Regulatory, noncoding DNA regions can have a variety of different functions, illustrated in Fig. 1 and variously classified as promoters, enhancers/silencers, super-enhancers, and insulators. Promoters are typically located within 1 to 2 kb of the transcriptional start site (TSS) of a gene. At a minimum, RNA-polymerase-II-dependent promoters contain binding sites for general transcription factors TBP and TFIIB, which form the core of the transcriptional complex. Within the promoter, transcription factor binding sites (TFBS) modulate gene expression by recruiting histone modifying enzymes and transcriptional coactivators or corepressors.

An enhancer/silencer is a short (50 to 1500 bp) region of DNA that can be bound by transcription factors to increase/decrease the likelihood that transcription of a particular gene will occur. Enhancers/ silencers can act both in cis (within a chromosome) and rarely in trans (between chromosomes), can be located up to 1 Mb away from the gene, and can be upstream or downstream from the TSS. Promoters physically interact with their associated enhancers or silencers via three-dimensional chromatin “looping,” facilitated by Mediator and Cohesin protein complexes (see Fig. 2). Genes may be regulated by several enhancers/silencers, and each enhancer/silencer may modulate expression of one or more genes. A super-enhancer is a cluster of physically and functionally associated enhancers that regulates genes critical for cell identity. Super-enhancers are marked by high levels of enhancer-associated histone modification and bind high levels of cell-type specific and lineage-defining transcription factors (known as “master” transcription factors).

By blocking the physical interactions between enhancers and promoters, insulators help to restrict the set of genes that can be modulated by an enhancer. Insulators are bound by cohesin and CTCF proteins and form boundaries between silenced and active genes. Clusters of insulators separate heterochromatin from euchromatin, and the segments of active chromatin bounded by these clusters are known as topological domains-genomic regions, within which regulation occurs.

Fig1. Functional chromatin domains and their characteristic histone modifications and protein-binding features

Fig2. Three-dimensional chromatin looping brings enhancers into close proximity with promoters via interactions with Cohesin and Mediator protein complexes.