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

ABSTRACT:

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 associat

SUBMITTER: Pancaldi V 

PROVIDER: S-EPMC4939006 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature