ArticleNature genetics2023
RNA polymerase II dynamics shape enhancer-promoter interactions.
Article in Nature genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed.
- Transcription and Three-Dimensional Genome Organization: Cause, Consequence, or Coordination?BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
- Nuclear exosome targeting complexes modulate cohesin binding and enhancer-promoter interactions in 3D.Nature communications · 2026Article
- Promoter strength and position govern promoter competition through transcript-dependent insulation.Nature genetics · 2026Article
- Exhausted CD8Nature immunology · 2026Article
- RNAPII and DNA supercoiling regulate cohesin engagement in neurons.Nucleic acids research · 2026Article
- A comparative analysis of promoter-proximal pausing reveals kinetic and distributional dimensions of variation.bioRxiv : the preprint server for biology · 2026Article
- The Semantics and Mechanisms of Enhancers and Promoters: "What Is True forAnnual review of biochemistry · 2026Review
- Transcription condensates are promoter hubs that enhance transcriptional bursts.bioRxiv : the preprint server for biology · 2026Article
- RNA-m5C regulatory atlas of human fetal tissues uncover the activities of Nsun2/Jarid2/Alyref axis.Journal of advanced research · 2026Article
- Graded versus ON/OFF control in quantitative gene expression and epigenetic memory.The EMBO journal · 2026Review
- Enhancer hubs govern chromatin topology and Th17 cell identity.bioRxiv : the preprint server for biology · 2026Article
- A functional overlap between actively transcribed genes and chromatin insulator elements.The EMBO journal · 2026Article
- Three-dimensional genome reorganization foreshadows zygotic genome activation in Drosophila.Nature genetics · 2026Article
- FACT depletion demonstrates a role for nucleosome organization in TAD formation.Molecular systems biology · 2026Article
- 3D genome folding in epigenetic regulation and cellular memory.Trends in cell biology · 2026Review
- Transcriptional pause release at enhancers mediates cell identity.NAR cancer · 2025Review
- Dynamics of microcompartment formation at the mitosis-to-G1 transition.Nature structural & molecular biology · 2025Article
- TOP2B modulates DNA supercoiling and chromatin contacts during transcriptional induction.Science advances · 2025Article
- Structural variants in the 3D genome as drivers of disease.Nature reviews. Genetics · 2025Review
- Deciphering histone mark-specific fine-scale chromatin organization at high resolution with Micro-C-ChIP.Nature communications · 2025Article
11 more citing papers are in PubMed but not listed here.
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11 authors.
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Abstract
How enhancers control target gene expression over long genomic distances remains an important unsolved problem. Here we investigated enhancer-promoter communication by integrating data from nucleosome-resolution genomic contact maps, nascent transcription and perturbations affecting either RNA polymerase II (Pol II) dynamics or the activity of thousands of candidate enhancers. Integration of new Micro-C experiments with published CRISPRi data demonstrated that enhancers spend more time in close proximity to their target promoters in functional enhancer-promoter pairs compared to nonfunctional pairs, which can be attributed in part to factors unrelated to genomic position. Manipulation of the transcription cycle demonstrated a key role for Pol II in enhancer-promoter interactions. Notably, promoter-proximal paused Pol II itself partially stabilized interactions. We propose an updated model in which elements of transcriptional dynamics shape the duration or frequency of interactions to facilitate enhancer-promoter communication.
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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.