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Question: How can network assortativity be applied in the three-dimensional analysis of the genome?

Context: Here, we use publicly available DNaseI-seq data to measure the assortativity signatures of genome-wide TFNs in 41 distinct human cell and tissue types. We find that all TFNs share a common assortativity signature and that this signature confers phenotypic robustness to model TFNs.
Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity
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
Polycomb group proteins and associated histone marks are the features with the highest chromatin assortativity in promoter-centered networks.
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.
Here, we use publicly available DNaseI-seq data to measure the assortativity signatures of genome-wide TFNs in 41 distinct human cell and tissue types.
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.
Our approach facilitates the study of multiple genome-wide epigenomic profiles, considering network topology and allowing the comparison of chromatin interaction networks.
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 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 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.
integrating epigenomic data and 3d genomic structure with a new measure of chromatin assortativity
Chromatin assortativity is a way 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.