enhancer
Definition
An enhancer is a regulatory DNA sequence, typically 50-1500 base pairs long, that increases transcription of target genes regardless of its orientation or distance from the promoter. Enhancers function by binding transcription factors and co-activators, forming chromatin loops that bring regulatory machinery into proximity with gene promoters, sometimes located hundreds of kilobases away. They are critical for cell-type-specific gene expression, developmental processes, and responses to environmental signals. Enhancers can be identified through epigenetic marks like H3K27ac and H3K4me1, open chromatin regions detected by ATAC-seq or DNase-seq, and transcription factor binding patterns from ChIP-seq data. Dysregulation of enhancer activity is implicated in various diseases, including cancer and developmental disorders, making them important therapeutic targets.
Visualize enhancer in Nodes Bio
Researchers can visualize enhancer-gene regulatory networks by connecting enhancers to their target genes, transcription factors, and associated chromatin modifiers. Network analysis in Nodes Bio enables identification of master regulatory enhancers (super-enhancers), visualization of tissue-specific enhancer landscapes, and mapping of disease-associated variants in enhancer regions to affected genes and pathways. This facilitates understanding of complex gene regulatory hierarchies and identification of potential therapeutic intervention points.
Visualization Ideas:
- Enhancer-gene interaction networks showing long-range chromatin contacts and target gene regulation
- Transcription factor binding networks at enhancer regions with tissue-specific activity patterns
- Disease variant-enhancer-gene pathways linking non-coding mutations to affected biological processes
Example Use Case
A cancer genomics team investigating acute myeloid leukemia identifies recurrent mutations in non-coding regions through whole-genome sequencing. By integrating H3K27ac ChIP-seq data, Hi-C chromatin interaction maps, and RNA-seq expression profiles, they discover that mutations disrupt a super-enhancer controlling MYC oncogene expression. Using network visualization, they map the enhancer's connections to multiple transcription factors including RUNX1 and GATA2, revealing a regulatory circuit that maintains leukemic cell identity. This network analysis guides development of targeted epigenetic therapies to disrupt the enhancer-MYC axis.