Title |
Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs
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Published in |
Cell Reports, January 2016
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DOI | 10.1016/j.celrep.2016.01.008 |
Pubmed ID | |
Authors |
David Juan, Juliane Perner, Enrique Carrillo de Santa Pau, Simone Marsili, David Ochoa, Ho-Ryun Chung, Martin Vingron, Daniel Rico, Alfonso Valencia |
Abstract |
Epigenetic communication through histone and cytosine modifications is essential for gene regulation and cell identity. Here, we propose a framework that is based on a chromatin communication model to get insight on the function of epigenetic modifications in ESCs. The epigenetic communication network was inferred from genome-wide location data plus extensive manual annotation. Notably, we found that 5-hydroxymethylcytosine (5hmC) is the most-influential hub of this network, connecting DNA demethylation to nucleosome remodeling complexes and to key transcription factors of pluripotency. Moreover, an evolutionary analysis revealed a central role of 5hmC in the co-evolution of chromatin-related proteins. Further analysis of regions where 5hmC co-localizes with specific interactors shows that each interaction points to chromatin remodeling, stemness, differentiation, or metabolism. Our results highlight the importance of cytosine modifications in the epigenetic communication of ESCs. |
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Geographical breakdown
Country | Count | As % |
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United States | 7 | 19% |
United Kingdom | 7 | 19% |
Spain | 4 | 11% |
Netherlands | 1 | 3% |
Canada | 1 | 3% |
Israel | 1 | 3% |
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India | 1 | 3% |
Hungary | 1 | 3% |
Other | 1 | 3% |
Unknown | 11 | 31% |
Demographic breakdown
Type | Count | As % |
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Members of the public | 20 | 56% |
Scientists | 13 | 36% |
Science communicators (journalists, bloggers, editors) | 3 | 8% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Germany | 2 | 1% |
United States | 2 | 1% |
Spain | 2 | 1% |
Sweden | 2 | 1% |
Italy | 1 | <1% |
New Caledonia | 1 | <1% |
United Kingdom | 1 | <1% |
Unknown | 146 | 93% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 52 | 33% |
Student > Ph. D. Student | 31 | 20% |
Student > Master | 15 | 10% |
Student > Bachelor | 12 | 8% |
Professor > Associate Professor | 6 | 4% |
Other | 22 | 14% |
Unknown | 19 | 12% |
Readers by discipline | Count | As % |
---|---|---|
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Agricultural and Biological Sciences | 56 | 36% |
Medicine and Dentistry | 4 | 3% |
Chemistry | 4 | 3% |
Computer Science | 3 | 2% |
Other | 4 | 3% |
Unknown | 22 | 14% |