ArticleScientific reports2017
Chromatin interaction networks revealed unique connectivity patterns of broad H3K4me3 domains and super enhancers in 3D chromatin.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 55 citations in OpenAlex.
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- KDM4C inhibition blocks tumor growth in basal breast cancer by promoting cathepsin L-mediated histone H3 cleavage.Nature genetics · 2025Article
- Node features of chromosome structure networks and their connections to genome annotation.Computational and structural biotechnology journal · 2024Article
- Decoding the epigenetics and chromatin loop dynamics of androgen receptor-mediated transcription.Nature communications · 2024Article
- Dynamic and distinct histone modifications facilitate human trophoblast lineage differentiation.Scientific reports · 2024Article
- Esearch3D: propagating gene expression in chromatin networks to illuminate active enhancers.Nucleic acids research · 2023Article
- Expanded Potential Stem Cells from Human Embryos Have an Open Chromatin Configuration with Enhanced Trophoblast Differentiation Ability.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Retinoblastoma-Binding Protein 5 Regulates H3K4 Methylation Modification to Inhibit the Proliferation of Melanoma Cells by Inactivating the Wnt/Journal of oncology · 2023Article
- High-resolution genome topology of human retina uncovers super enhancer-promoter interactions at tissue-specific and multifactorial disease loci.Nature communications · 2022Article
- Prediction of gene co-expression from chromatin contacts with graph attention network.Bioinformatics (Oxford, England) · 2022Article
- Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers.Genome research · 2022Article
- Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes.Genome research · 2022Article
- Histone H3K4me3 breadth in hypoxia reveals endometrial core functions and stress adaptation linked to endometriosis.iScience · 2022Article
- Chromatin Hubs: A biological and computational outlook.Computational and structural biotechnology journal · 2022Review
- The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes.Clinical epigenetics · 2021Review
- Transcriptionally Active Chromatin-Lessons Learned from the Chicken Erythrocyte Chromatin Fractionation.Cells · 2021Review
- Integrative analysis of liver-specific non-coding regulatory SNPs associated with the risk of coronary artery disease.American journal of human genetics · 2021Article
- Chromatin Network Analyses: Towards Structure-Function Relationships in Epigenomics.Frontiers in bioinformatics · 2021Article
- Chromatin network markers of leukemia.Bioinformatics (Oxford, England) · 2020Article
- Three-dimensional genome: developmental technologies and applications in precision medicine.Journal of human genetics · 2020Article
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
Broad domain promoters and super enhancers are regulatory elements that govern cell-specific functions and harbor disease-associated sequence variants. These elements are characterized by distinct epigenomic profiles, such as expanded deposition of histone marks H3K27ac for super enhancers and H3K4me3 for broad domains, however little is known about how they interact with each other and the rest of the genome in three-dimensional chromatin space. Using network theory methods, we studied chromatin interactions between broad domains and super enhancers in three ENCODE cell lines (K562, MCF7, GM12878) obtained via ChIA-PET, Hi-C, and Hi-CHIP assays. In these networks, broad domains and super enhancers interact more frequently with each other compared to their typical counterparts. Network measures and graphlets revealed distinct connectivity patterns associated with these regulatory elements that are robust across cell types and alternative assays. Machine learning models showed that these connectivity patterns could effectively discriminate broad domains from typical promoters and super enhancers from typical enhancers. Finally, targets of broad domains in these networks were enriched in disease-causing SNPs of cognate cell types. Taken together these results suggest a robust and unique organization of the chromatin around broad domains and super enhancers: loci critical for pathologies and cell-specific functions.
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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.