ArticleNature genetics2024
Enhancer-promoter interactions become more instructive in the transition from cell-fate specification to tissue differentiation.
Article in Nature genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers, 1 of them a synthesis that pooled it.
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Who cites it
46 citing papers in PubMed, 1 synthesis or guideline pooled it, 71 citations in OpenAlex.
- Cross-platform Hi-C meta-analysis identifies functional insulators that actively block enhancer-promoter interactions.Nature communications · 2026Pooled it
- Foundation model reveals the shared organization of transcription and topologically associating domains.Cell systems · 2026Article
- Dynamic control of cell state transitions during tissue morphogenesis.The EMBO journal · 2026Review
- 3D chromatin organisation contributes to the regulatory logic in differentiating lymphatic endothelium.EMBO reports · 2026Article
- The cardiac 4D nucleome: nuclear and chromatin dynamics across development, disease and ageing.Nature reviews. Cardiology · 2026Review
- Sodium Butyrate-Assisted Induction of Posterior Pre-Neural Progenitors from Pluripotent Stem Cells.International journal of molecular sciences · 2026Article
- Promoter reinforcement supports transcriptional resilience in drug-resistant cancer.Nature structural & molecular biology · 2026Article
- Enhancers integrate microenvironmental signals in muscle stem cells during regeneration in health, disease, and aging.Skeletal muscle · 2026Review
- UniversalEPI: robust prediction of cell type-specific and differential chromatin interactions from DNA sequence and chromatin accessibility.Nucleic acids research · 2026Article
- Hi-Compass: a depth-aware deep learning framework for predicting cell-type-specific 3D genome organization from single-cell to spatial resolution.Nature communications · 2026Article
- Boolean logic links chromatin accessibility states to gene expression variability across cell types.Nucleic acids research · 2026Article
- Identification of cis-regulatory elements provides insights into tissue-specific gene regulation in the sheep genome.Nature communications · 2026Article
- From Natural Discovery to AI-Guided Design: A Curated Collection of Compact Enhancers for Crop Engineering.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Hypoxia Preserves Chromatin Integrity and Delays Cellular Senescence through Epigenetic Regulation.Biomolecules & therapeutics · 2026Review
- Loop Extrusion Accelerates Long-Range Enhancer-Promoter Searches in Living Embryos.bioRxiv : the preprint server for biology · 2026Article
- Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding.Nature genetics · 2026Article
- LDB1 regulates gene expression and chromatin structure in pluripotency and lineage differentiation.Nucleic acids research · 2026Article
- Enhancer-dependent gene regulation in space, time, and malignancies.International journal of cancer · 2026Review
- Distal enhancers regulate mammalian early embryonic lineage differentiation through long-range interactions.Nucleic acids research · 2026Article
- Enhancer Trajectories in Lineage Commitment: Regulatory Logic of States and Cooperation.Biomolecules · 2026Review
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 4 countries.
Funding
Abstract
To regulate expression, enhancers must come in proximity to their target gene. However, the relationship between the timing of enhancer-promoter (E-P) proximity and activity remains unclear, with examples of uncoupled, anticorrelated and correlated interactions. To assess this, we selected 600 characterized enhancers or promoters with tissue-specific activity in Drosophila embryos and performed Capture-C in FACS-purified myogenic or neurogenic cells during specification and tissue differentiation. This enabled direct comparison between E-P proximity and activity transitioning from OFF-to-ON and ON-to-OFF states across developmental conditions. This showed remarkably similar E-P topologies between specified muscle and neuronal cells, which are uncoupled from activity. During tissue differentiation, many new distal interactions emerge where changes in E-P proximity reflect changes in activity. The mode of E-P regulation therefore appears to change as embryogenesis proceeds, from largely permissive topologies during cell-fate specification to more instructive regulation during terminal tissue differentiation, when E-P proximity is coupled to activation.
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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.