Investigating the functional architecture of microbial genomes with synthetic approaches

Project Information

SynarchiC

Grant agreement ID: 771813

DOI

10.3030/771813

Project closed

EC signature date 1 February 2018

Start date 1 April 2018

End date 31 March 2024

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 995 557,00

EU contribution

€ 1 995 557,00

Coordinated by

INSTITUT PASTEUR
France

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (29)

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

Author(s): Stéphane Pelleau, Tom Woudenberg, Jason Rosado, Françoise Donnadieu, Laura Garcia, Thomas Obadia, Soazic Gardais, Yasmine Elgharbawy, Aurelie Velay, Maria Gonzalez, Jacques Yves Nizou, Nizar Khelil, Konstantinos Zannis, Charlotte Cockram, Sarah Hélène Merkling, Annalisa Meola, Solen Kerneis, Benjamin Terrier, Jerome de Seze, Delphine Planas, Olivier Schwartz, François Dejardin, Stéphane Petr
Published in: The Journal of Infectious Diseases, Issue 224, 2021, Page(s) 1489-1499, ISSN 0022-1899
Publisher: University of Chicago Press
DOI: 10.1093/infdis/jiab375

A virally-encoded tRNA neutralizes the PARIS antiviral defence system

Author(s): Nathaniel Burman, Svetlana Belukhina, Florence Depardieu, Royce A. Wilkinson, Mikhail Skutel, Andrew Santiago-Frangos, Ava B. Graham, Alexei Livenskyi, Anna Chechenina, Natalia Morozova, Trevor Zahl, William S. Henriques, Murat Buyukyoruk, Christophe Rouillon, Baptiste Saudemont, Lena Shyrokova, Tatsuaki Kurata, Vasili Hauryliuk, Konstantin Severinov, Justine Groseille, Agnès Thierry, Romain Kosz
Published in: Nature, 2024, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-024-07874-3

Multiplex assays for the identification of serological signatures of SARS-CoV-2 infection: an antibody-based diagnostic and machine learning study

Author(s): Jason Rosado, Stéphane Pelleau, Charlotte Cockram, Sarah Hélène Merkling, Narimane Nekkab, Caroline Demeret, Annalisa Meola, Solen Kerneis, Benjamin Terrier, Samira Fafi-Kremer, Jerome de Seze, Timothée Bruel, François Dejardin, Stéphane Petres, Rhea Longley, Arnaud Fontanet, Marija Backovic, Ivo Mueller, Michael T White
Published in: The Lancet Microbe, Issue 2/2, 2021, Page(s) e60-e69, ISSN 2666-5247
Publisher: Elsevier
DOI: 10.1016/s2666-5247(20)30197-x

Depletion or cleavage of cohesin during anaphase differentially affects chromatin structure and segregation

Author(s): Jonay Garcia-Luis, Hélène Bordelet, Agnès Thierry, Romain Koszul, Luis Aragon
Published in: elife, 2022, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.80147

MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut

Author(s): Martial Marbouty, Agnès Thierry, Gaël A Millot, Romain Koszul
Published in: eLife, Issue 10, 2021, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.60608

Computer vision for pattern detection in chromosome contact maps

Author(s): Cyril Matthey-Doret, Lyam Baudry, Axel Breuer, Rémi Montagne, Nadège Guiglielmoni, Vittore Scolari, Etienne Jean, Arnaud Campeas, Philippe Henri Chanut, Edgar Oriol, Adrien Méot, Laurent Politis, Antoine Vigouroux, Pierrick Moreau, Romain Koszul, Axel Cournac
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-19562-7

Closed and High-Quality Bacterial Genome Sequences of the Oligo-Mouse-Microbiota Community

Author(s): Quentin Lamy-Besnier, Romain Koszul, Laurent Debarbieux, Martial Marbouty
Published in: Microbiology Resource Announcements, Issue 10, 2022, ISSN 2576-098X
Publisher: American Society for Microbiology
DOI: 10.1128/mra.01396-20

Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus

Author(s): Léa Meneu, Christophe Chapard, Jacques Serizay, Alex Westbrook, Etienne Routhier, Myriam Ruault, Manon Perrot, Alexandros Minakakis, Fabien Girard, Amaury Bignaud, Antoine Even, Géraldine Gourgues, Domenico Libri, Carole Lartigue, Aurèle Piazza, Agnès Thierry, Angela Taddei, Frédéric Beckouët, Julien Mozziconacci, Romain Koszul
Published in: Science, Issue 387, 2025, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.adm9466

Karyotype engineering reveals spatio-temporal control of replication firing and gene contacts

Author(s): Luciana Lazar-Stefanita; Jingchuan Luo; Remi Montagne; Agnes Thierry; Xiaoji Sun; Guillaume Mercy; Julien Mozziconacci; Romain Koszul; Jef D. Boeke
Published in: Cell Genomics, Issue 1, 2022, ISSN 2666-979X
Publisher: Elsevier
DOI: 10.1016/j.xgen.2022.100163

Anchoring of parasitic plasmids to inactive regions of eukaryotic chromosomes through nucleosome signal

Author(s): Fabien Girard, Antoine Even, Agnès Thierry, Myriam Ruault, Léa Meneu, Sandrine Adiba, Angela Taddei, Romain Koszul, Axel Cournac
Published in: Embo Journal, 2023, ISSN 0261-4189
Publisher: Nature Publishing Group
DOI: 10.1101/2023.10.04.558402

Neuroinvasion and anosmia are independent phenomena upon infection with SARS-CoV-2 and its variants

Author(s): Guilherme Dias de Melo, Victoire Perraud, Flavio Alvarez, Alba Vieites-Prado, Seonhee Kim, Lauriane Kergoat, Anthony Coleon, Bettina Salome, Magali Tichit, Aurèle Piazza, Agnès Thierry, David Hardy, Nicolas Wolff, Sandie Munier, Romain Koszul, Etienne Simon-Lorière, Volker Thiel, Marc Lecuit, Pierre-Marie Lledo, Nicolas Renier, Florence Larrous, Hervé Bourhy
Published in: Nature Communications, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-42800-7

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

Author(s): Matthey-Doret C, Colp MJ, Escoll P, Thierry A, Moreau P, Curtis B, Sahr T, Sarrasin M, Gray MW, Lang BF, Archibald JM, Buchrieser C, Koszul R.
Published in: Genome Research, 2022, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.276375.121

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

Author(s): Charlotte Cockram, Agnès Thierry, Aurore Gorlas, Roxane Lestini, Romain Koszul
Published in: Molecular Cell, 2020, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2020.12.013

FACT mediates cohesin function on chromatin

Author(s): Jonay Garcia-Luis, Luciana Lazar-Stefanita, Pilar Gutierrez-Escribano, Agnes Thierry, Axel Cournac, Alicia García, Sara González, Mar Sánchez, Adam Jarmuz, Alex Montoya, Marian Dore, Holger Kramer, Mohammad M. Karimi, Francisco Antequera, Romain Koszul, Luis Aragon
Published in: Nature Structural & Molecular Biology, Issue 26/10, 2019, Page(s) 970-979, ISSN 1545-9993
Publisher: Nature Publishing Group
DOI: 10.1038/s41594-019-0307-x

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

Author(s): Lyam Baudry, Théo Foutel-Rodier, Agnès Thierry, Romain Koszul, Martial Marbouty
Published in: Frontiers in Genetics, Issue 10, 2019, ISSN 1664-8021
Publisher: Frontiers Media
DOI: 10.3389/fgene.2019.00753

Generation of gene-level resolution chromosome contact maps in bacteria and archaea

Author(s): Charlotte Cockram, Agnès Thierry, Romain Koszul
Published in: STAR Protocols, Issue 2, 2022, Page(s) 100512, ISSN 2666-1667
Publisher: Cell Press Elsevier
DOI: 10.1016/j.xpro.2021.100512

Transcription-induced domains form the elementary constraining building blocks of bacterial chromosomes

Author(s): Amaury Bignaud, Charlotte Cockram, Céline Borde, Justine Groseille, Eric Allemand, Agnès Thierry, Martial Marbouty, Julien Mozziconacci, Olivier Espéli, Romain Koszul
Published in: Nature Structural & Molecular Biology, 2024, ISSN 1545-9993
Publisher: Nature Publishing Group
DOI: 10.1038/s41594-023-01178-2

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

Author(s): Quentin, Lamy-Besnier; Amaury, Bignaud; Julian R, Garneau; Marie, Titecat; Devon E, Conti; Alexandra, Von Strempel; Marc, Monot; Bärbel, Stecher; Romain, Koszul; Laurent, Debarbieux; Martial, Marbouty
Published in: Microbiome, Issue 7, 2023, ISSN 2049-2618
Publisher: Springer Nature
DOI: 10.1186/s40168-023-01541-x

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

Author(s): Héloïse Muller, Vittore F Scolari, Nicolas Agier, Aurèle Piazza, Agnès Thierry, Guillaume Mercy, Stéphane Descorps‐Declere, Luciana Lazar‐Stefanita, Olivier Espeli, Bertrand Llorente, Gilles Fischer, Julien Mozziconacci, Romain Koszul
Published in: Molecular Systems Biology, Issue 14/7, 2018, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.20188293

Regulation of Cohesin-Mediated Chromosome Folding by Eco1 and Other Partners

Author(s): Lise Dauban, Rémi Montagne, Agnès Thierry, Luciana Lazar-Stefanita, Nathalie Bastié, Olivier Gadal, Axel Cournac, Romain Koszul, Frédéric Beckouët
Published in: Molecular Cell, Issue 77/6, 2020, Page(s) 1279-1293.e4, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2020.01.019

Extended sister-chromosome catenation leads to massive reorganization of the E. coli genome

Author(s): Brenna Conin, Ingrid Billault-Chaumartin, Hafez El Sayyed, Charlotte Cockram, Romain Koszul, Olivier Espeli
Published in: Nucleic Acids Research, 2022, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkac105

instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder

Author(s): Lyam Baudry, Nadège Guiglielmoni, Hervé Marie-Nelly, Alexandre Cormier, Martial Marbouty, Komlan Avia, Yann Loe Mie, Olivier Godfroy, Lieven Sterck, J. Mark Cock, Christophe Zimmer, Susana M. Coelho, Romain Koszul
Published in: Genome Biology, 2020, ISSN 1474-7596
Publisher: BioMed Central
DOI: 10.1186/s13059-020-02041-z

Serpentine: a flexible 2D binning method for differential Hi-C analysis

Author(s): Lyam Baudry, Gaël A Millot, Agnes Thierry, Romain Koszul, Vittore F Scolari
Published in: Bioinformatics, Issue 36/12, 2020, Page(s) 3645-3651, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa249

Sir3 mediates long-range chromosome interactions in budding yeast

Author(s): Myriam Ruault, Vittore F. Scolari, Luciana Lazar-Stefanita, Antoine Hocher, Isabelle Loïodice, Romain Koszul, Angela Taddei
Published in: Genome Research, Issue 31/3, 2021, Page(s) 411-425, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.267872.120

Sister chromatid cohesion halts DNA loop expansion

Author(s): Nathalie Bastié, Christophe Chapard, Axel Cournac, Sanae Nejmi, Henri Mboumba, Olivier Gadal, Agnès Thierry, Frederic Beckouët, Romain Koszul
Published in: Molecular Cell, 2024, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2024.02.004

Absence of chromosome axis protein recruitment prevents meiotic recombination chromosome-wide in the budding yeast Lachancea kluyveri

Author(s): Sylvain Legrand, Asma Saifudeen, Hélène Bordelet, Julien Vernerey, Arnaud Guille, Amaury Bignaud, Agnès Thierry, Laurent Acquaviva, Maxime Gaudin, Aurore Sanchez, Dominic Johnson, Anne Friedrich, Joseph Schacherer, Matthew J Neale, Valérie Borde, Romain Koszul, Bertrand Llorente
Published in: Proc Natl Acad Sci U S A, 2024, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2312820121

Cohesin regulates homology search during recombinational DNA repair

Author(s): Aurèle Piazza, Hélène Bordelet, Agnès Dumont, Agnès Thierry, Jérôme Savocco, Fabien Girard, Romain Koszul
Published in: Nature Cellular Biology, 2021, ISSN 1476-4679
Publisher: Springer Nature
DOI: 10.1038/s41556-021-00783-x

Insights in bacterial genome folding

Author(s): Fares Osam Yáñez-Cuna; Romain Koszul
Published in: Current Opinion in Structural Biology, Issue 2, 2023, ISSN 0959-440X
Publisher: Elsevier BV
DOI: 10.1016/j.sbi.2023.102679

Orchestrating chromosome conformation capture analysis with Bioconductor

Author(s): Jacques Serizay, Cyril Matthey-Doret, Amaury Bignaud, Lyam Baudry, Romain Koszul
Published in: Nature Communications, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-44761-x

Non-peer reviewed articles (1)

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

Author(s): Nathalie Bastié, Christophe Chapard, Lise Dauban, Olivier Gadal, Frederic Beckouёt, Romain Koszul
Published in: Nature Structural & Molecular Biology, 2021, ISSN 1545-9993
Publisher: Nature Publishing Group
DOI: 10.1038/s41594-022-00780-0