2026-08-05T15:45:33Zhttps://repisalud.isciii.es/rest/oai/requestoai:repisalud.isciii.es:20.500.12105/85092024-11-29T20:32:32Zcom_20.500.12105_2173com_20.500.12105_2051col_20.500.12105_19597
Repisalud
author
Pancaldi, Vera
author
Carrillo-de-Santa-Pau, Enrique
author
Javierre, Biola Maria
author
Juan, David
author
Fraser, Peter
author
Spivakov, Mikhail
author
Valencia, Alfonso
author
Rico, Daniel
funder
Unión Europea
funder
Biotechnology and Biological Sciences Research Council (Reino Unido)
funder
Medical Research Council (Reino Unido)
funder
Instituto de Salud Carlos III
funder
Unión Europea. Fondo Europeo de Desarrollo Regional (FEDER/ERDF)
2019-10-21T10:50:08Z
2019-10-21T10:50:08Z
2016-07-08
Genome Biol. 2016;17(1):152
10.1186/s13059-016-1003-3
1474-760X
1474-760X
Genome biology
27391817
http://hdl.handle.net/20.500.12105/8509
BACKGROUND: Network analysis is a powerful way of modeling chromatin interactions. Assortativity is a network property used in social sciences to identify factors affecting how people establish social ties. We propose a new approach, using chromatin assortativity, to integrate the epigenomic landscape of a specific cell type with its chromatin interaction network and thus investigate which proteins or chromatin marks mediate genomic contacts. RESULTS: We use high-resolution promoter capture Hi-C and Hi-Cap data as well as ChIA-PET data from mouse embryonic stem cells to investigate promoter-centered chromatin interaction networks and calculate the presence of specific epigenomic features in the chromatin fragments constituting the nodes of the network. We estimate the association of these features with the topology of four chromatin interaction networks and identify features localized in connected areas of the network. Polycomb group proteins and associated histone marks are the features with the highest chromatin assortativity in promoter-centered networks. We then ask which features distinguish contacts amongst promoters from contacts between promoters and other genomic elements. We observe higher chromatin assortativity of the actively elongating form of RNA polymerase 2 (RNAPII) compared with inactive forms only in interactions between promoters and other elements. CONCLUSIONS: Contacts among promoters and between promoters and other elements have different characteristic epigenomic features. We identify a possible role for the elongating form of RNAPII in mediating interactions among promoters, enhancers, and transcribed gene bodies. Our approach facilitates the study of multiple genome-wide epigenomic profiles, considering network topology and allowing the comparison of chromatin interaction networks.
eng
3D genome
Assortativity
Chromatin Interaction Network
Embryonic stem cells
Enhancers
Epigenomics
Polycomb
Promoter Capture Hi-C
RNA polymerase
Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity
journal article
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