Epigenomics and chromosome architecture one cell at a time

Project Information

EpiScope

Grant agreement ID: 724429

DOI 10.3030/724429

Project closed

EC signature date 21 March 2017

Start date 1 September 2017

End date 31 August 2023

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 1 999 780,00

EU contribution € 1 999 780,00

Coordinated by

CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
France

Publications

Peer reviewed articles (13)

3D chromatin interactions involving Drosophila insulators are infrequent but preferential and arise before TADs and transcription

Author(s): Olivier Messina, Flavien Raynal, Julian Gurgo, Jean-Bernard Fiche, Vera Pancaldi, Marcelo Nollmann
Published in: Nature Communications, Issue in press, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/2022.12.12.520036

Multi-scale dynamic imaging reveals that cooperative motility behaviors promote efficient predation in bacteria

Author(s): Rombouts Sara, Anna Mas, Antoine Le Gall, Jean-Bernard Fiche, Tam Mignot, Marcelo Nollmann
Published in: Nature Communications, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/2022.12.20.521001

Multiple parameters shape the 3D chromatin structure of single nuclei at the doc locus in Drosophila

Author(s): Markus Goetz, Olivier Messina, Sergio Espinola, Jean-Bernard Fiche, Marcelo Nollmann
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-32973-y

Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging

Author(s): Franziska Barho, Jean-Bernard Fiche, Marion Bardou, Olivier Messina, Alexandre Martiniere, Christophe Houbron, Marcelo NOLLMANN
Published in: Open Research Europe, 2021, ISSN 2732-5121
Publisher: F1000 Research Limited on behalf of the European Commission
DOI: 10.12688/openreseurope.14641.1

bacto_tracker: a method for single-cell tracking of M. xanthus in dense and multispecies colonies

Author(s): Sara Rombouts, Jean-Bernard Fiche, Tam Mignot, Marcelo Nollmann
Published in: Open Research Europe, 2023, ISSN 2732-5121
Publisher: F1000 Research Limited on behalf of the European Commission
DOI: 10.12688/openreseurope.15255.1

Microscopy-Based Chromosome Conformation Capture Enables Simultaneous Visualization of Genome Organization and Transcription in Intact Organisms

Author(s): Andrés M. Cardozo Gizzi, Diego I. Cattoni, Jean-Bernard Fiche, Sergio M. Espinola, Julian Gurgo, Olivier Messina, Christophe Houbron, Yuki Ogiyama, Giorgio L. Papadopoulos, Giacomo Cavalli, Mounia Lagha, Marcelo Nollmann
Published in: Molecular Cell, Issue 74/1, 2019, Page(s) 212-222.e5, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2019.01.011

TADs are 3D structural units of higher-order chromosome organization in Drosophila

Author(s): Quentin Szabo, Daniel Jost, Jia-Ming Chang, Diego I. Cattoni, Giorgio L. Papadopoulos, Boyan Bonev, Tom Sexton, Julian Gurgo, Caroline Jacquier, Marcelo Nollmann, Frédéric Bantignies, Giacomo Cavalli
Published in: Science Advances, Issue 4/2, 2018, Page(s) eaar8082, ISSN 2375-2548
Publisher: Science
DOI: 10.1126/sciadv.aar8082

Direct and simultaneous observation of transcription and chromosome architecture in single cells with Hi-M

Author(s): Andrés M. Cardozo Gizzi, Sergio M. Espinola, Julian Gurgo, Christophe Houbron, Jean-Bernard Fiche, Diego I. Cattoni, Marcelo Nollmann
Published in: Nature Protocols, Issue 15/3, 2020, Page(s) 840-876, ISSN 1754-2189
Publisher: Nature Publishing Group
DOI: 10.1038/s41596-019-0269-9

TADs or no TADS: Lessons From Single-cell Imaging of Chromosome Architecture

Author(s): Andrés M. Cardozo Gizzi, Diego I. Cattoni, Marcelo Nollmann
Published in: Journal of Molecular Biology, Issue 432/3, 2020, Page(s) 682-693, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2019.12.034

Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions

Author(s): Diego I. Cattoni, Andrés M. Cardozo Gizzi, Mariya Georgieva, Marco Di Stefano, Alessandro Valeri, Delphine Chamousset, Christophe Houbron, Stephanie Déjardin, Jean-Bernard Fiche, Inma González, Jia-Ming Chang, Thomas Sexton, Marc A. Marti-Renom, Frédéric Bantignies, Giacomo Cavalli, Marcelo Nollmann
Published in: Nature Communications, Issue 8/1, 2017, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-017-01962-x

Contributions of 3D chromatin structure to cell-type-specific gene regulation

Author(s): Marie Schaeffer; Marcelo Nollmann
Published in: Current Opinion in Genetics & Development, 2022, ISSN 0959-437X
Publisher: Elsevier BV
DOI: 10.1016/j.gde.2023.102032

Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development

Author(s): Sergio Martin Espinola, Markus Götz, Maelle Bellec, Olivier Messina, Jean-Bernard Fiche, Christophe Houbron, Matthieu Dejean, Ingolf Reim, Andrés M. Cardozo Gizzi, Mounia Lagha, Marcelo Nollmann
Published in: Nature Genetics, Issue 53, pages 477-486, 2021, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-021-00816-z

ATP-Driven Separation of Liquid Phase Condensates in Bacteria

Author(s): B. Guilhas, J.C. Walter, J. Rech, G. David, N.-O. Walliser, J. Palmeri, C., Mathieu-Demaziere, A. Parmeggiani, J.Y. Bouet, A. Le Gall, Marcelo Nollmann
Published in: Mol Cell., Issue 2020 Jul 16;79(2):293-303.e4, 2020, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2020.06.034

Book chapters (1)

The Impact of Space and Time on the Functional Output of the Genome.

Author(s): Nollmann M, Bennabi I, Götz M, Gregor T.
Published in: Cold Spring Harb Perspect Biol, 2022, ISSN 1943-0264
Publisher: Cold Spring Harb
DOI: 10.1101/cshperspect.a040378

Non-peer reviewed articles (4)

pyHiM, a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging

Author(s): Devos Xavier, Fiche Jean-Bernard, Bardou Marion, Messina Olivier, Houbron Christophe, Gurgo Julian, Schaeffer Marie, Götz Markus, Walter Thomas, Mueller Florian, Nollmann Marcelo
Published in: BioRxiv, 2023, ISSN 2692-8205
Publisher: bioRxiv
DOI: 10.1101/2023.09.19.558412

Multiple parameters shape the 3D chromatin structure of single nuclei

Author(s): Markus Goetz, Olivier Messina, Sergio Espinola, Jean-Bernard Fiche, Marcelo Nollmann
Published in: BioRxiv, 2022, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.01.16.476319

Multiplexed chromatin imaging reveals predominantly pairwise long-range coordination between Drosophila Polycomb genes

Author(s): Julian Gurgo, Jean-Charles Walter, Jean-Bernard Fiche, Christophe Houbron, Marie Schaeffer, Giacomo Cavalli, Frédéric Bantignies, Marcelo Nollmann
Published in: BioRxiv, 2022, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratories
DOI: 10.1101/2022.05.16.492046

Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during development

Author(s): Sergio Martín Espínola; Markus Götz; Jean-Bernard Fiche; Maelle Bellec; Christophe Houbron; Andrés M. Cardozo Gizzi; Mounia Lagha; Marcelo Nollmann
Published in: Biorxiv, Issue 1, 2020, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratories
DOI: 10.1101/2020.07.07.191015