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DOI | 10.1186/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
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ISSN | 1471-2164 |
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 |
推荐引用方式 GB/T 7714 | 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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