Investigating the functional architecture of microbial genomes with synthetic approaches

Información del proyecto

SynarchiC

Identificador del acuerdo de subvención: 771813

DOI

10.3030/771813

Proyecto cerrado

Fecha de la firma de la CE 1 Febrero 2018

Fecha de inicio 1 Abril 2018

Fecha de finalización 31 Marzo 2024

Financiado con arreglo a

• EXCELLENT SCIENCE - European Research Council (ERC)

Coste total

€ 1 995 557,00

Aportación de la UE

€ 1 995 557,00

Coordinado por

INSTITUT PASTEUR
France

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Publicaciones

Peer reviewed articles (29)

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

Autores: 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
Publicado en: The Journal of Infectious Diseases, Edición 224, 2021, Página(s) 1489-1499, ISSN 0022-1899
Editor: University of Chicago Press
DOI: 10.1093/infdis/jiab375

A virally-encoded tRNA neutralizes the PARIS antiviral defence system

Autores: 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
Publicado en: Nature, 2024, ISSN 0028-0836
Editor: 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

Autores: 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
Publicado en: The Lancet Microbe, Edición 2/2, 2021, Página(s) e60-e69, ISSN 2666-5247
Editor: Elsevier
DOI: 10.1016/s2666-5247(20)30197-x

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

Autores: Jonay Garcia-Luis, Hélène Bordelet, Agnès Thierry, Romain Koszul, Luis Aragon
Publicado en: elife, 2022, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/elife.80147

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

Autores: Martial Marbouty, Agnès Thierry, Gaël A Millot, Romain Koszul
Publicado en: eLife, Edición 10, 2021, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/elife.60608

Computer vision for pattern detection in chromosome contact maps

Autores: 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
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-020-19562-7

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

Autores: Quentin Lamy-Besnier, Romain Koszul, Laurent Debarbieux, Martial Marbouty
Publicado en: Microbiology Resource Announcements, Edición 10, 2022, ISSN 2576-098X
Editor: American Society for Microbiology
DOI: 10.1128/mra.01396-20

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

Autores: 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
Publicado en: Science, Edición 387, 2025, ISSN 0036-8075
Editor: American Association for the Advancement of Science
DOI: 10.1126/science.adm9466

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

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

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

Autores: Fabien Girard, Antoine Even, Agnès Thierry, Myriam Ruault, Léa Meneu, Sandrine Adiba, Angela Taddei, Romain Koszul, Axel Cournac
Publicado en: Embo Journal, 2023, ISSN 0261-4189
Editor: 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

Autores: 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
Publicado en: Nature Communications, 2023, ISSN 2041-1723
Editor: 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

Autores: 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.
Publicado en: Genome Research, 2022, ISSN 1088-9051
Editor: 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

Autores: Charlotte Cockram, Agnès Thierry, Aurore Gorlas, Roxane Lestini, Romain Koszul
Publicado en: Molecular Cell, 2020, ISSN 1097-2765
Editor: Cell Press
DOI: 10.1016/j.molcel.2020.12.013

FACT mediates cohesin function on chromatin

Autores: 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
Publicado en: Nature Structural & Molecular Biology, Edición 26/10, 2019, Página(s) 970-979, ISSN 1545-9993
Editor: 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

Autores: Lyam Baudry, Théo Foutel-Rodier, Agnès Thierry, Romain Koszul, Martial Marbouty
Publicado en: Frontiers in Genetics, Edición 10, 2019, ISSN 1664-8021
Editor: Frontiers Media
DOI: 10.3389/fgene.2019.00753

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

Autores: Charlotte Cockram, Agnès Thierry, Romain Koszul
Publicado en: STAR Protocols, Edición 2, 2022, Página(s) 100512, ISSN 2666-1667
Editor: Cell Press Elsevier
DOI: 10.1016/j.xpro.2021.100512

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

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

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

Autores: 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
Publicado en: Microbiome, Edición 7, 2023, ISSN 2049-2618
Editor: Springer Nature
DOI: 10.1186/s40168-023-01541-x

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

Autores: 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
Publicado en: Molecular Systems Biology, Edición 14/7, 2018, ISSN 1744-4292
Editor: Nature Publishing Group
DOI: 10.15252/msb.20188293

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

Autores: Lise Dauban, Rémi Montagne, Agnès Thierry, Luciana Lazar-Stefanita, Nathalie Bastié, Olivier Gadal, Axel Cournac, Romain Koszul, Frédéric Beckouët
Publicado en: Molecular Cell, Edición 77/6, 2020, Página(s) 1279-1293.e4, ISSN 1097-2765
Editor: Cell Press
DOI: 10.1016/j.molcel.2020.01.019

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

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

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

Autores: 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
Publicado en: Genome Biology, 2020, ISSN 1474-7596
Editor: BioMed Central
DOI: 10.1186/s13059-020-02041-z

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

Autores: Lyam Baudry, Gaël A Millot, Agnes Thierry, Romain Koszul, Vittore F Scolari
Publicado en: Bioinformatics, Edición 36/12, 2020, Página(s) 3645-3651, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btaa249

Sir3 mediates long-range chromosome interactions in budding yeast

Autores: Myriam Ruault, Vittore F. Scolari, Luciana Lazar-Stefanita, Antoine Hocher, Isabelle Loïodice, Romain Koszul, Angela Taddei
Publicado en: Genome Research, Edición 31/3, 2021, Página(s) 411-425, ISSN 1088-9051
Editor: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.267872.120

Sister chromatid cohesion halts DNA loop expansion

Autores: Nathalie Bastié, Christophe Chapard, Axel Cournac, Sanae Nejmi, Henri Mboumba, Olivier Gadal, Agnès Thierry, Frederic Beckouët, Romain Koszul
Publicado en: Molecular Cell, 2024, ISSN 1097-2765
Editor: 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

Autores: 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
Publicado en: Proc Natl Acad Sci U S A, 2024, ISSN 0027-8424
Editor: National Academy of Sciences
DOI: 10.1073/pnas.2312820121

Cohesin regulates homology search during recombinational DNA repair

Autores: Aurèle Piazza, Hélène Bordelet, Agnès Dumont, Agnès Thierry, Jérôme Savocco, Fabien Girard, Romain Koszul
Publicado en: Nature Cellular Biology, 2021, ISSN 1476-4679
Editor: Springer Nature
DOI: 10.1038/s41556-021-00783-x

Insights in bacterial genome folding

Autores: Fares Osam Yáñez-Cuna; Romain Koszul
Publicado en: Current Opinion in Structural Biology, Edición 2, 2023, ISSN 0959-440X
Editor: Elsevier BV
DOI: 10.1016/j.sbi.2023.102679

Orchestrating chromosome conformation capture analysis with Bioconductor

Autores: Jacques Serizay, Cyril Matthey-Doret, Amaury Bignaud, Lyam Baudry, Romain Koszul
Publicado en: Nature Communications, 2024, ISSN 2041-1723
Editor: 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

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