Background: The field of 3D chromatin interaction mapping is changing our point of view on the genome, paving the way for new insights into URLanization. Network analysis is a natural and powerful way of modelling chromatin interactions. Assortativity is a network property that has been widely used in the social sciences to measure the probability of nodes with similar values of a specific feature to interact preferentially . We propose a new approach, using Chromatin feature Assortativity (ChAs), to integrate the epigenomic landscape of a specific cell type with its chromatin interaction network . Results: We use high-resolution Promoter Capture Hi-C and Hi-Cap data as well as ChIA-PET data from  embryonic stem cells to generate promoter-centered interaction networks. We calculate the presence of a collection of 78 chromatin features in the chromatin fragments constituting the nodes of the network. Based on the ChAs of these epigenomic features calculated in 4 different interaction networks , we find Polycomb Group proteins and associated histone marks to play a prominent role. Remarkably, in promoter-centered networks, we observe higher ChAs of the actively elongating form of RNA Polymerase 2  compared to inactive forms  in interactions between promoters and other elements. Conclusions: Contacts amongst promoters and between promoters and other elements have different characteristic epigenomic features. Using ChAs we identify a possible role of the elongating form of RNAPII in enhancer activity . Our approach facilitates the study of multiple genome-wide epigenomic profiles, considering network topology and allowing for the comparison of any number 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 to 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-centred 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 to 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.
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Background: The field of 3D chromatin interaction mapping is changing our point of view on the genome, paving the way for new insights into URLanization.
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natural and
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modelling
modeling
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that has been widely used in the
used in
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measure the probability of nodes with similar values of a specific feature to interact preferentially
identify factors affecting how people establish social ties
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Chromatin feature Assortativity (ChAs),
chromatin assortativity
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. Results:
and thus investigate which proteins or chromatin marks mediate genomic contacts.
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mouse
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generate
investigate
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interaction networks. We
chromatin interaction networks and
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a collection of 78 chromatin
specific epigenomic
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Based on the ChAs of these epigenomic features calculated in 4 different interaction networks , we find
We estimate the association of these features to the topology of four chromatin interaction networks and identify features localized in connected areas of the network.
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to play a prominent role. Remarkably, in promoter-centered networks, we observe higher ChAs
are the features with the highest chromatin assortativity in promoter-centred networks. We then ask which features distinguish contacts amongst promoters from contacts between promoters and other genomic elements. We observe higher chromatin assortativity
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(RNAPII)
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only
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Conclusions: Contacts amongst promoters
Contacts among promoters,
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Using ChAs we
We
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of
for
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enhancer activity
mediating interactions among promoters, enhancers and transcribed gene bodies
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for the comparison of any number
the comparison