ArticleNucleic acids research2024
Enhancer-promoter interactions can form independently of genomic distance and be functional across TAD boundaries.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 29 citations in OpenAlex.
- ELF5-Mediated Enhancer-Promoter Interaction Regulates LALBA Expression in Ovine Mammary Gland.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Transcription and Three-Dimensional Genome Organization: Cause, Consequence, or Coordination?BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
- Chromosomal inversions modulate 3D chromatin interactions and regulatory architecture inResearch square · 2026Article
- Allele-specific chromatin architecture shapes imprinted domains and coordinates a distal enhancer and antisense transcription at the mouse Mest-Copg2 domain.Nature communications · 2026Article
- Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer.Genome biology · 2026Article
- The cardiac 4D nucleome: nuclear and chromatin dynamics across development, disease and ageing.Nature reviews. Cardiology · 2026Review
- Genetic architecture of multiple myeloma: From somatic alterations to germline susceptibility and clinical implications.Translational oncology · 2026Review
- Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation.Nature communications · 2026Article
- Chromatin Remodeling in VSMC Phenotype Switching During Vascular Remodeling: From Mechanism to Therapeutic Potential.Biomolecules · 2026Review
- Configuring the Code: Enhancer-Promoter Arrangement and Transcriptional Regulation.Journal of molecular biology · 2026Review
- High-throughputbioRxiv : the preprint server for biology · 2025Article
- Allelic chromatin structure is a pervasive feature of imprinted domains and functions cooperatively with cis-acting long non-coding RNAs.bioRxiv : the preprint server for biology · 2025Article
- Comprehensive Single Molecule View of Transcriptional Dynamics in Development.bioRxiv : the preprint server for biology · 2025Article
- The inner nuclear membrane protein LEMD3 organizes the 3D chromatin architecture to maintain vascular smooth muscle cell identity.Nature communications · 2025Article
- Spatial-scERA: a method for reconstructing spatial single-cell enhancer activity in multicellular organisms.Nucleic acids research · 2025Article
- Bridging spatial and temporal scales of developmental gene regulation.Current opinion in genetics & development · 2025Review
- HoxBlinc: a key driver of chromatin dynamics in NUP98 fusion-driven leukemia.The Journal of clinical investigation · 2025Article
- Identification of druggable targets in acute kidney injury by proteome- and transcriptome-wide Mendelian randomization and bioinformatics analysis.Biology direct · 2025Article
- Article
- LDB1 establishes multi-enhancer networks to regulate gene expression.Molecular cell · 2025Article
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Authors and funding
7 authors at 1 institution in 2 countries.
Funding
Abstract
Topologically Associating Domains (TADs) have been suggested to facilitate and constrain enhancer-promoter interactions. However, the role of TAD boundaries in effectively restricting these interactions remains unclear. Here, we show that a significant proportion of enhancer-promoter interactions are established across TAD boundaries in Drosophila embryos, but that developmental genes are strikingly enriched in intra- but not inter-TAD interactions. We pursued this observation using the twist locus, a master regulator of mesoderm development, and systematically relocated one of its enhancers to various genomic locations. While this developmental gene can establish inter-TAD interactions with its enhancer, the functionality of these interactions remains limited, highlighting the existence of topological constraints. Furthermore, contrary to intra-TAD interactions, the formation of inter-TAD enhancer-promoter interactions is not solely driven by genomic distance, with distal interactions sometimes favored over proximal ones. These observations suggest that other general mechanisms must exist to establish and maintain specific enhancer-promoter interactions across large distances.
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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.