ArticleGenome biology2016
Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 67 citations in OpenAlex.
- Article
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- mosna Reveals Different Types of Cellular Interactions Predictive of Response to Immunotherapies and Survival in Cancer.Molecular & cellular proteomics : MCP · 2026Article
- Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs.Nature structural & molecular biology · 2026Article
- Analysis of Chromatin Structure Using Network Approaches: A Step-by-Step Guide.Methods in molecular biology (Clifton, N.J.) · 2026Article
- H3K36 Methylation as a Guardian of Epigenome Integrity.Nature communications · 2025Article
- Global chromatin reorganization and regulation of genes with specific evolutionary ages during differentiation and cancer.Nucleic acids research · 2025Article
- Integration of chromosome conformation and gene expression networks reveals regulatory mechanisms in triple negative breast cancer.Frontiers in cell and developmental biology · 2025Article
- Node features of chromosome structure networks and their connections to genome annotation.Computational and structural biotechnology journal · 2024Article
- Global chromatin reorganization and regulation of genes with specific evolutionary ages during differentiation and cancer.bioRxiv : the preprint server for biology · 2024Article
- Targeting the chromatin structural changes of antitumor immunity.Journal of pharmaceutical analysis · 2024Review
- Computational methods for analysing multiscale 3D genome organization.Nature reviews. Genetics · 2024Review
- Interplay between epigenome and 3D chromatin structure.BMB reports · 2023Review
- 3D chromatin interactions involving Drosophila insulators are infrequent but preferential and arise before TADs and transcription.Nature communications · 2023Article
- Esearch3D: propagating gene expression in chromatin networks to illuminate active enhancers.Nucleic acids research · 2023Article
- Mapping Multi-factor-mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-related Genes.Genomics, proteomics & bioinformatics · 2023Article
- 3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells.Nucleic acids research · 2022Article
- DAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Article
- Mapping nucleosome and chromatin architectures: A survey of computational methods.Computational and structural biotechnology journal · 2022Review
- STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells.Nucleic acids research · 2021Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundNetwork 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.
resultsWe 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.
conclusionsContacts 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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.