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dc.contributor.authorPancaldi, Vera
dc.contributor.authorCarrillo-de-Santa-Pau, Enrique
dc.contributor.authorJavierre, Biola Maria
dc.contributor.authorJuan, David
dc.contributor.authorFraser, Peter
dc.contributor.authorSpivakov, Mikhail
dc.contributor.authorValencia, Alfonso 
dc.contributor.authorRico, Daniel
dc.identifier.citationGenome Biol. 2016;17(1):152es_ES
dc.description.abstractBACKGROUND: 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 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. CONCLUSIONS: 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.es_ES
dc.description.sponsorshipThe research leading to these results has received funding from the European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement number 282510 (BLUEPRINT) and in the framework of the Platform for Biomolecular and Bioinformatics Resource PT 13/0001/0030 of the ISCIII, which is funded through the European Regional Development Fund (ERDF). This work was also supported by grants from the Biotechnology and Biological Sciences Research Council BBS/E/B/000C0404 and the Medical Research Council MR/L007150/1 to PF. VP acknowledges a FEBS Long-term fellowship.es_ES
dc.relation.isversionofPublisher's versiones_ES
dc.subject3D genomees_ES
dc.subjectChromatin Interaction Networkes_ES
dc.subjectEmbryonic stem cellses_ES
dc.subjectPromoter Capture Hi-Ces_ES
dc.subjectRNA polymerasees_ES
dc.subject.meshAnimals es_ES
dc.subject.meshChromatin es_ES
dc.subject.meshChromatin Assembly and Disassembly es_ES
dc.subject.meshComputational Biology es_ES
dc.subject.meshEmbryonic Stem Cells es_ES
dc.subject.meshGenome es_ES
dc.subject.meshHistone Code es_ES
dc.subject.meshHistones es_ES
dc.subject.meshHumans es_ES
dc.subject.meshMice es_ES
dc.subject.meshPromoter Regions, Genetices_ES
dc.subject.meshRegulatory Sequences, Nucleic Acides_ES
dc.subject.meshEpigenomics es_ES
dc.titleIntegrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativityes_ES
dc.rights.licenseAtribución-NoComercial-CompartirIgual 4.0 Internacional*
dc.contributor.funderEuropean Union (EU)es_ES
dc.contributor.funderBiotechnology and Biological Sciences Research Council (BBSRC)es_ES
dc.contributor.funderMedical Research Council UK (MRC)es_ES
dc.contributor.funderInstituto de Salud Carlos III- ISCIIIes_ES
dc.contributor.funderEuropean Regional Development Fund (ERDF/FEDER)es_ES
dc.identifier.journalGenome biologyes_ES
dc.repisalud.orgCNIOCNIO::Grupos de investigación::Antiguos CNIOes_ES

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