ArticleMolecular cell2019
Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods.
Article in Molecular cell, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed, 114 citations in OpenAlex.
- Single-cell 3D genome imaging shows super-enhancer hubs are rare, nonspecific, and neither necessary nor sufficient for transcriptional bursting.Cell genomics · 2026Article
- Entanglement dilution and high fractal dimension mediated by loop extrusion revealed in simulations of active polymer melts.bioRxiv : the preprint server for biology · 2026Article
- Conserved enhancer association of piRNAs and the implication in germ cell fate surveillance.Genome biology · 2026Article
- Integrative characterization of tissue-specific 3D genome organization and associated transcriptional regulation in pig liver and muscle.Functional & integrative genomics · 2026Article
- Postmitotic transcription and 3D regulation show locus-specific and differentiation-specific sensitivity to cohesin depletion.Nature genetics · 2026Article
- AP-1 promotes oncogenic transcription in lung cancer cells by bridging promoter-enhancer interactions.Cancer gene therapy · 2026Article
- Allele-specific chromatin dynamics underpin heterosis and shoot development in hybrid poplar 'Nanlin895'.Plant molecular biology · 2026Article
- Antecedent enhancer activity predicts future susceptibility to seizures in mice.Nature communications · 2026Article
- Rewiring of SINE-MIR enhancer topology and Esrrb modulation in expanded and naive pluripotency.Genome biology · 2025Article
- A cardiac transcriptional enhancer is repurposed during regeneration to activate an anti-proliferative program.Development (Cambridge, England) · 2025Article
- Long G4-rich enhancers target promoters via a G4 DNA-based mechanism.Nucleic acids research · 2025Article
- CatLearning: highly accurate gene expression prediction from histone mark.Briefings in bioinformatics · 2024Article
- Activity-driven chromatin organization during interphase: Compaction, segregation, and entanglement suppression.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Super-enhancer interactomes from single cells link clustering and transcription.bioRxiv : the preprint server for biology · 2024Article
- Enhancer-promoter interactions can form independently of genomic distance and be functional across TAD boundaries.Nucleic acids research · 2024Article
- Activity-driven chromatin organization during interphase: compaction, segregation, and entanglement suppression.bioRxiv : the preprint server for biology · 2024Article
- Transcriptional and epigenetic dysregulation impairs generation of proliferative neural stem and progenitor cells during brain aging.Nature aging · 2024Article
- 3D Enhancer-promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages.Nature structural & molecular biology · 2024Article
- The chromatin signatures of enhancers and their dynamic regulation.Nucleus (Austin, Tex.) · 2023Review
- Methylation-directed regulatory networks determine enhancing and silencing of mutation disease driver genes and explain inter-patient expression variation.Genome biology · 2023Article
Corrections and comments
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
Abstract
Metazoan chromosomes are sequentially partitioned into topologically associating domains (TADs) and then into smaller sub-domains. One class of sub-domains, insulated neighborhoods, are proposed to spatially sequester and insulate the enclosed genes through self-association and chromatin looping. However, it has not been determined functionally whether promoter-enhancer interactions and gene regulation are broadly restricted to within these loops. Here, we employed published datasets from murine embryonic stem cells (mESCs) to identify insulated neighborhoods that confine promoter-enhancer interactions and demarcate gene regulatory regions. To directly address the functionality of these regions, we depleted estrogen-related receptor β (Esrrb), which binds the Mediator co-activator complex, to impair enhancers of genes within 222 insulated neighborhoods without causing mESC differentiation. Esrrb depletion reduces Mediator binding, promoter-enhancer looping, and expression of both nascent RNA and mRNA within the insulated neighborhoods without significantly affecting the flanking genes. Our data indicate that insulated neighborhoods represent functional regulons in mammalian genomes.
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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.