Arid
DOI10.1186/s12864-015-1786-8
Distinct polymer physics principles govern chromatin dynamics in mouse and Drosophila topological domains
Ea, Vuthy1; Sexton, Tom2; Gostan, Thierry1; Herviou, Laurie1; Baudement, Marie-Odile1; Zhang, Yunzhe3,4; Berlivet, Soizik1; Le Lay-Taha, Marie-Noelle1; Cathala, Guy1,5; Lesne, Annick1,5,6; Victor, Jean-Marc1,5,6; Fan, Yuhong3,4; Cavalli, Giacomo2,5; Fome, Thierry1,5
通讯作者Fome, Thierry
来源期刊BMC GENOMICS
ISSN1471-2164
出版年2015
卷号16
英文摘要

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.


英文关键词Chromatin dynamics Polymer models Topological domains Epigenetics H1 histone
类型Article
语种英语
国家France ; USA
收录类别SCI-E
WOS记录号WOS:000359526100001
WOS关键词CHROMOSOME CONFORMATION ; HISTONE H1 ; GENOME ; ORGANIZATION ; FIBER ; MODEL ; PLURIPOTENT ; COMPLEXITY ; LANDSCAPE ; SUPPORT
WOS类目Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS研究方向Biotechnology & Applied Microbiology ; Genetics & Heredity
资源类型期刊论文
条目标识符http://119.78.100.177/qdio/handle/2XILL650/186298
作者单位1.Univ Montpellier, CNRS, UMR5535, Inst Genet Mol Montpellier, F-34293 Montpellier 5, France;
2.CNRS, UPR 1142, Inst Genet Humaine, Montpellier, France;
3.Georgia Inst Technol, Sch Biol, Atlanta, GA 30332 USA;
4.Georgia Inst Technol, Petit Inst Bioengn & Biosci, Atlanta, GA 30332 USA;
5.Univ Paris 04, UPMC, CNRS, GDR 3536, Paris, France;
6.Univ Paris 04, UPMC, CNRS, UMR 7600,Lab Phys Matiere Condensee, Paris, France
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Ea, Vuthy,Sexton, Tom,Gostan, Thierry,et al. Distinct polymer physics principles govern chromatin dynamics in mouse and Drosophila topological domains[J],2015,16.
APA Ea, Vuthy.,Sexton, Tom.,Gostan, Thierry.,Herviou, Laurie.,Baudement, Marie-Odile.,...&Fome, Thierry.(2015).Distinct polymer physics principles govern chromatin dynamics in mouse and Drosophila topological domains.BMC GENOMICS,16.
MLA Ea, Vuthy,et al."Distinct polymer physics principles govern chromatin dynamics in mouse and Drosophila topological domains".BMC GENOMICS 16(2015).
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