ArticleProceedings of the National Academy of Sciences of the United States of America2017
Network analysis identifies chromosome intermingling regions as regulatory hotspots for transcription.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Image2Reg: Linking chromatin images to gene regulation using genetic and chemical perturbation screens.Cell systems · 2025Article
- Engineering aortic valves via transdifferentiating fibroblasts into valvular endothelial cells without using viruses or iPS cells.Bioactive materials · 2025Article
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- Remodeling of cytoskeleton, chromatin, and gene expression during mechanical rejuvenation of aged human dermal fibroblasts.Molecular biology of the cell · 2025Article
- The effect of trisomic chromosomes on spatial genome organization and global transcription in embryonic stem cells.Cell proliferation · 2024Article
- Transcriptional changes are tightly coupled to chromatin reorganization during cellular aging.Aging cell · 2024Article
- Adhesome Receptor Clustering is Accompanied by the Colocalization of the Associated Genes in the Cell Nucleus.bioRxiv : the preprint server for biology · 2023Article
- Mesoscale, long-time mixing of chromosomes and its connection to polymer dynamics.PLoS computational biology · 2023Article
- Integrative chromatin domain annotation through graph embedding of Hi-C data.Bioinformatics (Oxford, England) · 2023Article
- Long-distance association of topological boundaries through nuclear condensates.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Article
- Chromatin Hubs: A biological and computational outlook.Computational and structural biotechnology journal · 2022Review
- Cytogenomic Characterization of Giant Ring or Rod Marker Chromosome in Four Cases of Well-Differentiated and Dedifferentiated Liposarcoma.Case reports in genetics · 2022Article
- Effects of forces on chromatin.APL bioengineering · 2021Review
- Reciprocal regulation of cellular mechanics and metabolism.Nature metabolism · 2021Review
- Rapid nucleus-scale reorganization of chromatin in neurons enables transcriptional adaptation for memory consolidation.PloS one · 2021Article
- Non-Canonical Functions of the Gamma-Tubulin Meshwork in the Regulation of the Nuclear Architecture.Cancers · 2020Review
- Association between fetal sex and maternal plasma microRNA responses to prenatal alcohol exposure: evidence from a birth outcome-stratified cohort.Biology of sex differences · 2020Article
- Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platform.GigaScience · 2020Article
- Predicting cell lineages using autoencoders and optimal transport.PLoS computational biology · 2020Article
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5 authors.
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Abstract
The 3D structure of the genome plays a key role in regulatory control of the cell. Experimental methods such as high-throughput chromosome conformation capture (Hi-C) have been developed to probe the 3D structure of the genome. However, it remains a challenge to deduce from these data chromosome regions that are colocalized and coregulated. Here, we present an integrative approach that leverages 1D functional genomic features (e.g., epigenetic marks) with 3D interactions from Hi-C data to identify functional interchromosomal interactions. We construct a weighted network with 250-kb genomic regions as nodes and Hi-C interactions as edges, where the edge weights are given by the correlation between 1D genomic features. Individual interacting clusters are determined using weighted correlation clustering on the network. We show that intermingling regions generally fall into either active or inactive clusters based on the enrichment for RNA polymerase II (RNAPII) and H3K9me3, respectively. We show that active clusters are hotspots for transcription factor binding sites. We also validate our predictions experimentally by 3D fluorescence in situ hybridization (FISH) experiments and show that active RNAPII is enriched in predicted active clusters. Our method provides a general quantitative framework that couples 1D genomic features with 3D interactions from Hi-C to probe the guiding principles that link the spatial organization of the genome with regulatory control.
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