Super-enhancer

Cell differentiation in multicellular organisms with different cell types is determined, in each cell type, by the expression of genes under the regulatory control of typical enhancers and super-enhancers. A typical enhancer (TE), as illustrated in the top panel of the Figure, is a several hundred base pair region of DNA that can bind transcription factors to sequence motifs on the enhancer. The typical enhancer can come in proximity to its target gene through a large chromosome loop. A Mediator complex (consisting of about 26 proteins in an interacting structure) communicates regulatory signals from the enhancer-located DNA-bound transcription factors to the promoter of a gene, regulating RNA transcription of the target gene. A super-enhancer, illustrated in the lower panel of the Figure, is a region of the mammalian genome comprising multiple typical enhancers that is collectively bound by an array of transcription factor proteins to drive transcription of genes involved in cell identity, or of genes involved in cancer. Because super-enhancers frequently occur near genes important for controlling and defining cell identity, they may be used to quickly identify key nodes regulating cell identity. Super-enhancers are also central to mediating dysregulation of signaling pathways and promoting cancer cell growth. Super-enhancers differ from typical enhancers, however, in that they are strongly dependent on additional specialized proteins that create and maintain their formation, including BRD4 (shown in the lower panel of Figure) and co-factors including p300. Enhancers have several quantifiable traits that have a range of values, and these traits are generally elevated at super-enhancers. Super-enhancers are bound by higher levels of transcription-regulating proteins and are associated with genes that are more highly expressed. Expression of genes associated with super-enhancers is particularly sensitive to perturbations, which may facilitate cell state transitions or explain sensitivity of super-enhancer–associated genes to small molecules that target transcription.

Frequency of super-enhancers In many cell types, only a minority of activated enhancers are located in Super-Enhancers (SEs). For specialized tissue, such as skeletal muscle, a reduced number of genes are expressed and a low number of specialized and activated super-enhancers are found. In human skeletal muscle, there are nine identified types of cells. On average, the number of expressed genes in these nine cell types is 1,331. There are also about 22 super-enhancers specific to skeletal muscle cells among the nine types of skeletal muscle cells, indicating that specialized super-enhancers in these cells are about 1.7% of the number of typical enhancers (TEs). In immune-system B cells, a study identified 140 SEs and 4,290 TEs in non-stimulated B cells (SEs were 3.2% of activated transcription areas). In stimulated B cells SEs were 3.6% of activated transcription areas. Similarly, in mouse embryonic stem cells, 231 SEs were found, compared to 8,794 TEs, with SEs comprising 2.6% of activated chromatin regions. A study of neural stem cells found 445 SEs and 9436 TEs, so that SEs were 4.7% of active enhancer regions.

Formation of super-enhancers Hundreds of thousands of sites in the human genome can potentially act as enhancers. In one large 2020 study, 78 different types of human cells were examined for links between activated enhancers and genes coding for messenger RNA to produce gene products. Distributed among the 78 types of cells there were a total of 449,627 activated enhancers linked to 17,643 protein-coding genes. With this large number of potentially active enhancers, there are some genome regions with a cluster of enhancers that, when all are activated they can all loop to the same promoter and produce a super-enhancer, driving a gene to have very high messenger RNA output. One well-studied gene, MYC, has amplified expression in as many as 70% of all cancers. While about 28% of its over-expressions are due to genetic focal amplifications or translocations, the majority of cases of over-expression of MYC are due to activated super-enhancers. There are more than 10 different super-enhancers that can cause MYC over-expression. For each of 4 tumor types of cells grown in culture (HCT-116, MCF7, K562 and Jurkat) there were three to five super-enhancers specific to each tumor cell type.

In one 2013 study, the length of typical enhancers was found to be about 700 base pairs while in the case of super-enhancers the length was about 9,000 base pairs (encompassing multiple single enhancers). A later study, in 2020, indicated that typical enhancers were about 200 nucleotides long and that there may be as many as 3.6 million potentially active enhancers occupying 21.55% of the human genome. In the nucleus of mammalian cells, almost all the DNA is wrapped around regularly spaced protein complexes, called nucleosomes (see top panel in Figure "Chromatin"). The protein complexes are composed of 4 pairs of histones, H2A, H2B, H3 and H4. The DNA plus these protein complexes is called chromatin (see Figure illustrating chromatin). Enhancer regions, as described above, are several hundred nucleotides long. To be activated, the enhancer region must have the nucleosomes evicted from the DNA so that the multiple transcription factors that bind to that enhancer DNA would have access to their binding sites (see bottom panel in Figure "Chromatin"). (To be an active enhancer, more than 10 different binding sites must be occupied by different transcription factors in the enhancer.)

In eviction of nucleosomes from enhancer DNA, a pioneer transcription factor first loosens up the attachment of DNA to the nucleosome of an enhancer region. For instance, one transcription factor that does this is the pioneer transcription factor NF-κB. Five steps follow this:

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