Toggle Main Menu Toggle Search

Open Access padlockePrints

Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity

Lookup NU author(s): Dr Daniel Rico RodriguezORCiD



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


BackgroundNetwork 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.ResultsWe 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.ConclusionsContacts 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.

Publication metadata

Author(s): Pancaldi V, Carrillo-de-Santa-Pau E, Javierre BM, Juan D, Fraser P, Valencia A, Rico D

Publication type: Article

Publication status: Published

Journal: Genome Biology

Year: 2016

Volume: 17

Online publication date: 08/07/2016

Acceptance date: 07/06/2016

Date deposited: 12/10/2016

ISSN (electronic): 1474-760X

Publisher: BioMed Central Ltd


DOI: 10.1186/s13059-016-1003-3

PubMed id: 27391817


Altmetrics provided by Altmetric


Funder referenceFunder name
PT 13/0001/0030