Enhancers

Enhancers are cis-regulatory DNA elements that increase transcription of a gene. They can be located far from the promoter, upstream or downstream, and can function in either orientation and at variable distances.

Enhancers function by binding transcription factors that recruit coactivators and the transcriptional machinery to the promoter, often via chromatin looping bringing the enhancer in contact with the promoter. They can act in a tissue-specific or developmental stage-specific manner, contributing to precise spatial and temporal gene expression.

Basal histone marks: active enhancers show H3K27ac and H3K4me1 (poised have H3K4me1 only). They are DNase I hypersensitive and often enriched for transcription factor binding.

Promoter vs enhancer: Promoters are proximal to transcription start site; enhancers can work at distance and are orientation-independent, and can influence multiple promoters.

Discovery and study: genome-wide mapping uses ChIP-seq for histone marks and TFs, ATAC-seq/DNase-seq for accessibility, Hi-C for interactions; functional testing uses reporter assays and CRISPR-based perturbations; eRNAs are non-coding RNAs transcribed from some active enhancers.

Clinical and evolutionary relevance: variants in enhancers can alter gene expression and contribute to developmental disorders or disease susceptibility; enhancers can evolve between species; shadow enhancers provide redundant regulation for robustness.

Super-enhancers are clusters of active enhancers with high TF occupancy and strong regulatory activity, implicated in cell identity and disease.