein antigens, two antigens for the nucleoproteins of the 229E and NL63 seasonal coronaviruses, and three non-coronavirus antigens. Antibodies were measured in serum samples from patients in French hospitals with RT-qPCR confirmed SARS-CoV-2 infection (n= 259), and negative control serum samples collected before the start of the SARS-CoV-2 epidemic (n= 335). A random forests algorithm was trained with the multiplex data to classify individuals with previous SARS-CoV-2 infection. A mathematical model of antibody kinetics informed by prior information from other coronaviruses was used to estimate time-varying antibody responses and assess the potential sensitivity and classification performance of serological diagnostics during the first year following symptom onset. A statistical estimator is presented that can provide estimates of seroprevalence in very low transmission settings.ResultsIgG antibody responses to trimeric Spike protein identified individuals with previous RT-qPCR confirmed SARS-CoV-2 infection with 91.6% sensitivity (95% confidence interval (CI); 87.5%, 94.5%) and 99.1% specificity (95% CI; 97.4%, 99.7%). Using a serological signature of IgG and IgM to multiple antigens, it was possible to identify infected individuals with 98.8% sensitivity (95% CI; 96.5%, 99.6%) and 99.3% specificity (95% CI; 97.6%, 99.8%). Informed by prior data from other coronaviruses, we estimate that one year following infection a monoplex assay with optimal anti-StriIgG cutoff has 88.7% sensitivity (95% CI: 63.4%, 97.4%), and that a multiplex assay can increase sensitivity to 96.4% (95% CI: 80.9%, 100.0%). When applied to population-level serological surveys, statistical analysis of multiplex data allows estimation of seroprevalence levels less than 1%, below the false positivity rate of many other assays.ConclusionSerological signatures based on antibody responses to multiple antigens can provide accurate and robust serological classification of individuals with previous SARS-CoV-2 infection. This provides potential solutions to two pressing challenges for SARS-CoV-2 serological surveillance: classifying individuals who were infected greater than six months ago, and measuring seroprevalence in serological surveys in very low transmission settings.
Published: 2020

27. Chromosomal resolution reveals symbiotic virus colonization of parasitic wasp genomes

Author: Gauthier, Jérémy, BOULAIN, Hélène, van Vugt, Joke J.F.A., Baudry, Lyam, Persyn, Emma, Aury, Jean-Marc, Noel, Benjamin, Bretaudeau, Anthony, Legeai, Fabrice, Warris, Sven, Chebbi, Mohamed Amine, Dubreuil, Géraldine, Duvic, Bernard, Kremer, Natacha, Gayral, Philippe, Musset, Karine, Josse, Thibaut, Bigot, Diane, Bressac, Christophe, Moreau, Sébastien, Periquet, Georges, Harry, Myriam, Montagne, Nicolas, Boulogne, Isabelle, Sabeti-Azad, Mahnaz, Maïbèche, Martine, Chertemps, Thomas, Hilliou, Frédérique, Siaussat, David, Amselem, Joëlle, Luyten, Isabelle, Capdevielle-Dulac, Claire, Labadie, Karine, Merlin, Bruna Laís, Barbe, Valérie, de Boer, Jetske, Marbouty, Martial, Cônsoli, Fernando Luis, Vet, Louise E.M., Cônsoli, Fernando, Dupas, Stéphane, Hua Van, Aurélie, Le Goff, Gaëlle, Bézier, Annie, Jacquin-Joly, Emmanuelle, Whitfield, James, Vet, Louise, Smid, Hans, Kaiser-Arnault, Laure, Koszul, Romain, Huguet, Elisabeth, Herniou, Elisabeth, Drezen, Jean-Michel, Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Collège Doctoral, Sorbonne Université (SU), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Unité de Recherche Génomique Info (URGI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), France Génomique (UMS CNRS 3628 - INRAE 1396 - Inserm 026), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nederlands Instituut Voor Ecologie - NIOO (NETHERLANDS), Université de Tours-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AGROCAMPUS OUEST, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Collège doctoral [Sorbonne universités], Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Nice Sophia Antipolis (... - 2019) (UNS), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 0303 health sciences, food.ingredient, Host (biology), [SDV]Life Sciences [q-bio], fungi, Duurzame gewasbescherming, Parasitism, Biology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Genome, Virus, Wespen, Parasitoid wasp, Parasitoid, 03 medical and health sciences, food, Evolutionary biology, Bracovirus, Gene, 030304 developmental biology
Abstract: Most endogenous viruses, an important proportion of eukaryote genomes, are doomed to slowly decay. Little is known, however, on how they evolve when they confer a benefit to their host. Bracoviruses are essential for the parasitism success of parasitoid wasps, whose genomes they integrated ~103 million years ago. Here we show, from the assembly of a parasitoid wasp genome, for the first time at a chromosomal scale, that symbiotic bracovirus genes spread to and colonized all the chromosomes. Moreover, large viral clusters are stably maintained suggesting strong evolutionary constraints. Genomic comparison with another wasps revealed that this organization was already established ~53 mya. Transcriptomic analyses highlight temporal synchronization of viral gene expression, leading to particle production. Immune genes are not induced, however, indicating the virus is not perceived as foreign by the wasp. This recognition suggests that no conflicts remain between symbiotic partners when benefits to them converge.
Published: 2020
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28. Regulation of Cohesin-Mediated Chromosome Folding by Eco1 and Other Partners

Author: Romain Koszul, Luciana Lazar-Stefanita, Olivier Gadal, Nathalie Bastié, Agnès Thierry, Rémi Montagne, Lise Dauban, Axel Cournac, Frédéric Beckouët, Laboratoire de biologie moléculaire eucaryote (LBME), Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-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), L.D. was supported by ARC fellowships. L.L.S. was partially supported by a fellowship from Fondation pour la Recherche Médicale (SPE201801005113). This research was supported by funding to R.K. from the European Research Council under the Horizon 2020 Program (ERC grant agreement 260822)., We thank T.U. Tanaka, Kerstin Bystricky, and K. Nasmyth for sharing strains and K. Shiahige for the Smc3 antibody. We thank Aurèle Piazza, Dave Lane, Luis Aragon, Julien Mozziconacci, Christophe Chapard, Olivier Cuvier, Tony Marchal, and O.G. and R.K. teams for discussions and comments on the manuscript., European Project: 260822,EC:FP7:ERC,ERC-2010-StG_20091118,DICIG(2011), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Saccharomyces cerevisiae Proteins, Chromosomal Proteins, Non-Histone, [SDV]Life Sciences [q-bio], Pds5, Cell Cycle Proteins, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Biology, Chromatids, 03 medical and health sciences, 0302 clinical medicine, Acetyltransferases, Hi-C, Wapl, Chromosome Segregation, Centromere, Translocase, Sister chromatids, saccharomyces cerevisiae, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Eco1, Molecular Biology, Mitosis, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, mitosis, 0303 health sciences, chromatin loop, [SDV.GEN]Life Sciences [q-bio]/Genetics, loop extrusion, Cohesin, Chromosome, Nuclear Proteins, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell Biology, Cell biology, Chromatin, chromosome organization, biology.protein, Chromatin Loop, cell cycle, biological phenomena, cell phenomena, and immunity, Chromosomes, Fungal, 030217 neurology & neurosurgery
Abstract: International audience; Cohesin, a member of the SMC complex family, holds sister chromatids together but also shapes chromosomes by promoting the formation of long-range intra-chromatid loops, a process proposed to be mediated by DNA loop extrusion. Here we describe the roles of three cohesin partners, Pds5, Wpl1, and Eco1, in loop formation along either unreplicated or mitotic Saccharomyces cerevisiae chromosomes. Pds5 limits the size of DNA loops via two different pathways: the canonical Wpl1-mediated releasing activity and an Eco1-dependent mechanism. In the absence of Pds5, the main barrier to DNA loop expansion appears to be the centromere. Our data also show that Eco1 acetyl-transferase inhibits the translocase activity that powers loop formation and contributes to the positioning of loops through a mechanism that is distinguishable from its role in cohesion establishment. This study reveals that the mechanisms regulating cohesin-dependent chromatin loops are conserved among eukaryotes while promoting different functions.
Published: 2020

29. Perspectives on Chromosome Organization

Author: Marcelo Nollmann, Romain Koszul, Koszul, Romain, Centre de Biochimie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-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), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genetics, Biomedical Research, Macromolecular Substances, [SDV]Life Sciences [q-bio], Molecular Conformation, Chromosome Organization, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Biology, Chromatin, [SDV] Life Sciences [q-bio], Structural Biology, [SDV.BC.BC] Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Molecular Biology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2020

30. The silencing factor Sir3 is a molecular bridge that sticks together distant loci

Author: Romain Koszul, Luciana Lazar-Stefanita, Isabelle Loïodice, Vittore F. Scolari, Angela Taddei, Myriam Ruault, Antoine Hocher, Camille Noûs, Taddei, Angela, Initiative d'excellence - Paris Sciences et Lettres - - PSL2010 - ANR-10-IDEX-0001 - IDEX - VALID, Investigating the functional architecture of microbial genomes with synthetic approaches - SynarchiC - - ERC-2017-COG2018-04-01 - 2023-09-30 - 771813 - VALID, Dynamique du noyau [Institut Curie], Institut Curie [Paris]-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Cogitamus, A.T. team was financially supported by funding from the Labex DEEP (ANR-11-LABEX-0044 DEEP and ANR-10-IDEX-0001-02 PSL), from the ANR DNA-Life (ANR-15-CE12-0007), Fondation pour la Recherche Médicale (DEP20151234398), and CNRS grant 80prime PhONeS, the authors greatly acknowledge the PICT-IBiSA@Pasteur Imaging Facility of the Institut Curie, member of the France Bioimaging National Infrastructure (ANR-10-INBS-04).V.S. is the recipient of a Roux-Cantarini Pasteur fellowship. L.L.S. was supported in part by a fellowship from the Fondation pour la Recherche Médicale. This research was supported by funding to R.K. from the European Research Council under the Horizon 2020 Program (ERC grant agreement 771813)., ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), European Project: 771813,ERC-2017-COG,SynarchiC(2018), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and European Project: 771813,SynarchiC
Subjects: 0303 health sciences, Heterochromatin, [SDV]Life Sciences [q-bio], heterochromatin, Chromosome, Context (language use), Biology, Subtelomere, telomeres, Genome, Telomere, [SDV] Life Sciences [q-bio], 03 medical and health sciences, 0302 clinical medicine, Evolutionary biology, Hi-C, yeast nuclear organization, Gene silencing, Allele, nucleolus, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: Physical contacts between distant loci contribute to regulate genome function. However, the molecular mechanisms responsible for settling and maintaining such interactions remain poorly understood. Here we investigate the well conserved interactions between heterochromatin loci. In budding yeast, the 32 telomeres cluster in 3-5 foci in exponentially growing cells. This clustering is functionally linked to the formation of heterochromatin in subtelomeric regions through the recruitment of the silencing complex SIR composed of Sir2/3/4. Combining microscopy and Hi-C on strains expressing different alleles ofSIR3, we show that the binding of Sir3 directly promotes long range contacts between distant regions, including the rDNA, telomeres, and internal Sir3 bound sites. Furthermore, we unveil a new property of Sir3 in promoting rDNA compaction. Finally, using a synthetic approach we demonstrate that Sir3 can bond loci belonging to different chromosomes together, when targeted to these loci, independently of its interaction with its known partners (Rap1, and Sir4), Sir2 activity or chromosome context. Altogether these data suggest that Sir3 represents an uncommon example of protein able to bridge directly distant loci.
Published: 2020

31. Crosstalk between Hepatitis B Virus and the 3D Genome Structure

Author: João Diogo Dias, Nazim Sarica, Axel Cournac, Romain Koszul, Christine Neuveut, Institut de génétique humaine (IGH), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), and This research was funded by Agence Nationale de Recherches sur le Sida et les Hépatites Virales (ANRS), grant number EZT88522. J.D.D. was supported by ANRS.
Subjects: Hepatitis B virus, Carcinoma, Hepatocellular, MESH: Hepatitis B, Chronic, [SDV]Life Sciences [q-bio], viruses, spatial nuclear organization, [SDV.CAN]Life Sciences [q-bio]/Cancer, Genome, Viral, Virus Replication, Hepatitis B, Chronic, Virology, HBV, Animals, Humans, MESH: Animals, MESH: Carcinoma, Hepatocellular, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Humans, MESH: Hepatitis B, HBV cccDNA, MESH: Virus Replication, Hepatitis B, MESH: DNA, Viral, MESH: Hepatitis B virus, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, DNA, Viral, MESH: DNA, Circular, MESH: Genome, Viral, DNA, Circular, DNA viruses, gene regulation
Abstract: International audience; Viruses that transcribe their DNA within the nucleus have to adapt to the existing cellular mechanisms that govern transcriptional regulation. Recent technological breakthroughs have highlighted the highly hierarchical organization of the cellular genome and its role in the regulation of gene expression. This review provides an updated overview on the current knowledge on how the hepatitis B virus interacts with the cellular 3D genome and its consequences on viral and cellular gene expression. We also briefly discuss the strategies developed by other DNA viruses to co-opt and sometimes subvert cellular genome spatial organization.
Published: 2022

32. Tridimensional infiltration of DNA viruses into the host genome shows preferential contact with active chromatin

Author: Martial Marbouty, Stefano Cairo, Christine Neuveut, Romain Koszul, Agnès Thierry, Gianna Aurora Palumbo, Marc Lavigne, Shogofa Mortaza, Axel Cournac, Pierrick Moreau, Hépacivirus et Immunité innée, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Régulation spatiale des Génomes - Spatial Regulation of Genomes, XenTech [Évry], Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Département de Virologie - Department of Virology, Institut Pasteur [Paris], This work was supported by funding to C.N. from the Agence Nationale de la Recherche sur le Sida et les Hépatites Virales (ANRS) and Fondation pour la Recherche sur le Cancer (ARC). This research was also supported by funding to R.K. from the European Research Council under the 7th and H2020 Framework Program (FP7/2007-2013, ERC grant agreement 260822 and H2020 ERC grant agreement DLV-771813), and from Agence Nationale pour la Recherche (MeioRec ANR-13-BSV6-0012). P.M. was supported by ANRS and Institut Carnot. This study makes use of data generated by the ENCODE Consortium and the ENCODE production laboratories., We thank C. Seeger and S. Urban for kindly providing cell lines used in this study. We thank the UTechS PBI (Imagopole)-DTPS/C2RT, part of the France-BioImaging infrastructure network supported by the ANR (ANR-10-INSB-04, Investments for theFuture), for the use of the Zeiss widefield apotome microscope., ANR-13-BSV6-0012,MeioRec,Dynamique chromosomique et recombinaison au cours de la méiose(2013), European Project: 260822,EC:FP7:ERC,ERC-2010-StG_20091118,DICIG(2011), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut Pasteur [Paris] (IP), THIERRY, AGNES, Blanc 2013 - Dynamique chromosomique et recombinaison au cours de la méiose - - MeioRec2013 - ANR-13-BSV6-0012 - Blanc 2013 - VALID, and Dynamic Interplay between Eukaryotic Chromosomes: Impact on Genome Stability - DICIG - - EC:FP7:ERC2011-06-01 - 2017-05-31 - 260822 - VALID
Subjects: 0301 basic medicine, Transcription, Genetic, viruses, General Physics and Astronomy, MESH: Base Sequence, Genome, chemistry.chemical_compound, MESH: Chromatin / metabolism, 0302 clinical medicine, Transcription (biology), Adenovirus, Viral Regulatory and Accessory Proteins, lcsh:Science, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Multidisciplinary, Virus–host interactions, Hep G2 Cells, MESH: Gene Expression Regulation, Chromatin, 3. Good health, Cell biology, Up-Regulation, CpG site, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Transcription Initiation Site, Transcription Initiation Site, Plasmids, Hepatitis B virus, Science, MESH: Hep G2 Cells, Biology, Models, Biological, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, MESH: Plasmids / metabolism, MESH: Genome, Human, MESH: Up-Regulation / genetics, Humans, MESH: DNA, Viral / genetics, Enhancer, Gene, Transcription factor, MESH: Humans, Base Sequence, Genome, Human, MESH: Transcription, Genetic, MESH: Models, Biological, General Chemistry, MESH: Hepatitis B virus / physiology, MESH: CpG Islands / genetics, MESH: Hepatocytes / virology, MESH: Trans-Activators / metabolism, 030104 developmental biology, chemistry, Gene Expression Regulation, DNA, Viral, Hepatocytes, Trans-Activators, CpG Islands, lcsh:Q, 030217 neurology & neurosurgery, DNA
Abstract: Whether non-integrated viral DNAs distribute randomly or target specific positions within the higher-order architecture of mammalian genomes remains largely unknown. Here we use Hi-C and viral DNA capture (CHi-C) in primary human hepatocytes infected by either hepatitis B virus (HBV) or adenovirus type 5 (Ad5) virus to show that they adopt different strategies in their respective positioning at active chromatin. HBV contacts preferentially CpG islands (CGIs) enriched in Cfp1 a factor required for its transcription. These CGIs are often associated with highly expressed genes (HEG) and genes deregulated during infection. Ad5 DNA interacts preferentially with transcription start sites (TSSs) and enhancers of HEG, as well as genes upregulated during infection. These results show that DNA viruses use different strategies to infiltrate genomic 3D networks and target specific regions. This targeting may facilitate the recruitment of transcription factors necessary for their own replication and contribute to the deregulation of cellular gene expression., Whether DNA viruses contact specific regions of host genomes or make random contacts is unclear. Here, the authors use Hi-C and show that HBV cccDNA and Ad5 DNA contact preferentially active chromatin at CpG islands for the former and at transcription start sites and enhancers for the latter.
Published: 2018

33. Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL, a proximity ligation-based scaffolder

Author: Hervé Marie-Nelly, Nadège Guiglielmoni, Susana M. Coelho, Romain Koszul, Alexandre Cormier, Komlan Avia, Christophe Zimmer, Martial Marbouty, Mie Yl, Sterck L, Lyam Baudry, Olivier Godfroy, J. M. Cock, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Collège Doctoral, Sorbonne Université (SU), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université libre de Bruxelles (ULB), Imagerie et Modélisation - Imaging and Modeling, This research was supported by funding to R.K. and S.M.C. from the European Research Council under the Horizon 2020 Program (ERC grant agreements 260822 and 638240, respectively) and from Agence Nationale pour la Recherche (JPI-EC-AMR STARCS ANR-16-JPEC-0003-05) to R.K. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 764840, 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), European Project: 638240,H2020,ERC-2014-STG,SEXSEA(2015), European Project: 764840,IGNITE, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Collège doctoral [Sorbonne universités]
Subjects: Scaffold, MCMC, Computer science, media_common.quotation_subject, [SDV]Life Sciences [q-bio], GPU, Sequence assembly, Locus (genetics), Computational biology, Hi-C scaffolding, Genome, 03 medical and health sciences, 0302 clinical medicine, Chromosome (genetic algorithm), Quality (business), 030304 developmental biology, media_common, 0303 health sciences, Contig, biology, business.industry, parallel computing, Chromosome, Ectocarpus, Modular design, biology.organism_classification, Hi-C genome assembly, Ligation, business, 030217 neurology & neurosurgery, Desmarestia herbacea
Abstract: Hi-C has become a popular technique in recent genome assembly projects. Hi-C exploits contact frequencies between pairs of loci to bridge and order contigs in draft genomes, resulting in chromosome-level assemblies. However, application of this approach is currently hampered by a lack of robust programs that are capable of effectively treating this type of data, particularly open source programs. We developed instaGRAAL, a complete overhaul of the GRAAL program, which has adapted the latter to allow efficient assembly of large genomes. Both GRAAL, and instaGRAAL use a Markov Chain Monte Carlo algorithm to perform Hi-C scaffolding, but instaGRAAL features a number of improvements including a modular polishing approach that optionally integrates independent data. To validate the program, we used it to generate chromosome-level assemblies for two brown algae, Desmarestia herbacea and the model Ectocarpus sp., and quantified improvements compared to the initial draft for the latter. Overall, instaGRAAL is a program able to generate, using default parameters with minimal human intervention, near-complete assemblies.
Published: 2019
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34. Proximity ligation scaffolding and comparison of two Trichoderma reesei strains genomes

Author: Jourdier, Etienne, Baudry, Lyam, Poggi-Parodi, Dante, Vicq, Yoan, Koszul, Romain, Margeot, Antoine, Marbouty, Martial, Bidard, Frédérique, IFP Energies nouvelles (IFPEN), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Chromosome conformation capture, Genome assembly, GRAAL, Trichoderma reesei, lcsh:Biotechnology, Centromere, Karyotype, Chromosomal contact, Translocation, lcsh:Fuel, lcsh:TP315-360, Hi-C, lcsh:TP248.13-248.65, [CHIM]Chemical Sciences
Abstract: International audience; Background: The presence of low complexity and repeated regions in genomes often results in difficulties to assemblesequencing data into full chromosomes. However, the availability of full genome scaffolds is essential to severalinvestigations, regarding for instance the evolution of entire clades, the analysis of chromosome rearrangements,and is pivotal to sexual crossing studies. In non-conventional but industrially relevant model organisms, such as theascomycete Trichoderma reesei, a complete genome assembly is seldom available.Results: The chromosome scaffolds of T. reesei QM6a and Rut-C30 strains have been generated using a contactgenomic/proximity ligation genomic approach. The original reference assembly, encompassing dozens of scaffolds,was reorganized into two sets of seven chromosomes. Chromosomal contact data also allowed to characterize10–40 kb, gene-free, AT-rich (76%) regions corresponding to the T. reesei centromeres. Large chromosomal rearrangements(LCR) in Rut-C30 were then characterized, in agreement with former studies, and the position of LCRbreakpoints used to assess the likely chromosome structure of other T. reesei strains [QM9414, CBS999.97 (1-1, re), andQM9978]. In agreement with published results, we predict that the numerous chromosome rearrangements found inhighly mutated industrial strains may limit the efficiency of sexual reproduction for their improvement.Conclusions: The GRAAL program allowed us to generate the karyotype of the Rut-C30 strain, and from there topredict chromosome structure for most T. reesei strains for which sequence is available. This method that exploitsproximity ligation sequencing approach is a fast, cheap, and straightforward way to characterize both chromosomestructure and centromere sequences and is likely to represent a popular convenient alternative to expensive andwork-intensive resequencing projects.
Published: 2017

35. A major role for Eco1 in regulating cohesin-mediated mitotic chromosome folding

Author: Romain Koszul, Olivier Gadal, Lise Dauban, Axel Cournac, Luciana Lazar-Stefanita, Frédéric Beckouët, Rémi Montagne, Agnès Thierry, Laboratoire de biologie moléculaire eucaryote (LBME), Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0303 health sciences, Cohesin complex, Cohesin, [SDV]Life Sciences [q-bio], Chromosome, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Biology, Chromatin, Cell biology, 03 medical and health sciences, 0302 clinical medicine, Centromere, Sister chromatids, Chromatid, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, biological phenomena, cell phenomena, and immunity, Mitosis, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: Understanding how chromatin organizes spatially into chromatid and how sister chromatids are maintained together during mitosis is of fundamental importance in chromosome biology. Cohesin, a member of the Structural Maintenance of Chromosomes (SMC) complex family, holds sister chromatids together 1–3 and promotes long-range intra-chromatid DNA looping 4,5. These cohesin-mediated DNA loops are important for both higher-order mitotic chromatin compaction6,7 and, in some organisms, compartmentalization of chromosomes during interphase into topologically associating domains (TADs) 8,9. Our understanding of the mechanism(s) by which cohesin generates large DNA loops remains incomplete. It involves a combination of molecular partners and active expansion/extrusion of DNA loops. Here we dissect the roles on loop formation of three partners of the cohesin complex: Pds5 10, Wpl1 11 and Eco1 acetylase 12, during yeast mitosis. We identify a new function for Eco1 in negatively regulating cohesin translocase activity, which powers loop extrusion. In the absence of negative regulation, the main barrier to DNA loop expansion appears to be the centromere. Those results provide new insights on the mechanisms regulating cohesin dependent DNA looping.
Published: 2019

36. FACT mediates cohesin function on chromatin

Author: Mohammad M. Karimi, Jonay García-Luis, Mar Sánchez, Luis Aragón, Luciana Lazar-Stefanita, Pilar Gutiérrez-Escribano, Adam Jarmuz, Axel Cournac, Alicia García, Alex Montoya, Sara Serrate González, Francisco Antequera, Holger B. Kramer, Marian Dore, Agnès Thierry, Romain Koszul, MRC London Institute of Medical Sciences (LMC), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Instituto de Biología Funcional y Genómica [Salamanca, Spain] (IBFG), Universidad de Salamanca-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), The work in the L.A. laboratory was supported by a Wellcome Trust Senior Investigator award to L.A. (100955, ‘Functional dissection of mitotic chromatin’) and the London Institute of Medical Research (LMS), which receives its core funding from the UK Medical Research Council. This research was further supported by funding from The European Research Council (R.K.), Agence Nationale pour la Recherche (R.K.) and the the Spanish Ministerio de Economía, Industria y Competitividad (BFU2017-89622-P, F.A.)., We thank the members of the L.A., R.K. and P.A. laboratories for fruitful discussions and advice., Wellcome Trust, Medical Research Council (UK), European Commission, European Research Council, Agence Nationale de la Recherche (France), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Saccharomyces cerevisiae Proteins, Chromosomal Proteins, Non-Histone, MESH: Chromosomal Proteins, Non-Histone / metabolism, Cell Cycle Proteins, Chromatin remodelling, Saccharomyces cerevisiae, Article, MESH: Chromatin / metabolism, Chromosome segregation, 03 medical and health sciences, MESH: Cell Cycle Proteins / metabolism, 0302 clinical medicine, Structural Biology, Chromosome condensation, MESH: Saccharomyces cerevisiae / metabolism, Nucleosome, MESH: High Mobility Group Proteins / metabolism, Protein Interaction Maps, MESH: Saccharomyces cerevisiae / cytology, Molecular Biology, Metaphase, MESH: Protein Interaction Maps, 030304 developmental biology, 0303 health sciences, Nuclear organization, biology, Cohesin, Chemistry, High Mobility Group Proteins, Chromosome, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, MESH: DNA-Binding Proteins / metabolism, Chromatin, 3. Good health, Cell biology, DNA-Binding Proteins, Establishment of sister chromatid cohesion, Histone, MESH: Transcriptional Elongation Factors / metabolism, biology.protein, MESH: Saccharomyces cerevisiae Proteins / metabolism, Transcriptional Elongation Factors, biological phenomena, cell phenomena, and immunity, 030217 neurology & neurosurgery
Abstract: Cohesin is a regulator of genome architecture with roles in sister chromatid cohesion and chromosome compaction. The recruitment and mobility of cohesin complexes on DNA is restricted by nucleosomes. Here, we show that the role of cohesin in chromosome organization requires the histone chaperone FACT (‘facilitates chromatin transcription’) in Saccharomyces cerevisiae. We find that FACT interacts directly with cohesin, and is dynamically required for its localization on chromatin. Depletion of FACT in metaphase cells prevents cohesin accumulation at pericentric regions and causes reduced binding on chromosome arms. Using the Hi-C technique, we show that cohesin-dependent TAD (topological associated domain)-like structures in G1 and metaphase chromosomes are reduced in the absence of FACT. Sister chromatid cohesion is intact in FACT-depleted cells, although chromosome segregation failure is observed. Our data show that FACT contributes to the formation of cohesin-dependent TADs, thus uncovering a new role for this complex in nuclear organization during interphase and mitotic chromosome folding., The work in the L.A. laboratory was supported by a Wellcome Trust Senior Investigator award to L.A. (100955, ‘Functional dissection of mitotic chromatin’) and the London Institute of Medical Research (LMS), which receives its core funding from the UK Medical Research Council. This research was further supported by funding from The European Research Council (R.K.), Agence Nationale pour la Recherche (R.K.) and the the Spanish Ministerio de Economía, Industria y Competitividad (BFU2017-89622-P; F.A.).
Published: 2019

37. MetaTOR: A Computational Pipeline to Recover High-Quality Metagenomic Bins From Mammalian Gut Proximity-Ligation (meta3C) Libraries

Author: Lyam Baudry, Théo Foutel-Rodier, Agnès Thierry, Romain Koszul, Martial Marbouty, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Sorbonne Université (SU), LB is supported by an AMX fellowship from the French Ministry of Higher Education, Research and Innovation. TFR is supported by an ENS fellowship by the French Ministry of Higher Education, Research and Innovation. This research was supported by funding to RK from the European Research Council under the Horizon 2020 Program (ERC grant agreement 260822) and from the Agence Nationale pour la Recherche (JPI-EC-AMR STARCS ANR-16-JPEC-0003-05)., 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]-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, lcsh:QH426-470, metagenome-assembled genomes, Computer science, [SDV]Life Sciences [q-bio], metagenomics Hi-C, gut microbiome, Computational biology, metagenomics binning, Genome, DNA sequencing, Chromosome conformation capture, 03 medical and health sciences, 0302 clinical medicine, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Hi-C, Genetics, Genetics (clinical), Original Research, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Contig, metagenomic analysis, Pipeline (software), Gut microbiome, lcsh:Genetics, 030104 developmental biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Metagenomics, 030220 oncology & carcinogenesis, binning algorithm, Molecular Medicine
Abstract: International audience; Characterizing the complete genomic structure of complex microbial communities would represent a key step toward the understanding of their diversity, dynamics, and evolution. Current metagenomics approaches aiming at this goal are typically done by analyzing millions of short DNA sequences directly extracted from the environment. New experimental and computational approaches are constantly sought for to improve the analysis and interpretation of such data. We developed MetaTOR, an open-source computational solution that bins DNA contigs into individual genomes according to their 3D contact frequencies. Those contacts are quantified by chromosome conformation capture experiments (3C, Hi-C), also known as proximity-ligation approaches, applied to metagenomics samples (meta3C). MetaTOR was applied on 20 meta3C libraries of mice gut microbiota. We quantified the program ability to recover high-quality metagenome-assembled genomes (MAGs) from metagenomic assemblies generated directly from the meta3C libraries. Whereas nine high-quality MAGs are identified in the 148-Mb assembly generated using a single meta3C library, MetaTOR identifies 82 high-quality MAGs in the 763-Mb assembly generated from the merged 20 meta3C libraries, corresponding to nearly a third of the total assembly. Compared to the hybrid binning softwares MetaBAT or CONCOCT, MetaTOR recovered three times more high-quality MAGs. These results underline the potential of 3C-/Hi-C-based approaches in metagenomic projects.
Published: 2019

38. Condensin-Mediated Chromosome Folding and Internal Telomeres Drive Dicentric Severing by Cytokinesis

Author: Natalja Barinova, Romain Koszul, Stéphane Marcand, Alice Deshayes, Claire Béneut, Karine Dubrana, Virginia Lopez, Agnès Thierry, Thomas Guerin, Luciana Lazar-Stefanita, Stabilité génétique, cellules souches et radiations (SGCSR (U_1274 / UMR_E_008)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Université Paris Cité (UPCité), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), This work was supported by funding to S.M. from Fondation ARC, EDF, CEA Radiobiology call, DRF-Impulsion (4D-DSB-DIC), and ANR (DICENs-ANR-14-CE10-0021-01), to K.D. from the European Research Council under the Seventh Framework Program (FP7/2007 2013/ERC grant agreement 281287), and to R.K. from the European Research Council under the Horizon 2020 Program (ERC grant agreement 260822). T.M.G. was supported by a PhD fellowship from CEA, ANR, and a Fondation ARC young researcher grant., We thank Angela Taddei for lacI, lacI∗∗, and lacO array plasmids and suggestions, Frank Uhlmann and Thomas Kuilman for the G20 plasmid, Helle Ulrich for the AID tool kit, Didier Busso and Eléa Dizet (CIGEX platform) for the Rap1 sites plasmids, Pascale Lesage for the anti-Dps1 antibody, Rémi Montagne for assistance with the Hi-C data, Romain Le Bars (IMAGE-GIF platform) and Lamya Irbah (IRCM microscopy platform) for assistance with higher-resolution microscopy, Dan Throsby for text editing, and John Marko, Damien D’Amours, Sarah Lambert, François-Xavier Barre, Pablo Radicella, Eric Coïc, Laurent Maloisel, Paul-Henri Roméo, Mathias Toulouze, and Maoussi Lhuillier-Akakpo for fruitful discussions and suggestions., ANR-14-CE10-0021,DICENs,Prévention et résolution des chromosomes dicentriques(2014), European Project: 281287,EC:FP7:ERC,ERC-2011-StG_20101109,NDOGS(2012), European Project: 260822,EC:FP7:ERC,ERC-2010-StG_20091118,DICIG(2011), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Université de Paris (UP), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Condensin, Gene Expression, yeast, Shelterin Complex, MESH: Telomere-Binding Proteins, chemistry.chemical_compound, Chromosome Breakpoints, 0302 clinical medicine, MESH: Saccharomyces cerevisiae Proteins, Hi-C, MESH: Models, Genetic, DNA, Fungal, Adenosine Triphosphatases, 0303 health sciences, biology, SMC, MESH: Karyotype, MESH: Chromosome Breakpoints, MESH: Transcription Factors, Telomere, MESH: Saccharomyces cerevisiae, MESH: Chromosomes, Fungal, Cell biology, DNA-Binding Proteins, Chromosomes, Fungal, mutagenesis, lacI, MESH: Cytokinesis, Saccharomyces cerevisiae Proteins, MESH: Gene Expression, Saccharomyces cerevisiae, Karyotype, Telomere-Binding Proteins, 03 medical and health sciences, Dicentric chromosome, MESH: Adenosine Triphosphatases, Telophase, Molecular Biology, Mitosis, 030304 developmental biology, Cytokinesis, mitosis, Models, Genetic, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell Biology, MESH: Multiprotein Complexes, biology.organism_classification, telophase, abscission, MESH: DNA, Fungal, enzymes and coenzymes (carbohydrates), chemistry, Multiprotein Complexes, biology.protein, MESH: Telomere, 030217 neurology & neurosurgery, DNA, MESH: DNA-Binding Proteins, Transcription Factors, condensing
Abstract: International audience; In Saccharomyces cerevisiae, dicentric chromosomes stemming from telomere fusions preferentially break at the fusion. This process restores a normal karyotype and protects chromosomes from the detrimental consequences of accidental fusions. Here, we address the molecular basis of this rescue pathway. We observe that tandem arrays tightly bound by the telomere factor Rap1 or a heterologous high-affinity DNA binding factor are sufficient to establish breakage hotspots, mimicking telomere fusions within dicentrics. We also show that condensins generate forces sufficient to rapidly refold dicentrics prior to breakage by cytokinesis and are essential to the preferential breakage at telomere fusions. Thus, the rescue of fused telomeres results from a condensin- and Rap1-driven chromosome folding that favors fusion entrapment where abscission takes place. Because a close spacing between the DNA-bound Rap1 molecules is essential to this process, Rap1 may act by stalling condensins.
Published: 2019

39. Exploration des dynamiques de chromosomes par assemblage Hi-C

Author: Baudry, Lyam, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, and Romain Koszul
Subjects: Génomique, Hi-C, Assemblage, Structure, Genomics, Metagenomics, Assembling, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Métagénomique
Abstract: The advent of high-throughput DNA sequencing technologies has set off an expanding trend in genome assembling and scaffolding. Such genome quality is an essential preliminary to understand interactions between and among chromosomes. We built upon a computational and technological framework that let us tackle genome assembly problems of increasing complexity. Our methods are mainly based on chromosome conformation capture technologies such as Hi-C. In a Hi-C experiment, DNA molecules are cross-linked with the surrounding proteins and form a large, static protein-DNA complex. This captures the spatial conformation by trapping together molecules that are physically close to each other. Therefore, Hi-C is very suitable for 3D genome structure analysis, which lets us infer a wealth of information about the genome. It was indeed shown that the tridimensional structure of the genome can be unambiguously linked to its 1D structure thanks to the physical properties of DNA polymers. Moreover, such 3D proximity also gives access to cell compartment information, thus opening the way for an additional approach for metagenomic binning, known as meta3C. In this work, we expand upon these methods and apply them to use cases with more and more complexity. We first improve on tools for genome assembly and demonstrate their validity with the scaffolding of Ectocarpus sp., then unveil rearrangements in joint scaffoldings of Trichoderma reesei and Cataglyphis hispanica. Lastly, we use the same approach with metagenomic binning on live mouse microbiome samples to reconstruct hundreds of genomes.; L'avènement des technologies de séquençage ADN à haut-debit a initié une tendance grandissante dans l'assemblage de génomes. La qualité de ces génomes est un prérequis essentiel pour comprendre les interactions au sein de et entre ces chromosomes. Nos méthodes se basent principalement sur les technologies de capture de conformation de chromosomes comme le Hi-C. Lors d'un protocole de Hi-C, les molécules d'ADN sont réticulées avec les protéines environnantes pour former un complexe protéine-ADN statique et volumineux. Ceci permet de capturer la conformation spatiale en piégeant les molécules physiquement proches dans l'espace. Ainsi, le Hi-C est très approprié pour l'analyse de la structure 3D des génomes, ce qui permet d'obtenir un certain nombre d'informations sur le génome. Il a été ainsi montré que sa structure tridimensionnelle peut être reliée directement à sa structure 1D grâce aux propriétés physiques des polymères d'ADN. De plus, une telle proximité en 3D donne également accès à des informations de compartimentation, ce qui a ouvert la voie à une nouvelle approche de binning métagénomique, connue sous le nom de meta3C. Au cours de ce travail, nous étendons ces méthodes à des études de cas présentant une complexité grandissante. Tout d'abord, nous améliorons les outils d'assemblage de génomes et démontrons leur validité avec l'assemblage de Ectocarpus sp., puis nous mettons en évidence des réarrangements chromosomiques au sein d'assemblages joints de Trichoderma reesei et Cataglyphis hispanica. Enfin, nous utilisons la même approche avec le binning métagénomique sur des échantillons de souris in vivo afin de reconstruire des centaines de génomes.
Published: 2019

40. Investigating chromosome dynamics through Hi-C assembly

Author: Baudry, Lyam, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Romain Koszul, and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Génomique, Hi-C, Assemblage, Structure, Genomics, Metagenomics, Assembling, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Métagénomique
Abstract: The advent of high-throughput DNA sequencing technologies has set off an expanding trend in genome assembling and scaffolding. Such genome quality is an essential preliminary to understand interactions between and among chromosomes. We built upon a computational and technological framework that let us tackle genome assembly problems of increasing complexity. Our methods are mainly based on chromosome conformation capture technologies such as Hi-C. In a Hi-C experiment, DNA molecules are cross-linked with the surrounding proteins and form a large, static protein-DNA complex. This captures the spatial conformation by trapping together molecules that are physically close to each other. Therefore, Hi-C is very suitable for 3D genome structure analysis, which lets us infer a wealth of information about the genome. It was indeed shown that the tridimensional structure of the genome can be unambiguously linked to its 1D structure thanks to the physical properties of DNA polymers. Moreover, such 3D proximity also gives access to cell compartment information, thus opening the way for an additional approach for metagenomic binning, known as meta3C. In this work, we expand upon these methods and apply them to use cases with more and more complexity. We first improve on tools for genome assembly and demonstrate their validity with the scaffolding of Ectocarpus sp., then unveil rearrangements in joint scaffoldings of Trichoderma reesei and Cataglyphis hispanica. Lastly, we use the same approach with metagenomic binning on live mouse microbiome samples to reconstruct hundreds of genomes.; L'avènement des technologies de séquençage ADN à haut-debit a initié une tendance grandissante dans l'assemblage de génomes. La qualité de ces génomes est un prérequis essentiel pour comprendre les interactions au sein de et entre ces chromosomes. Nos méthodes se basent principalement sur les technologies de capture de conformation de chromosomes comme le Hi-C. Lors d'un protocole de Hi-C, les molécules d'ADN sont réticulées avec les protéines environnantes pour former un complexe protéine-ADN statique et volumineux. Ceci permet de capturer la conformation spatiale en piégeant les molécules physiquement proches dans l'espace. Ainsi, le Hi-C est très approprié pour l'analyse de la structure 3D des génomes, ce qui permet d'obtenir un certain nombre d'informations sur le génome. Il a été ainsi montré que sa structure tridimensionnelle peut être reliée directement à sa structure 1D grâce aux propriétés physiques des polymères d'ADN. De plus, une telle proximité en 3D donne également accès à des informations de compartimentation, ce qui a ouvert la voie à une nouvelle approche de binning métagénomique, connue sous le nom de meta3C. Au cours de ce travail, nous étendons ces méthodes à des études de cas présentant une complexité grandissante. Tout d'abord, nous améliorons les outils d'assemblage de génomes et démontrons leur validité avec l'assemblage de Ectocarpus sp., puis nous mettons en évidence des réarrangements chromosomiques au sein d'assemblages joints de Trichoderma reesei et Cataglyphis hispanica. Enfin, nous utilisons la même approche avec le binning métagénomique sur des échantillons de souris in vivo afin de reconstruire des centaines de génomes.
Published: 2019

41. Au-delà des limites de l’évolution : les chromosomes synthétiques… Comment et pourquoi faire ?

Author: Romain Koszul, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This research is supported by funding from ERASynBio and the 'Agence nationale pour la recherche' (IESY ANR-14-SYNB-0001-03 and MeioRec ANR-13-BSV6-0012-02)., ANR-14-SYNB-0001,IESY,Induced Evolution of Synthetic Yeast genomes(2014), and ANR-13-BSV6-0012,MeioRec,Dynamique chromosomique et recombinaison au cours de la méiose(2013)
Subjects: 0106 biological sciences, 0301 basic medicine, Brouillage, Saccharomyces cerevisiae, Oligonucleotides, Sequence assembly, Oligonucléotides, Computational biology, Biology, 01 natural sciences, Chromosomes, Artificial, Human, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Synthetic biology, Genome editing, Immunology and Microbiology(all), 010608 biotechnology, Animals, Humans, Levure, Gene, Organism, Medicine(all), 2. Zero hunger, Genetics, [SDV.GEN]Life Sciences [q-bio]/Genetics, Agricultural and Biological Sciences(all), General Immunology and Microbiology, Biochemistry, Genetics and Molecular Biology(all), DNA, General Medicine, 3D organization, biology.organism_classification, Yeast, Scrambling, Homologous Recombination Pathway, ComputingMethodologies_PATTERNRECOGNITION, 030104 developmental biology, Assemblage de séquences, Synthetic Biology, Organisation tridimensionnelle, Directed Molecular Evolution, General Agricultural and Biological Sciences
Abstract: International audience; Chromosome synthesis is still at its early stage. The budding yeast Saccharomyces cerevisiae is an organism of choice with respect to this field, thanks to its efficient homologous recombination pathway. By iteratively concatenating short DNA molecules to ultimately generate large sequences of megabase size, these approaches allow piecing together multiple genes and genetic elements in a way designed by an individual prior to their assembly. They therefore hold important promises as a tool to design complex genetic systems or assemble new genetic pathways that allow addressing fundamental and applied questions. The constant drop in DNA synthesis costs, fed by the development of new technologies, opens new perspectives with respect to the conceptual way these questions can be addressed. Thanks to its properties, S. cerevisiae may provide solutions for chromosome synthesis in other organisms, in combination with genome editing techniques.; Les chromosomes synthétiques sont une technique récente. La levure de boulangerie Saccharomyces cerevisiae est un organisme de choix dans ce domaine, notamment grâce à une voie de recombinaison homologue très efficace. Par concaténation itérative de molécules d’ADN courte, ces approches permettent de générer finalement de grandes séquences de plus d’un million de bases. Les gènes et éléments génétiques présents sur ces molécules sont définis par un individu préalablement à leur assemblage. Elles représentent donc d’importantes promesses comme outils pour concevoir des systèmes génétiques complexes ou assembler de nouvelles voies génétiques qui permettent de répondre à des questions fondamentales et appliquées. La baisse constante des coûts de synthèse d’ADN, alimentée par le développement de nouvelles technologies, ouvre de nouvelles perspectives par rapport à la manière conceptuelle dont ces questions peuvent être abordées. Grace à ses propriétés, S. cerevisiae pourrait vraisemblablement représenter une solution à la synthèse de chromosomes dans d’autres d’espèces, notamment en combinaison avec des techniques d’édition de génome.
Published: 2016

42. Metagenome Analysis Exploiting High-Throughput Chromosome Conformation Capture (3C) Data

Author: Romain Koszul, Martial Marbouty, 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 R.K. from the European Research Council under the 7th Framework Program (FP7/2007-2013)/ERC grant agreement 260822., European Project: 260822,EC:FP7:ERC,ERC-2010-StG_20091118,DICIG(2011), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genetics, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: High-Throughput Screening Assays, [SDV]Life Sciences [q-bio], Chromosome, Computational biology, MESH: Metagenome, Biology, Genome, Chromosomes, Article, DNA sequencing, High-Throughput Screening Assays, Chromosome conformation capture, chemistry.chemical_compound, Plasmid, chemistry, Metagenomics, Metagenome, MESH: Chromosomes, Mobile genetic elements, DNA
Abstract: Microbial communities are extremely complex and constitute critical actors of our environment. Genomic analyses of these populations are a dynamic research area but remain limited by the difficulty to assemble full genomes of individual species. Recently, a new method for metagenome assembly/analysis based on chromosome conformation capture has emerged (meta3C). This approach quantifies the collisions experienced by DNA molecules to identify those sharing the same cellular compartments, allowing the characterization of genomes present within complex mixes of species. The exploitation of these chromosome 3D signatures holds important premises regarding reaching at the genome sequences from discrete species in complex populations. It also has the potential to correctly assign extra-chromosomal elements, such as plasmids, mobile elements and phages, to their host cells.
Published: 2015

43. Dynamic Processing of Displacement Loops During Recombinational DNA Repair

Author: Steven K Gore, Romain Koszul, Shanaya Shital Shah, Aurèle Piazza, Wolf Dietrich Heyer, William Douglass Wright, University of California, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), A.P. was supported by fellowships from the ARC Foundation, the EMBO (ALTF-238-2013), and the Framework Project 7 of the European Union (Marie Skłodowska-Curie International Outgoing Fellowship 628355) and received financial support from the Philippe Foundation. This research used core services supported by P30 CA93373 and was supported by NIH grants GM58015 and CA92276 to W.-D.H. and the Agence Nationale pour la Recherche grant ANR-13-BSV6-0012-02 to R.K., ANR-13-BSV6-0012,MeioRec,Dynamique chromosomique et recombinaison au cours de la méiose(2013), European Project: 628355,EC:FP7:PEOPLE,FP7-PEOPLE-2013-IOF,MULTIPLE SEARCH, University of California (UC), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV]Life Sciences [q-bio], homologous recombination, Medical and Health Sciences, DEAD-box RNA Helicases, chemistry.chemical_compound, 0302 clinical medicine, D-loop, DNA, Fungal, Double strand, topoisomerase, 0303 health sciences, RecQ Helicases, biology, Mph1, 030302 biochemistry & molecular biology, Biological Sciences, Rdh54, Cell biology, helicase, Fungal, heteroduplex DNA, Heteroduplex, Biotechnology, Saccharomyces cerevisiae Proteins, DNA repair, 1.1 Normal biological development and functioning, Saccharomyces cerevisiae, Article, Structure-Activity Relationship, 03 medical and health sciences, Underpinning research, Genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Srs2, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, Sgs1, Topoisomerase, fungi, DNA Helicases, Wild type, Recombinational DNA Repair, Helicase, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell Biology, DNA, Kinetics, chemistry, Rad54, biology.protein, Nucleic Acid Conformation, Homologous recombination, 030217 neurology & neurosurgery, DNA Topoisomerases, DNA Damage, Developmental Biology
Abstract: Displacement-loops (D-loops) are pivotal intermediates of homologous recombination (HR), a universal DNA double strand break (DSB) repair pathway. We developed a versatile assay for the physical detection of D-loopsin vivo, which enabled studying the kinetics of their formation and defining the network of D-loop formation and reversal pathways. Nascent D-loops are detected within 2 hrs of DSB formation and extended over the next 2 hrs in a system allowing break-induced replication. The majority of D-loops are disrupted in wild type cells by two pathways: one supported by the Srs2 helicase and the other by the Mph1 helicase and the Sgs1-Top3-Rmi1 helicase-topoisomerase complex. Both pathways operate without significant overlap and are delineated by the Rad54 paralog Rdh54 in an ATPase-independent fashion. This study uncovers a novel layer of HR control in cells relying on nascent D-loop dynamics, revealing unsuspected complexities, and identifying a surprising role for a conserved Rad54 paralog.
Published: 2018
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44. Kinetic Signature of Cooperativity in the Irreversible Collapse of a Polymer

Author: Romain Koszul, Guillaume Mercy, Julien Mozziconacci, Annick Lesne, Vittore F. Scolari, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Institut de Génétique Moléculaire de Montpellier (IGMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université de Montpellier (UM), This research was supported by funding to R. K. from the European Research Council under the 7th Framework Program (H2020 ERC grant agreement DLV-771813), and by Agence Nationale pour la Recherche (HiResBac ANR-15-CE11-0023-03) to R. K. and J. M.. V. F. S. is recipi, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Length scale, Materials science, Polymers, Kinetics, Molecular Conformation, General Physics and Astronomy, Thermodynamics, FOS: Physical sciences, Cooperativity, Condensed Matter - Soft Condensed Matter, Kinetic energy, Instability, Chromosomes, 03 medical and health sciences, chemistry.chemical_compound, Aggregation, Yeasts, A-DNA, Physics - Biological Physics, DNA, Fungal, Condensed Matter - Statistical Mechanics, chemistry.chemical_classification, [PHYS]Physics [physics], Condensed Matter - Materials Science, Quantitative Biology::Biomolecules, Statistical Mechanics (cond-mat.stat-mech), Irreversible processes, digestive, oral, and skin physiology, Materials Science (cond-mat.mtrl-sci), Polymer, Chromatin, Condensed Matter::Soft Condensed Matter, 030104 developmental biology, Monomer, chemistry, Models, Chemical, Biological Physics (physics.bio-ph), Soft Condensed Matter (cond-mat.soft), Nucleic Acid Conformation, Nonequilibrium & irreversible thermodynamics, Monte Carlo Method
Abstract: We investigate the kinetics of a polymer collapse due to the formation of irreversible crosslinks between its monomers. Using the contact probability $P(s)$ as a scale-dependent order parameter depending on the chemical distance $s$, our simulations show the emergence of a cooperative pearling instability. Namely, the polymer undergoes a sharp conformational transition to a set of absorbing states characterized by a length scale $\xi$ corresponding to the mean pearl size. This length and the transition time depend on the polymer equilibrium dynamics and the crosslinking rate. We confirm experimentally this transition using a DNA conformation capture experiment in yeast., Comment: Article: 12 pages, 4 figures. Supplementary material: 22 pages, 7 supplementary figures
Published: 2018

45. Characterizing meiotic chromosomes' structure and pairing using a designer sequence optimized for Hi‐C

Author: Stéphane Descorps-Declère, Romain Koszul, Olivier Espéli, Julien Mozziconacci, Nicolas Agier, Agnès Thierry, Luciana Lazar-Stefanita, Bertrand Llorente, Guillaume Mercy, Gilles Fischer, Vittore F. Scolari, Héloïse Muller, Aurèle Piazza, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-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), Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Vittore Scolari and Héloïse Muller were recipients of Pasteur Roux Cantarini fellowships, and Aurèle Piazza was supported by the Framework Project 7 of the European Union (Marie Curie International Outgoing Fellowship 628355). This research was supported by funding to R.K. from the European Research Council under the 7th Framework Program (H2020 ERC grant agreement DLV‐771813) and from ERASynBio and Agence Nationale pour la Recherche (IESY ANR‐14‐SYNB‐0001‐03), and to R.K., O.E., and B.L. from Agence Nationale pour la Recherche (MeioRec ANR‐13‐BSV6‐0012)., ANR-14-SYNB-0001,IESY,Induced Evolution of Synthetic Yeast genomes(2014), ANR-13-BSV6-0012,MeioRec,Dynamique chromosomique et recombinaison au cours de la méiose(2013), European Project: 628355,EC:FP7:PEOPLE,FP7-PEOPLE-2013-IOF,MULTIPLE SEARCH, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Aix Marseille Université (AMU), and Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)
Subjects: 0301 basic medicine, synthetic chromosome, cohesin, Computational biology, Methods & Resources, Biology, Chromatin, Epigenetics, Genomics & Functional Genomics, General Biochemistry, Genetics and Molecular Biology, Article, Chromosome conformation capture, 03 medical and health sciences, Prophase, Meiosis, Genome Size, Centromere, Schizosaccharomyces, Homologous chromosome, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, chromatin loop, General Immunology and Microbiology, Applied Mathematics, Systems Biology, Rec8, Articles, Restriction site, 030104 developmental biology, Computational Theory and Mathematics, Genome-Scale & Integrative Biology, Chromatin Loop, Ploidy, Chromosomes, Fungal, General Agricultural and Biological Sciences, Information Systems
Abstract: International audience; In chromosome conformation capture experiments (Hi-C), the accuracy with which contacts are detected varies due to the uneven distribution of restriction sites along genomes. In addition, repeated sequences or homologous regions remain indistinguishable because of the ambiguities they introduce during the alignment of the sequencing reads. We addressed both limitations by designing and engineering 144 kb of a yeast chromosome with regularly spaced restriction sites (Syn-HiC design). In the Syn-HiC region, Hi-C signal-to-noise ratio is enhanced and can be used to measure the shape of an unbiased distribution of contact frequencies , allowing to propose a robust definition of a Hi-C experiment resolution. The redesigned region is also distinguishable from its native homologous counterpart in an otherwise isogenic diploid strain. As a proof of principle, we tracked homologous chromosomes during meiotic prophase in synchronized and pachytene-arrested cells and captured important features of their spatial reorganization, such as chromatin restructuration into arrays of Rec8-delimited loops, centromere declustering, individualization, and pairing. Overall, we illustrate the promises held by redesigning genomic regions to explore complex biological questions.
Published: 2018

46. 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

47. L'organisation 3D des chromosomes synthétiques de levure

Author: Mercy, Guillaume, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, and Romain Koszul
Subjects: Synthetic yeast, Hi-C, Carte génomique, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Projet Sc2.0, Levure synthétique, Chromosome organization, Scramble, Organisation chromosomique
Abstract: The international project Sc2.0 started 10 years ago by the Pr. Jef Boeke aims to build a fully synthetic genome of S. cerevisiae which increases the genome stability by removing all repeated sequences (tRNA, transposable elements, etc.), and implements SCRaMbLE (for Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution), an inducible, high-throughput chromosome rearrangement system. This design is highly conservative with respect to gene content, the deletion of several classes of repeated sequences and the introduction of thousands of designer changes. However, it may affect genome organization and potentially alter cellular functions. To determine wether those modifications affected the three-dimensional conformation of synthetic chromosmes, we investigated it using chromosomes conformation capture coupled to second generation sequencing method (Hi-C). Currently, eight synthetic chromosomes (synI, synII, synIII, synV, synVI, synIX-R, synX et synXII) have been fully assembled. Using these strains we observed that 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 exploited the contact maps to detect rearrangements induced in these SCRaMbLE strains.; Le projet international de synthèse des chromosomes de S. cerevisiae (projet Sc2.0) a débuté il y a une dizaine d'années en suivant des principes établis par le Pr. Jef Boeke. Les chromosomes synthétiques ont été conçus pour augmenter la stabilité du génome en supprimant toutes les séquences répétées (ARNt, éléments transposables...), tout en y ajoutant un système d'évolution inductible dépendant du système Cré/LoxP (système SCRaMbLE), permettant de générer rapidement des réarrangements chromosomiques. Bien que le design du projet Sc2.0 soit très conservateur en ce qui concerne le contenu des gènes, la suppression de plusieurs classes de séquences répétées peut affecter l'organisation du génome et potentiellement altérer les fonctions cellulaires. En utilisant la méthode de capture de conformation de chromosome couplée au séquençage de seconde génération (Hi-C), mon objectif a été de caractériser l'organisation 3D des génomes des souches synthétiques et évoluées. À ce jour, huit chromosomes (syn I, II, III, V, VI, IX-R, X et XII) ont été entièrement assemblés séparément. En utilisant les souches contenant un ou plusieurs de ces chromosomes, nous avons pu montrer que leur organisation génomique n'est globalement pas affectée par leur présence. Quelques exceptions subsistent, avec synIII dont les cassettes HML et HMR ont été retirées, et synXII d'où l'ADNr a été déplacé sur un autre chromosome. À ce stade, nous concluons que l'ADN répétitif dispersé ne conduit pas la conformation moyenne globale du génome de S. cerevisiae. Nous avons aussi exploité les cartes de contacts pour identifier les réarrangements dans les souches SCRaMbLE.
Published: 2018

48. 3D organisation of synthetic yeast chromosomes

Author: Mercy, Guillaume, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Romain Koszul, and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Synthetic yeast, Hi-C, Carte génomique, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Projet Sc2.0, Levure synthétique, Chromosome organization, Scramble, Organisation chromosomique
Abstract: The international project Sc2.0 started 10 years ago by the Pr. Jef Boeke aims to build a fully synthetic genome of S. cerevisiae which increases the genome stability by removing all repeated sequences (tRNA, transposable elements, etc.), and implements SCRaMbLE (for Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution), an inducible, high-throughput chromosome rearrangement system. This design is highly conservative with respect to gene content, the deletion of several classes of repeated sequences and the introduction of thousands of designer changes. However, it may affect genome organization and potentially alter cellular functions. To determine wether those modifications affected the three-dimensional conformation of synthetic chromosmes, we investigated it using chromosomes conformation capture coupled to second generation sequencing method (Hi-C). Currently, eight synthetic chromosomes (synI, synII, synIII, synV, synVI, synIX-R, synX et synXII) have been fully assembled. Using these strains we observed that 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 exploited the contact maps to detect rearrangements induced in these SCRaMbLE strains.; Le projet international de synthèse des chromosomes de S. cerevisiae (projet Sc2.0) a débuté il y a une dizaine d'années en suivant des principes établis par le Pr. Jef Boeke. Les chromosomes synthétiques ont été conçus pour augmenter la stabilité du génome en supprimant toutes les séquences répétées (ARNt, éléments transposables...), tout en y ajoutant un système d'évolution inductible dépendant du système Cré/LoxP (système SCRaMbLE), permettant de générer rapidement des réarrangements chromosomiques. Bien que le design du projet Sc2.0 soit très conservateur en ce qui concerne le contenu des gènes, la suppression de plusieurs classes de séquences répétées peut affecter l'organisation du génome et potentiellement altérer les fonctions cellulaires. En utilisant la méthode de capture de conformation de chromosome couplée au séquençage de seconde génération (Hi-C), mon objectif a été de caractériser l'organisation 3D des génomes des souches synthétiques et évoluées. À ce jour, huit chromosomes (syn I, II, III, V, VI, IX-R, X et XII) ont été entièrement assemblés séparément. En utilisant les souches contenant un ou plusieurs de ces chromosomes, nous avons pu montrer que leur organisation génomique n'est globalement pas affectée par leur présence. Quelques exceptions subsistent, avec synIII dont les cassettes HML et HMR ont été retirées, et synXII d'où l'ADNr a été déplacé sur un autre chromosome. À ce stade, nous concluons que l'ADN répétitif dispersé ne conduit pas la conformation moyenne globale du génome de S. cerevisiae. Nous avons aussi exploité les cartes de contacts pour identifier les réarrangements dans les souches SCRaMbLE.
Published: 2018

49. A Proximity Ligation-Based Method for Quantitative Measurement of D-Loop Extension in S. cerevisiae

Author: Wolf Dietrich Heyer, Romain Koszul, Aurèle Piazza, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), University of California (UC), A.P. was supported by fellowships from the Fondation ARC pour la Recherche sur le Cancer, the EMBO (ALTF-238-2013), and the Framework Project 7 of the European Union (Marie Curie International Outgoing Fellowship 628355) administered by the Institut Pasteur, France, and received financial support from the Philippe Foundation. This research was supported by MeioRec ANR-13-BSV6-0012-02 to R.K. and NIH grants GM58015 and CA92276 to W.-D.H., ANR-13-BSV6-0012,MeioRec,Dynamique chromosomique et recombinaison au cours de la méiose(2013), European Project: 628355,EC:FP7:PEOPLE,FP7-PEOPLE-2013-IOF,MULTIPLE SEARCH, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and University of California
Subjects: 0301 basic medicine, MESH: DNA Ligases, DNA Ligases, [SDV]Life Sciences [q-bio], Saccharomyces cerevisiae, DSB repair, Article, 03 medical and health sciences, chemistry.chemical_compound, D-loop, Dsb repair, Homologous chromosome, A-DNA, DNA Breaks, Single-Stranded, Homologous recombination, DNA, Fungal, DNA synthesis, MESH: DNA Breaks, Single-Stranded, Chemistry, Recombinational DNA Repair, MESH: Saccharomyces cerevisiae, MESH: DNA, Fungal, MESH: Recombinational DNA Repair, MESH: Genetic Techniques, 030104 developmental biology, Genetic Techniques, Biophysics, Ligation, DNA
Abstract: Methods in enzymology (0076-6879); International audience; Homologous recombination faithfully restores the sequence information interrupted by a DNA double-strand break by referencing an intact DNA molecule as a template for repair DNA synthesis. DNA synthesis is primed from 3'-OH end of the invading DNA strand in the displacement loop (D-loop). Here, we describe a simple and quantitative proximity ligation-based assay to study the initiation of homologous recombination-associated DNA synthesis initiated at the D-loop and final product formation. The D-loop extension assay overcomes the semiquantitative nature and some limitations of the current PCR-based technique and facilitates the study of the recombination-associated DNA synthesis.
Published: 2018

50. Generation of a Metagenomics Proximity Ligation 3C Library of a Mammalian Gut Microbiota

Author: Romain Koszul, Théo Foutel-Rodier, Agnès Thierry, Martial Marbouty, 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), Sorbonne Université (SU), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, MESH: Sequence Analysis, DNA, Base pair, Assembly, Computational biology, Biology, MESH: Genome, Bacterial, Genome, Human gut, DNA sequencing, MESH: Gastrointestinal Microbiome, 03 medical and health sciences, 0302 clinical medicine, Plasmid, Meta Hi-C, Metagenomics binning, MESH: Animals, Microbiome, Gene, MESH: High-Throughput Nucleotide Sequencing, Meta3C, Contig, MESH: Metagenome, 030104 developmental biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Metagenomics, MESH: Metagenomics, 030217 neurology & neurosurgery
Abstract: International audience; Microbial species thrive in very diverse environments and play fundamental roles in their equilibrium and dynamics. Metagenomics consists in extracting, sequencing, and studying the DNA present in ecosystems to better understand their regulation. Ideally, the maximal amount of information would be gathered from the full sequences of the genomes, episomes, and phages present in the microbial communities. Current high-throughput DNA sequencing produces reads ranging in size from a few dozen base pairs for the most commonly used technologies to several kb for emerging single-molecule real-time sequencing techniques. Although valuable information can be extracted from processing these DNA sequences into contigs, reconstructing full genomes remains a difficult task. Clustering contigs according to their similarities or read coverage covariations gives some insights on these genomes, but remains limited as viral sequences, or recent horizontal gene transfers, often differ from their host genomes. We recently developed meta3C, a proximity ligation approach that bins contigs in a sequence-independent way by quantifying and exploiting their tridimensional collisions frequencies in vivo. This technique has demonstrated a great potential to reconstruct genomes as well as to assign plasmids and phages to their hosts. It nevertheless requires a specific processing of the microbial samples before sequencing, which has to be carefully planned.
Published: 2018

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