Investigating the functional architecture of microbial genomes with synthetic approaches

Informazioni relative al progetto

SynarchiC

ID dell’accordo di sovvenzione: 771813

DOI

10.3030/771813

Progetto chiuso

Data della firma CE 1 Febbraio 2018

Data di avvio 1 Aprile 2018

Data di completamento 31 Marzo 2024

Finanziato da

• EXCELLENT SCIENCE - European Research Council (ERC)

Costo totale

€ 1 995 557,00

Contributo UE

€ 1 995 557,00

Coordinato da

INSTITUT PASTEUR
France

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Pubblicazioni

Peer reviewed articles (29)

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

Autori: 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
Pubblicato in: The Journal of Infectious Diseases, Numero 224, 2021, Pagina/e 1489-1499, ISSN 0022-1899
Editore: University of Chicago Press
DOI: 10.1093/infdis/jiab375

A virally-encoded tRNA neutralizes the PARIS antiviral defence system

Autori: 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
Pubblicato in: Nature, 2024, ISSN 0028-0836
Editore: 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

Autori: 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
Pubblicato in: The Lancet Microbe, Numero 2/2, 2021, Pagina/e e60-e69, ISSN 2666-5247
Editore: Elsevier
DOI: 10.1016/s2666-5247(20)30197-x

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

Autori: Jonay Garcia-Luis, Hélène Bordelet, Agnès Thierry, Romain Koszul, Luis Aragon
Pubblicato in: elife, 2022, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.80147

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

Autori: Martial Marbouty, Agnès Thierry, Gaël A Millot, Romain Koszul
Pubblicato in: eLife, Numero 10, 2021, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.60608

Computer vision for pattern detection in chromosome contact maps

Autori: 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
Pubblicato in: Nature Communications, Numero 11/1, 2020, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-020-19562-7

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

Autori: Quentin Lamy-Besnier, Romain Koszul, Laurent Debarbieux, Martial Marbouty
Pubblicato in: Microbiology Resource Announcements, Numero 10, 2022, ISSN 2576-098X
Editore: American Society for Microbiology
DOI: 10.1128/mra.01396-20

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

Autori: 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
Pubblicato in: Science, Numero 387, 2025, ISSN 0036-8075
Editore: American Association for the Advancement of Science
DOI: 10.1126/science.adm9466

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

Autori: Luciana Lazar-Stefanita; Jingchuan Luo; Remi Montagne; Agnes Thierry; Xiaoji Sun; Guillaume Mercy; Julien Mozziconacci; Romain Koszul; Jef D. Boeke
Pubblicato in: Cell Genomics, Numero 1, 2022, ISSN 2666-979X
Editore: Elsevier
DOI: 10.1016/j.xgen.2022.100163

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

Autori: Fabien Girard, Antoine Even, Agnès Thierry, Myriam Ruault, Léa Meneu, Sandrine Adiba, Angela Taddei, Romain Koszul, Axel Cournac
Pubblicato in: Embo Journal, 2023, ISSN 0261-4189
Editore: 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

Autori: 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
Pubblicato in: Nature Communications, 2023, ISSN 2041-1723
Editore: 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

Autori: 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.
Pubblicato in: Genome Research, 2022, ISSN 1088-9051
Editore: 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

Autori: Charlotte Cockram, Agnès Thierry, Aurore Gorlas, Roxane Lestini, Romain Koszul
Pubblicato in: Molecular Cell, 2020, ISSN 1097-2765
Editore: Cell Press
DOI: 10.1016/j.molcel.2020.12.013

FACT mediates cohesin function on chromatin

Autori: 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
Pubblicato in: Nature Structural & Molecular Biology, Numero 26/10, 2019, Pagina/e 970-979, ISSN 1545-9993
Editore: 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

Autori: Lyam Baudry, Théo Foutel-Rodier, Agnès Thierry, Romain Koszul, Martial Marbouty
Pubblicato in: Frontiers in Genetics, Numero 10, 2019, ISSN 1664-8021
Editore: Frontiers Media
DOI: 10.3389/fgene.2019.00753

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

Autori: Charlotte Cockram, Agnès Thierry, Romain Koszul
Pubblicato in: STAR Protocols, Numero 2, 2022, Pagina/e 100512, ISSN 2666-1667
Editore: Cell Press Elsevier
DOI: 10.1016/j.xpro.2021.100512

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

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

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

Autori: 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
Pubblicato in: Microbiome, Numero 7, 2023, ISSN 2049-2618
Editore: Springer Nature
DOI: 10.1186/s40168-023-01541-x

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

Autori: 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
Pubblicato in: Molecular Systems Biology, Numero 14/7, 2018, ISSN 1744-4292
Editore: Nature Publishing Group
DOI: 10.15252/msb.20188293

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

Autori: Lise Dauban, Rémi Montagne, Agnès Thierry, Luciana Lazar-Stefanita, Nathalie Bastié, Olivier Gadal, Axel Cournac, Romain Koszul, Frédéric Beckouët
Pubblicato in: Molecular Cell, Numero 77/6, 2020, Pagina/e 1279-1293.e4, ISSN 1097-2765
Editore: Cell Press
DOI: 10.1016/j.molcel.2020.01.019

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

Autori: Brenna Conin, Ingrid Billault-Chaumartin, Hafez El Sayyed, Charlotte Cockram, Romain Koszul, Olivier Espeli
Pubblicato in: Nucleic Acids Research, 2022, ISSN 1362-4962
Editore: Oxford University Press
DOI: 10.1093/nar/gkac105

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

Autori: 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
Pubblicato in: Genome Biology, 2020, ISSN 1474-7596
Editore: BioMed Central
DOI: 10.1186/s13059-020-02041-z

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

Autori: Lyam Baudry, Gaël A Millot, Agnes Thierry, Romain Koszul, Vittore F Scolari
Pubblicato in: Bioinformatics, Numero 36/12, 2020, Pagina/e 3645-3651, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btaa249

Sir3 mediates long-range chromosome interactions in budding yeast

Autori: Myriam Ruault, Vittore F. Scolari, Luciana Lazar-Stefanita, Antoine Hocher, Isabelle Loïodice, Romain Koszul, Angela Taddei
Pubblicato in: Genome Research, Numero 31/3, 2021, Pagina/e 411-425, ISSN 1088-9051
Editore: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.267872.120

Sister chromatid cohesion halts DNA loop expansion

Autori: Nathalie Bastié, Christophe Chapard, Axel Cournac, Sanae Nejmi, Henri Mboumba, Olivier Gadal, Agnès Thierry, Frederic Beckouët, Romain Koszul
Pubblicato in: Molecular Cell, 2024, ISSN 1097-2765
Editore: 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

Autori: 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
Pubblicato in: Proc Natl Acad Sci U S A, 2024, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2312820121

Cohesin regulates homology search during recombinational DNA repair

Autori: Aurèle Piazza, Hélène Bordelet, Agnès Dumont, Agnès Thierry, Jérôme Savocco, Fabien Girard, Romain Koszul
Pubblicato in: Nature Cellular Biology, 2021, ISSN 1476-4679
Editore: Springer Nature
DOI: 10.1038/s41556-021-00783-x

Insights in bacterial genome folding

Autori: Fares Osam Yáñez-Cuna; Romain Koszul
Pubblicato in: Current Opinion in Structural Biology, Numero 2, 2023, ISSN 0959-440X
Editore: Elsevier BV
DOI: 10.1016/j.sbi.2023.102679

Orchestrating chromosome conformation capture analysis with Bioconductor

Autori: Jacques Serizay, Cyril Matthey-Doret, Amaury Bignaud, Lyam Baudry, Romain Koszul
Pubblicato in: Nature Communications, 2024, ISSN 2041-1723
Editore: 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

Autori: Nathalie Bastié, Christophe Chapard, Lise Dauban, Olivier Gadal, Frederic Beckouёt, Romain Koszul
Pubblicato in: Nature Structural & Molecular Biology, 2021, ISSN 1545-9993
Editore: Nature Publishing Group
DOI: 10.1038/s41594-022-00780-0