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Epigenomic Co-localization and Co-evolution Reveal a key role for 5hmC as a Communication Hub in the Chromatin Network of ESCs

Lookup NU author(s): Dr Daniel Rico RodriguezORCiD

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).

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.

Publication metadata

Author(s): Juan D, Perner D, Carrillo de Santa Pau E, Marsili S, Ochoa D, Chung HR, Vingron M, Rico D, Valencia A

Publication type: Article

Publication status: Published

Journal: Cell Reports

Year: 2016

Volume: 14

Issue: 5

Pages: 1246-1257

Print publication date: 09/02/2016

Online publication date: 28/01/2016

Acceptance date: 29/12/2015

Date deposited: 31/10/2016

ISSN (print): 2211-1247

Publisher: Cell Press

URL: http://dx.doi.org/10.1016/j.celrep.2016.01.008

DOI: 10.1016/j.celrep.2016.01.008

PubMed id: 26832418

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