2015/12/01 by Véra Pancaldi, Enrique Carrillo de Santa Pau, Pancaldi, Vera +14
Biochemistry, Genetics and Molecular Biology · #Bioinformatics and Genomic Networks #Epigenetics and DNA Methylation #FOS: Biological sciences #Genomics (q-bio.GN) #Genomics and Chromatin Dynamics #Molecular Networks (q-bio.MN)
paper · pdf · doi:10.48550/arxiv.1512.00268
openalex publication_date 2015/12/01 · openalex created_date 2022/10/04 · openalex updated_date 2026/07/28
Network analysis is a powerful way of modeling chromatin interactions.\nAssortativity is a network property used in social sciences to identify factors\naffecting how people establish social ties. We propose a new approach, using\nchromatin assortativity to integrate the epigenomic landscape of a specific\ncell type with its chromatin interaction network and thus investigate which\nproteins or chromatin marks mediate genomic contacts. We use high-resolution\nPromoter Capture Hi-C and Hi-Cap data as well as ChIA-PET data from mouse\nembryonic stem cells to investigate promoter-centered chromatin interaction\nnetworks and calculate the presence of specific epigenomic features in the\nchromatin fragments constituting the nodes of the network. We estimate the\nassociation of these features to the topology of four chromatin interaction\nnetworks and identify features localized in connected areas of the network.\nPolycomb Group proteins and associated histone marks are the features with the\nhighest chromatin assortativity in promoter-centred networks. We then ask which\nfeatures distinguish contacts amongst promoters from contacts between promoters\nand other genomic elements. We observe higher chromatin assortativity of the\nactively elongating form of RNA Polymerase 2 (RNAPII) compared to inactive\nforms only in interactions between promoters and other elements. Contacts among\npromoters, and between promoters and other elements have different\ncharacteristic epigenomic features. We identify a possible role for the\nelongating form of RNAPII in mediating interactions among promoters, enhancers\nand transcribed gene bodies. Our approach facilitates the study of multiple\ngenome-wide epigenomic profiles, considering network topology and allowing the\ncomparison of chromatin interaction networks.\n