ArticleNature structural & molecular biology2025
CTCF depletion decouples enhancer-mediated gene activation from chromatin hub formation.
Article in Nature structural & molecular biology, 2025. 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.
- Mechanisms and functional implications of long-range enhancer-dependent gene regulation.Nature genetics · 2026Review
- Nonlinearities and Switch-Like Behavior in Gene Expression: From Genetics to Biochemistry and Back.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Review
- Origins and consequences of oncogenic 3D chromatin remodelling.Nature reviews. Cancer · 2026Review
- Senescent cells cluster CTCF on nuclear speckles to instruct an alternative splicing program.Nature aging · 2026Article
- Transcription factors as drivers of 3D enhancer-promoter interactions.Current opinion in structural biology · 2026Review
- Cis-regulation ofGenes & diseases · 2026Article
- Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation.Nature communications · 2026Article
- Cohesin bridging as a physical principle of enhancer-promoter communication.bioRxiv : the preprint server for biology · 2026Article
- Cohesin extrudes chromatin loop unidirectionally through two modes of mechanisms in human cells.bioRxiv : the preprint server for biology · 2026Article
- Acute NIPBL depletion reveals in vivo dynamics of loop extrusion and its role in transcription activation.Nature genetics · 2026Article
- Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs.Nature structural & molecular biology · 2026Article
- A functional overlap between actively transcribed genes and chromatin insulator elements.The EMBO journal · 2026Article
- Phase separation of β-catenin assembles active loop hubs in colorectal cancer.Genome biology · 2026Article
- SMCHD1 loss re-wires MYOD1 enhancer nexuses and chromatin accessibility landscapes in muscle cells.bioRxiv : the preprint server for biology · 2026Article
- FACT depletion demonstrates a role for nucleosome organization in TAD formation.Molecular systems biology · 2026Article
- Single-cell RNA sequencing pseudobulk analysis and machine learning identify candidate biomarkers for ischemic cardiomyopathy.Frontiers in cardiovascular medicine · 2026Article
- Spatial Chromatin Organization Across the Cell Cycle: Insights from Auxin-Inducible Protein Depletion.Cells · 2025Review
- Nanoscale dynamics of enhancer-promoter interactions during exit from pluripotency.Nucleic acids research · 2025Article
- 3D Genome Engineering: Current Advances and Therapeutic Opportunities in Human Diseases.Research (Washington, D.C.) · 2025Review
- Multiscale information processing in the immune system.Frontiers in immunology · 2025Review
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Enhancers and promoters interact in three-dimensional (3D) chromatin structures to regulate gene expression. Here we characterize the mechanisms that drive the formation and function of these structures in a lymphoid-to-myeloid transdifferentiation system. Based on analyses at base pair resolution, we demonstrate a close correlation between binding of regulatory proteins, formation of chromatin interactions and gene expression. Multi-way interaction analyses and computational modeling show that tissue-specific gene loci are organized into chromatin hubs, characterized by cooperative interactions between multiple enhancers, promoters and CTCF-binding sites. While depletion of CTCF strongly impairs the formation of these chromatin hubs, the effects of CTCF depletion on gene expression are modest and can be explained by rewired enhancer-promoter interactions. These findings demonstrate a role for enhancer-promoter interactions in gene regulation that is independent of cooperative interactions in chromatin hubs. Together, these results contribute to our understanding of the structure-function relationship of the genome during cellular differentiation.
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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.