enhancer promoter interaction
Definition
Enhancer-promoter interactions are physical contacts between distal regulatory DNA elements (enhancers) and gene promoters that control transcriptional activity. These interactions occur through chromatin looping, bringing enhancers located thousands to millions of base pairs away into close spatial proximity with target gene promoters. Mediated by protein complexes including transcription factors, coactivators, and architectural proteins like CTCF and cohesin, these interactions are cell-type specific and dynamically regulated. Understanding enhancer-promoter interactions is crucial for deciphering gene regulation, as disruptions can lead to developmental disorders and diseases. Technologies like Hi-C, ChIA-PET, and Capture-C map these three-dimensional genome interactions, revealing how non-coding variants in enhancers can affect disease-associated genes.
Visualize enhancer promoter interaction in Nodes Bio
Researchers can visualize enhancer-promoter interaction networks where nodes represent genomic regions (enhancers and promoters) and edges represent validated physical interactions. By integrating ChIP-seq data for histone marks, transcription factor binding sites, and chromatin accessibility, users can map regulatory landscapes across different cell types or disease states, identifying key regulatory hubs and understanding how genetic variants in non-coding regions influence gene expression through long-range interactions.
Visualization Ideas:
- Bipartite network showing enhancers connected to their target gene promoters with edge weights representing interaction frequency
- Multi-layer network comparing enhancer-promoter interactions across different cell types or disease conditions
- Integrated regulatory network combining enhancer-promoter contacts with transcription factor binding and gene expression data
Example Use Case
A cancer genomics team investigating non-coding mutations in colorectal cancer identifies SNPs in putative enhancer regions through GWAS. Using Hi-C and H3K27ac ChIP-seq data, they map enhancer-promoter interactions to identify target genes affected by these variants. Network visualization reveals that a single enhancer contacts multiple oncogene promoters, and the disease-associated SNP disrupts binding of a key transcription factor. This analysis explains how a non-coding variant 500kb upstream drives overexpression of MYC, providing a mechanistic understanding of cancer predisposition.