ArticlePLoS genetics2024
Transcription decouples estrogen-dependent changes in enhancer-promoter contact frequencies and spatial proximity.
Article in PLoS genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Increased chromatin accessibility following 1α,25-dihydroxyvitamin DToxicology and applied pharmacology · 2026Article
- Live-cell imaging of enhancer-promoter dynamics reveals transient contact-driven gene activation.bioRxiv : the preprint server for biology · 2026Article
- Review
- Connecting multiway enhancer-promoter interactions to changes in gene expression in cancer.bioRxiv : the preprint server for biology · 2026Article
- Article
- A methodology to reduce the localization error in multi-loci microscopy provides new insights into enhancer biology.PLoS computational biology · 2025Article
- Is enhancer-driven gene regulation all wrapped up?Nature reviews. Genetics · 2025Article
- Molecular mechanisms altering cell identity in cancer.Oncogene · 2025Review
- Regulation of RNA polymerase II transcription through re-initiation and bursting.Molecular cell · 2025Review
- Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements.Genome research · 2025Article
- Liquid condensates: a new barrier to loop extrusion?Cellular and molecular life sciences : CMLS · 2025Review
- Epigenetics in Neurodegenerative Diseases.Sub-cellular biochemistry · 2025Review
- Transcription-coupled changes in genomic region proximities during transcriptional bursting.Science advances · 2024Article
- Enhancer selectivity in space and time: from enhancer-promoter interactions to promoter activation.Nature reviews. Molecular cell biology · 2024Review
- Cell type- and transcription-independent spatial proximity between enhancers and promoters.Molecular biology of the cell · 2024Article
- Enhancer-promoter interactions become more instructive in the transition from cell-fate specification to tissue differentiation.Nature genetics · 2024Article
- Image-based 3D genomics through chromatin tracing.Nature reviews. Methods primers · 2024Article
- Noncoding function of super enhancer derived mRNA in modulating neighboring gene expression and TAD interaction.bioRxiv : the preprint server for biology · 2023Article
- Ultra-long-range interactions between active regulatory elements.Genome research · 2023Article
- Integrative approaches to study enhancer-promoter communication.Current opinion in genetics & development · 2023Review
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
How enhancers regulate their target genes in the context of 3D chromatin organization is extensively studied and models which do not require direct enhancer-promoter contact have recently emerged. Here, we use the activation of estrogen receptor-dependent enhancers in a breast cancer cell line to study enhancer-promoter communication at two loci. This allows high temporal resolution tracking of molecular events from hormone stimulation to efficient gene activation. We examine how both enhancer-promoter spatial proximity assayed by DNA fluorescence in situ hybridization, and contact frequencies resulting from chromatin in situ fragmentation and proximity ligation, change dynamically during enhancer-driven gene activation. These orthogonal methods produce seemingly paradoxical results: upon enhancer activation enhancer-promoter contact frequencies increase while spatial proximity decreases. We explore this apparent discrepancy using different estrogen receptor ligands and transcription inhibitors. Our data demonstrate that enhancer-promoter contact frequencies are transcription independent whereas altered enhancer-promoter proximity depends on transcription. Our results emphasize that the relationship between contact frequencies and physical distance in the nucleus, especially over short genomic distances, is not always a simple one.
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