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

BMC Genomics

Research Article

Tom Sexton¹  Giacomo Cavalli²  Marie-Noëlle Le Lay-Taha³  Laurie Herviou³  Marie-Odile Baudement³  Vuthy Ea³  Soizik Berlivet³  Thierry Gostan³  Thierry Forné⁴  Guy Cathala⁴  Annick Lesne⁵  Jean-Marc Victor⁵  Yunzhe Zhang⁶  Yuhong Fan⁶ 

[1] Institut de Génétique Humaine, UPR 1142, CNRS, Montpellier, France;Institut de Génétique Humaine, UPR 1142, CNRS, Montpellier, France;CNRS GDR 3536 UPMC, Sorbonne universités, Paris, France;Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France;Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France;CNRS GDR 3536 UPMC, Sorbonne universités, Paris, France;Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France;CNRS GDR 3536 UPMC, Sorbonne universités, Paris, France;Laboratoire de Physique de la Matière Condensée, CNRS UMR 7600, UPMC, Sorbonne universités, Paris, France;School of Biology and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA;

关键词: Chromatin dynamics;    Polymer models;    Topological domains;    Epigenetics;    H1 histone;   

DOI  :  10.1186/s12864-015-1786-8

 received in 2015-02-06, accepted in 2015-07-20,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundIn 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.ResultsHere, 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.ConclusionsModels 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.

【 授权许可】

CC BY   
© Ea et al. 2015