ArticleNucleic acids research2021
A model of active transcription hubs that unifies the roles of active promoters and enhancers.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed.
- Article
- Transcription condensates are promoter hubs that enhance transcriptional bursts.bioRxiv : the preprint server for biology · 2026Article
- Epigenetic mechanism of HDAC5 in sepsis-induced acute intestinal injury through KLF4-mediated intestinal epithelial cell ferroptosis.Inflammation research : official journal of the European Histamine Research Society ... [et al.] · 2026Article
- Connecting multiway enhancer-promoter interactions to changes in gene expression in cancer.bioRxiv : the preprint server for biology · 2026Article
- High-resolution map of chromatin accessibility - insights into the focused binding of a large number of transcription factors.Epigenetics & chromatin · 2026Article
- Epigenome and interactome profiling uncovers principles of distal regulation in the barley genome.Cell genomics · 2026Article
- Comprehensive Mapping of Functional Enhancers in Chinese Hamster Ovary Cells.Biotechnology and bioengineering · 2026Article
- ChromTag: an interactive R-shiny platform for analysis and visualization of CUT&Tag and ChIP-seq peak profiling data.Frontiers in bioinformatics · 2026Article
- Discovering the complete enhancer map of human herpesviruses using a natural language processing model.Nature communications · 2025Article
- Disruption of histone acetylation homeostasis reveals multilayered chromatin regulation for transcriptional resiliency.Epigenetics & chromatin · 2025Article
- Identification of IL-34 and Slc7al as potential key regulators in MASLD progression through epigenomic profiling.Epigenomics · 2025Article
- FOXM1 expression reverts aging chromatin profiles through repression of the senescence-associated pioneer factor AP-1.Nature communications · 2025Article
- Genome-wide CRISPR screening identifies PHF8 as an effective therapeutic target for KRAS- or BRAF-mutant colorectal cancers.Journal of experimental & clinical cancer research : CR · 2025Article
- Decoding the epigenetics and chromatin loop dynamics of androgen receptor-mediated transcription.Nature communications · 2024Article
- Article
- How Transcription Factor Clusters Shape the Transcriptional Landscape.Biomolecules · 2024Review
- Transcription Factor Condensates Mediate Clustering ofbioRxiv : the preprint server for biology · 2024Article
- Multiscale Bayesian simulations reveal functional chromatin condensation of gene loci.PNAS nexus · 2024Article
- Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns.BMC genomics · 2024Article
- The potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer.Nature structural & molecular biology · 2024Article
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Abstract
An essential questions of gene regulation is how large number of enhancers and promoters organize into gene regulatory loops. Using transcription-factor binding enrichment as an indicator of enhancer strength, we identified a portion of H3K27ac peaks as potentially strong enhancers and found a universal pattern of promoter and enhancer distribution: At actively transcribed regions of length of ∼200-300 kb, the numbers of active promoters and enhancers are inversely related. Enhancer clusters are associated with isolated active promoters, regardless of the gene's cell-type specificity. As the number of nearby active promoters increases, the number of enhancers decreases. At regions where multiple active genes are closely located, there are few distant enhancers. With Hi-C analysis, we demonstrate that the interactions among the regulatory elements (active promoters and enhancers) occur predominantly in clusters and multiway among linearly close elements and the distance between adjacent elements shows a preference of ∼30 kb. We propose a simple rule of spatial organization of active promoters and enhancers: Gene transcriptions and regulations mainly occur at local active transcription hubs contributed dynamically by multiple elements from linearly close enhancers and/or active promoters. The hub model can be represented with a flower-shaped structure and implies an enhancer-like role of active promoters.
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