enhancerpromoter

In molecular biology, enhancers are DNA elements that increase transcription, while promoters are DNA elements where transcription by RNA polymerase II begins. The term enhancer-promoter describes the functional interaction between these regulatory elements, or DNA sequences that combine both activities.

Enhancers can act at a distance, upstream or downstream of the promoter, and in various orientations. Their effect depends on bound transcription factors, coactivators, and the local chromatin context that permits looping to the promoter.

Promoters contain core elements that recruit RNA polymerase II and general transcription factors to initiate transcription. Enhancers influence promoter activity by increasing initiation frequency, altering chromatin accessibility, and stabilizing transcription complexes via mediator and other coactivators.

Physical contact between enhancer-bound complexes and promoters is often mediated by chromatin looping and higher-order genome organization, including topologically associating domains. Insulators and architectural proteins can constrain or direct these interactions.

Technologies such as ChIP-seq, ATAC-seq, Hi-C, and CRISPR-based perturbations (deletions, repression, or activation) are used to map and test enhancer-promoter interactions. Some sequences exhibit dual promoter and enhancer activity, and many genes rely on multiple enhancers, including shadow and super-enhancers.

Understanding enhancer-promoter communication informs gene regulation, development, and disease, and supports applications in synthetic biology and gene therapy by enabling rational design of regulatory elements.