Distinct polymer physics principles govern chromatin dynamics in mouse and Drosophila topological domains

Autor: Ea, Vuthy, Sexton, Tom, Gostan, Thierry, Herviou, Laurie, Baudement, Marie-Odile, Zhang, Yunzhe, Berlivet, Soizik, Le Lay-Taha, Marie-Noëlle, Cathala, Guy, Lesne, Annick, Victor, Jean-Marc, Fan, Yuhong, Cavalli, Giacomo, Forné, Thierry
Přispěvatelé: Institut de Génétique Moléculaire de Montpellier ( IGMM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Montpellier ( UM ), Institut de génétique humaine ( IGH ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), School of Physics and Nuclear Energy Engineering, Laboratoire de Physique Théorique de la Matière Condensée ( LPTMC ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), School of Biology and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA, Institut de Génétique Moléculaire de Montpellier (IGMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Georgia Institute of Technology [Atlanta], GDR 3536 Architecture et Dynamique Nucléaires (ADN), Université Pierre et Marie Curie - Paris 6 (UPMC), Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
Jazyk: angličtina
Rok vydání: 2015
Předmět:
Zdroj: BMC Genomics
BMC Genomics, BioMed Central, 2015, 16, pp.607. 〈10.1186/s12864-015-1786-8〉
BMC Genomics, BioMed Central, 2015, 16, pp.607. ⟨10.1186/s12864-015-1786-8⟩
BMC Genomics, 2015, 16, pp.607. ⟨10.1186/s12864-015-1786-8⟩
ISSN: 1471-2164
DOI: 10.1186/s12864-015-1786-8〉
Popis: International audience; Background: In higher eukaryotes, the genome is partitioned into large "Topologically Associating Domains" (TADs) in which the chromatin displays favoured long-range contacts. While a crumpled/fractal globule organization has received experimental supports at higher-order levels, the organization principles that govern chromatin dynamics within these TADs remain unclear. Using simple polymer models, we previously showed that, in mouse liver cells, gene-rich domains tend to adopt a statistical helix shape when no significant locus-specific interaction takes place. Results: Here, we use data from diverse 3C-derived methods to explore chromatin dynamics within mouse and Drosophila TADs. In mouse Embryonic Stem Cells (mESC), that possess large TADs (median size of 840 kb), we show that the statistical helix model, but not globule models, is relevant not only in gene-rich TADs, but also in gene-poor and gene-desert TADs. Interestingly, this statistical helix organization is considerably relaxed in mESC compared to liver cells, indicating that the impact of the constraints responsible for this organization is weaker in pluripotent cells. Finally, depletion of histone H1 in mESC alters local chromatin flexibility but not the statistical helix organization. In Drosophila, which possesses TADs of smaller sizes (median size of 70 kb), we show that, while chromatin compaction and flexibility are finely tuned according to the epigenetic landscape, chromatin dynamics within TADs is generally compatible with an unconstrained polymer configuration. Conclusions: Models issued from polymer physics can accurately describe the organization principles governing chromatin dynamics in both mouse and Drosophila TADs. However, constraints applied on this dynamics within mammalian TADs have a peculiar impact resulting in a statistical helix organization.
Databáze: OpenAIRE
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