Super-enhancer

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.{{cite journal |vauthors=Cameron A, Wakelin G, Gaulton N, Young LV, Wotherspoon S, Hodson N, Lees MJ, Moore DR, Johnston AP |title=Identification of underexplored mesenchymal and vascular-related cell populations in human skeletal muscle |journal=Am J Physiol Cell Physiol |volume=323 |issue=6 |pages=C1586–C1600 |date=December 2022 |pmid=36342160 |doi=10.1152/ajpcell.00364.2022 |url=}} 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).{{cite journal |vauthors=Ehrlich KC, Paterson HL, Lacey M, Ehrlich M |title=DNA Hypomethylation in Intragenic and Intergenic Enhancer Chromatin of Muscle-Specific Genes Usually Correlates with their Expression |journal=Yale J Biol Med |volume=89 |issue=4 |pages=441–455 |date=December 2016 |pmid=28018137 |pmc=5168824 |doi= |url=}} 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.{{cite journal |vauthors=Michida H, Imoto H, Shinohara H, Yumoto N, Seki M, Umeda M, Hayashi T, Nikaido I, Kasukawa T, Suzuki Y, Okada-Hatakeyama M |title=The Number of Transcription Factors at an Enhancer Determines Switch-like Gene Expression |journal=Cell Rep |volume=31 |issue=9 |pages=107724 |date=June 2020 |pmid=32492432 |doi=10.1016/j.celrep.2020.107724 |url=|doi-access=free }} Similarly, in mouse embryonic stem cells, 231 SEs were found, compared to 8,794 TEs, with SEs comprising 2.6% of activated chromatin regions.{{cite journal |vauthors=Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, Kagey MH, Rahl PB, Lee TI, Young RA |title=Master transcription factors and mediator establish super-enhancers at key cell identity genes |journal=Cell |volume=153 |issue=2 |pages=307–19 |date=April 2013 |pmid=23582322 |pmc=3653129 |doi=10.1016/j.cell.2013.03.035 |url=}} A study of neural stem cells found 445 SEs and 9436 TEs, so that SEs were 4.7% of active enhancer regions.{{cite journal |vauthors=Quevedo M, Meert L, Dekker MR, Dekkers DH, Brandsma JH, van den Berg DL, Ozgür Z, van IJcken WF, Demmers J, Fornerod M, Poot RA |title=Mediator complex interaction partners organize the transcriptional network that defines neural stem cells |journal=Nat Commun |volume=10 |issue=1 |pages=2669 |date=June 2019 |pmid=31209209 |pmc=6573065 |doi=10.1038/s41467-019-10502-8 |bibcode=2019NatCo..10.2669Q |url=}}

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.{{cite journal |vauthors=Mills C, Muruganujan A, Ebert D, Marconett CN, Lewinger JP, Thomas PD, Mi H |title=PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence |journal=PLOS ONE |volume=15 |issue=12 |pages=e0243791 |date=2020 |pmid=33320871 |pmc=7737992 |doi=10.1371/journal.pone.0243791 |doi-access=free |bibcode=2020PLoSO..1543791M |url=}} 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.{{cite journal |vauthors=Duffy MJ, O'Grady S, Tang M, Crown J |title=MYC as a target for cancer treatment |journal=Cancer Treat Rev |volume=94 |issue= |pages=102154 |date=March 2021 |pmid=33524794 |doi=10.1016/j.ctrv.2021.102154 |url=|doi-access=free }} While about 28% of its over-expressions are due to genetic focal amplifications or translocations,{{cite journal |vauthors=Schaub FX, Dhankani V, Berger AC, Trivedi M, Richardson AB, Shaw R, Zhao W, Zhang X, Ventura A, Liu Y, Ayer DE, Hurlin PJ, Cherniack AD, Eisenman RN, Bernard B, Grandori C |title=Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas |journal=Cell Syst |volume=6 |issue=3 |pages=282–300.e2 |date=March 2018 |pmid=29596783 |pmc=5892207 |doi=10.1016/j.cels.2018.03.003 |url=}} the majority of cases of over-expression of MYC are due to activated super-enhancers.{{cite journal |vauthors=Schuijers J, Manteiga JC, Weintraub AS, Day DS, Zamudio AV, Hnisz D, Lee TI, Young RA |title=Transcriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism |journal=Cell Rep |volume=23 |issue=2 |pages=349–360 |date=April 2018 |pmid=29641996 |pmc=5929158 |doi=10.1016/j.celrep.2018.03.056 |url=}} 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.

File:Chromatin and chromatin with nucleosome eviction.jpg

In one 2013 study,{{cite journal |vauthors=Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-André V, Sigova AA, Hoke HA, Young RA |title=Super-enhancers in the control of cell identity and disease |journal=Cell |volume=155 |issue=4 |pages=934–47 |date=November 2013 |pmid=24119843 |pmc=3841062 |doi=10.1016/j.cell.2013.09.053 |url=}} 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.{{cite journal |vauthors=Singh G, Mullany S, Moorthy SD, Zhang R, Mehdi T, Tian R, Duncan AG, Moses AM, Mitchell JA |title=A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells |journal=Genome Res |volume=31 |issue=4 |pages=564–575 |date=April 2021 |pmid=33712417 |pmc=8015845 |doi=10.1101/gr.272468.120 |url=}}

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").{{cite journal |vauthors=Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE |title=High-resolution mapping and characterization of open chromatin across the genome |journal=Cell |volume=132 |issue=2 |pages=311–22 |date=January 2008 |pmid=18243105 |pmc=2669738 |doi=10.1016/j.cell.2007.12.014 |url=}} 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.{{cite journal |vauthors=Singh G, Mullany S, Moorthy SD, Zhang R, Mehdi T, Tian R, Duncan AG, Moses AM, Mitchell JA |title=A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells |journal=Genome Res |volume=31 |issue=4 |pages=564–575 |date=April 2021 |pmid=33712417 |pmc=8015845 |doi=10.1101/gr.272468.120 |url=}})

File:Nucleosome at enhancer with H3K122 acetylated.jpg

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-kB .{{cite journal |vauthors=Stormberg T, Filliaux S, Baughman HE, Komives EA, Lyubchenko YL |title=Transcription factor NF-κB unravels nucleosomes |journal=Biochim Biophys Acta Gen Subj |volume=1865 |issue=9 |pages=129934 |date=September 2021 |pmid=34029641 |pmc=8277743 |doi=10.1016/j.bbagen.2021.129934 |url=}} Five steps follow this: (1) NF-kB is acetylated by p300/CBP. (2) Acetylated NF-kB recruits a specific histone acetyltransferase enzyme, BRD4.{{cite journal |vauthors=Huang B, Yang XD, Zhou MM, Ozato K, Chen LF |title=Brd4 coactivates transcriptional activation of NF-kappaB via specific binding to acetylated RelA |journal=Mol Cell Biol |volume=29 |issue=5 |pages=1375–87 |date=March 2009 |pmid=19103749 |pmc=2643823 |doi=10.1128/MCB.01365-08 |url=}} (3) BRD4 acetylates histone 3 at histone 3 lysine 122 (see Figure “Nucleosome at enhancer with H3K122 acetylated”). (4) When histone 3 lysine 122 is acetylated the nucleosome is evicted from the enhancer sequence.{{cite journal |vauthors=Devaiah BN, Case-Borden C, Gegonne A, Hsu CH, Chen Q, Meerzaman D, Dey A, Ozato K, Singer DS |title=BRD4 is a histone acetyltransferase that evicts nucleosomes from chromatin |journal=Nat Struct Mol Biol |volume=23 |issue=6 |pages=540–8 |date=June 2016 |pmid=27159561 |pmc=4899182 |doi=10.1038/nsmb.3228 |url=}} (5) Opening up the enhancer DNA allows binding of the other transcription factors needed to form an activated enhancer. Presumably, when the activating signal for NF-kB is very strong, much more NF-kB is activated, and then greatly increased NF-kB can start the process of activating multiple nearby enhancers at the same time, forming a super-enhancer.

As described above, in forming a super-enhancer, BRD4 is complexed with NF-kB. This complex also recruits and forms a further complex with cyclin T1 and Cdk9. Cyclin T1/Cdk9 is also known as P-TEFb. P-TEFb acts as a kinase that phosphorylates RNA polymerase II (RNAP II), which then activates (in conjunction with the Mediator complex described below) the polymerase on the promoter of a gene to initiate transcription and to continue transcription (instead of pausing).{{cite journal |vauthors=Jang MK, Mochizuki K, Zhou M, Jeong HS, Brady JN, Ozato K |title=The bromodomain protein Brd4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase II-dependent transcription |journal=Mol Cell |volume=19 |issue=4 |pages=523–34 |date=August 2005 |pmid=16109376 |doi=10.1016/j.molcel.2005.06.027 |url=|doi-access=free }}

The transcription factors, bound to their sites on each enhancer within the super-enhancer, recruit the Mediator complex between each enhancer and the RNA polymerase II that will initiate transcription of the gene to be actively transcribed (see Figure at top of article that illustrates a super-enhancer). The Mediator complex in humans is 1.4 MDa in size and includes 26 sub-units.{{cite journal |vauthors=Richter WF, Nayak S, Iwasa J, Taatjes DJ |title=The Mediator complex as a master regulator of transcription by RNA polymerase II |journal=Nat Rev Mol Cell Biol |volume=23 |issue=11 |pages=732–749 |date=November 2022 |pmid=35725906 |pmc=9207880 |doi=10.1038/s41580-022-00498-3 |url=}} The tail modules of the Mediator complex protein sub-units interact with the activation domains of transcription factors bound at enhancers and the head and middle modules interact with the pre-initiation complex (PIC) at gene promoters.{{cite journal |vauthors=Ramasamy S, Aljahani A, Karpinska MA, Cao TB, Velychko T, Cruz JN, Lidschreiber M, Oudelaar AM |title=The Mediator complex regulates enhancer-promoter interactions |journal=Nat Struct Mol Biol |volume=30 |issue=7 |pages=991–1000 |date=July 2023 |pmid=37430065 |pmc=10352134 |doi=10.1038/s41594-023-01027-2 |url=}} The Mediator complex, when certain sub-units are phosphorylated and up-activated by particular cyclin-dependent kinases (Cdk8, Cdk9, Cdk19, etc.) it will then promote higher levels of transcription.

The regulation of transcription by enhancers has been studied since the 1980s.{{cite journal | vauthors = Banerji J, Rusconi S, Schaffner W | title = Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences | journal = Cell | volume = 27 | issue = 2 Pt 1 | pages = 299–308 | date = December 1981 | pmid = 6277502 | doi = 10.1016/0092-8674(81)90413-x | s2cid = 54234674 }}{{cite journal | vauthors = Benoist C, Chambon P | title = In vivo sequence requirements of the SV40 early promoter region | journal = Nature | volume = 290 | issue = 5804 | pages = 304–10 | date = March 1981 | pmid = 6259538 | doi = 10.1038/290304a0 | bibcode = 1981Natur.290..304B | s2cid = 4263279 }}{{cite journal | vauthors = Gruss P, Dhar R, Khoury G | title = Simian virus 40 tandem repeated sequences as an element of the early promoter | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 78 | issue = 2 | pages = 943–7 | date = February 1981 | pmid = 6262784 | pmc = 319921 | doi = 10.1073/pnas.78.2.943 | bibcode = 1981PNAS...78..943G | doi-access = free }}{{cite journal | vauthors = Evans T, Felsenfeld G, Reitman M | title = Control of globin gene transcription | journal = Annual Review of Cell Biology | volume = 6 | pages = 95–124 | date = 1990 | pmid = 2275826 | doi = 10.1146/annurev.cb.06.110190.000523 | url = https://zenodo.org/record/1234945 }}{{cite journal | vauthors = Cellier M, Belouchi A, Gros P | title = Resistance to intracellular infections: comparative genomic analysis of Nramp | journal = Trends in Genetics | volume = 12 | issue = 6 | pages = 201–4 | date = June 1996 | pmid = 8928221 | doi = 10.1016/0168-9525(96)30042-5 }} Large or multi-component transcription regulators with a range of mechanistic properties, including locus control regions, clustered open regulatory elements, and transcription initiation platforms, were observed shortly thereafter.{{cite journal |authorlink4=George Stamatoyannopoulos| vauthors = Li Q, Peterson KR, Fang X, Stamatoyannopoulos G | title = Locus control regions | journal = Blood | volume = 100 | issue = 9 | pages = 3077–86 | date = November 2002 | pmid = 12384402 | pmc = 2811695 | doi = 10.1182/blood-2002-04-1104 }}{{cite journal | vauthors = Grosveld F, van Assendelft GB, Greaves DR, Kollias G | title = Position-independent, high-level expression of the human beta-globin gene in transgenic mice | journal = Cell | volume = 51 | issue = 6 | pages = 975–85 | date = December 1987 | pmid = 3690667 | doi = 10.1016/0092-8674(87)90584-8 | hdl = 1765/2425 | s2cid = 1150699 | url = http://repub.eur.nl/pub/2425 | hdl-access = free }}{{cite journal | vauthors = Gaulton KJ, Nammo T, Pasquali L, Simon JM, Giresi PG, Fogarty MP, Panhuis TM, Mieczkowski P, Secchi A, Bosco D, Berney T, Montanya E, Mohlke KL, Lieb JD, Ferrer J | display-authors = 6 | title = A map of open chromatin in human pancreatic islets | journal = Nature Genetics | volume = 42 | issue = 3 | pages = 255–9 | date = March 2010 | pmid = 20118932 | pmc = 2828505 | doi = 10.1038/ng.530 }}{{cite journal | vauthors = Koch F, Fenouil R, Gut M, Cauchy P, Albert TK, Zacarias-Cabeza J, Spicuglia S, de la Chapelle AL, Heidemann M, Hintermair C, Eick D, Gut I, Ferrier P, Andrau JC | title = Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters | journal = Nature Structural & Molecular Biology | volume = 18 | issue = 8 | pages = 956–63 | date = August 2011 | pmid = 21765417 | doi = 10.1038/nsmb.2085 | s2cid = 12778976 }} More recent research has suggested that these different categories of regulatory elements may represent subtypes of super-enhancer.{{cite journal | vauthors = Pott S, Lieb JD | title = What are super-enhancers? | journal = Nature Genetics | volume = 47 | issue = 1 | pages = 8–12 | date = January 2015 | pmid = 25547603 | doi = 10.1038/ng.3167 | s2cid = 205349376 }}

In 2013, two labs identified large enhancers near several genes especially important for establishing cell identities. While Richard A. Young and colleagues identified super-enhancers, Francis Collins and colleagues identified stretch enhancers. Both super-enhancers and stretch enhancers are clusters of enhancers that control cell-specific genes and may be largely synonymous.{{cite journal | vauthors = Hnisz D, Schuijers J, Lin CY, Weintraub AS, Abraham BJ, Lee TI, Bradner JE, Young RA | title = Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers | journal = Molecular Cell | volume = 58 | issue = 2 | pages = 362–70 | date = April 2015 | pmid = 25801169 | pmc = 4402134 | doi = 10.1016/j.molcel.2015.02.014 }}

As currently defined, the term “super-enhancer” was introduced by Young’s lab to describe regions identified in mouse embryonic stem cells (ESCs). These particularly large, potent enhancer regions were found to control the genes that establish the embryonic stem cell identity, including Oct-4, Sox2, Nanog, Klf4, and Esrrb. Perturbation of the super-enhancers associated with these genes showed a range of effects on their target genes’ expression. Super-enhancers have been since identified near cell identity-regulators in a range of mouse and human tissues. {{cite journal | vauthors = Di Micco R, Fontanals-Cirera B, Low V, Ntziachristos P, Yuen SK, Lovell CD, Dolgalev I, Yonekubo Y, Zhang G, Rusinova E, Gerona-Navarro G, Cañamero M, Ohlmeyer M, Aifantis I, Zhou MM, Tsirigos A, Hernando E | display-authors = 6 | title = Control of embryonic stem cell identity by BRD4-dependent transcriptional elongation of super-enhancer-associated pluripotency genes | journal = Cell Reports | volume = 9 | issue = 1 | pages = 234–47 | date = October 2014 | pmid = 25263550 | pmc = 4317728 | doi = 10.1016/j.celrep.2014.08.055 }}{{cite journal | vauthors = Ji X, Dadon DB, Powell BE, Fan ZP, Borges-Rivera D, Shachar S, Weintraub AS, Hnisz D, Pegoraro G, Lee TI, Misteli T, Jaenisch R, Young RA | title = 3D Chromosome Regulatory Landscape of Human Pluripotent Cells | journal = Cell Stem Cell | volume = 18 | issue = 2 | pages = 262–75 | date = February 2016 | pmid = 26686465 | doi = 10.1016/j.stem.2015.11.007 | pmc = 4848748 }}{{cite journal | vauthors = Tsankov AM, Gu H, Akopian V, Ziller MJ, Donaghey J, Amit I, Gnirke A, Meissner A | title = Transcription factor binding dynamics during human ES cell differentiation | journal = Nature | volume = 518 | issue = 7539 | pages = 344–9 | date = February 2015 | pmid = 25693565 | pmc = 4499331 | doi = 10.1038/nature14233 | bibcode = 2015Natur.518..344T }}{{cite journal | vauthors = Fang Z, Hecklau K, Gross F, Bachmann I, Venzke M, Karl M, Schuchhardt J, Radbruch A, Herzel H, Baumgrass R | title = Transcription factor co-occupied regions in the murine genome constitute T-helper-cell subtype-specific enhancers | journal = European Journal of Immunology | volume = 45 | issue = 11 | pages = 3150–7 | date = November 2015 | pmid = 26300430 | doi = 10.1002/eji.201545713 | doi-access = free }}{{cite journal | vauthors = Vahedi G, Kanno Y, Furumoto Y, Jiang K, Parker SC, Erdos MR, Davis SR, Roychoudhuri R, Restifo NP, Gadina M, Tang Z, Ruan Y, Collins FS, Sartorelli V, O'Shea JJ | title = Super-enhancers delineate disease-associated regulatory nodes in T cells | journal = Nature | volume = 520 | issue = 7548 | pages = 558–62 | date = April 2015 | pmid = 25686607 | pmc = 4409450 | doi = 10.1038/nature14154 | bibcode = 2015Natur.520..558V }}{{cite journal | vauthors = Koues OI, Kowalewski RA, Chang LW, Pyfrom SC, Schmidt JA, Luo H, Sandoval LE, Hughes TB, Bednarski JJ, Cashen AF, Payton JE, Oltz EM | title = Enhancer sequence variants and transcription-factor deregulation synergize to construct pathogenic regulatory circuits in B-cell lymphoma | journal = Immunity | volume = 42 | issue = 1 | pages = 186–98 | date = January 2015 | pmid = 25607463 | pmc = 4302272 | doi = 10.1016/j.immuni.2014.12.021 }}{{cite journal | vauthors = Adam RC, Yang H, Rockowitz S, Larsen SB, Nikolova M, Oristian DS, Polak L, Kadaja M, Asare A, Zheng D, Fuchs E | title = Pioneer factors govern super-enhancer dynamics in stem cell plasticity and lineage choice | journal = Nature | volume = 521 | issue = 7552 | pages = 366–70 | date = May 2015 | pmid = 25799994 | pmc = 4482136 | doi = 10.1038/nature14289 | bibcode = 2015Natur.521..366A }}{{cite journal | vauthors = Siersbæk R, Baek S, Rabiee A, Nielsen R, Traynor S, Clark N, Sandelin A, Jensen ON, Sung MH, Hager GL, Mandrup S | title = Molecular architecture of transcription factor hotspots in early adipogenesis | journal = Cell Reports | volume = 7 | issue = 5 | pages = 1434–42 | date = June 2014 | pmid = 24857666 | doi = 10.1016/j.celrep.2014.04.043 | pmc = 6360525 }}{{cite journal | vauthors = Siersbæk R, Rabiee A, Nielsen R, Sidoli S, Traynor S, Loft A, La Cour Poulsen L, Rogowska-Wrzesinska A, Jensen ON, Mandrup S | title = Transcription factor cooperativity in early adipogenic hotspots and super-enhancers | journal = Cell Reports | volume = 7 | issue = 5 | pages = 1443–55 | date = June 2014 | pmid = 24857652 | doi = 10.1016/j.celrep.2014.04.042 | doi-access = free }}{{cite journal | vauthors = Harms MJ, Ishibashi J, Wang W, Lim HW, Goyama S, Sato T, Kurokawa M, Won KJ, Seale P | display-authors = 6 | title = Prdm16 is required for the maintenance of brown adipocyte identity and function in adult mice | journal = Cell Metabolism | volume = 19 | issue = 4 | pages = 593–604 | date = April 2014 | pmid = 24703692 | pmc = 4012340 | doi = 10.1016/j.cmet.2014.03.007 }}{{cite journal | vauthors = Loft A, Forss I, Siersbæk MS, Schmidt SF, Larsen AS, Madsen JG, Pisani DF, Nielsen R, Aagaard MM, Mathison A, Neville MJ, Urrutia R, Karpe F, Amri EZ, Mandrup S | title = Browning of human adipocytes requires KLF11 and reprogramming of PPARγ superenhancers | journal = Genes & Development | volume = 29 | issue = 1 | pages = 7–22 | date = January 2015 | pmid = 25504365 | pmc = 4281566 | doi = 10.1101/gad.250829.114 }}{{cite journal | vauthors = Pasquali L, Gaulton KJ, Rodríguez-Seguí SA, Mularoni L, Miguel-Escalada I, Akerman I, Tena JJ, Morán I, Gómez-Marín C, van de Bunt M, Ponsa-Cobas J, Castro N, Nammo T, Cebola I, García-Hurtado J, Maestro MA, Pattou F, Piemonti L, Berney T, Gloyn AL, Ravassard P, Gómez-Skarmeta JL, Müller F, McCarthy MI, Ferrer J | display-authors = 6 | title = Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants | journal = Nature Genetics | volume = 46 | issue = 2 | pages = 136–43 | date = February 2014 | pmid = 24413736 | pmc = 3935450 | doi = 10.1038/ng.2870 }}{{cite journal | vauthors = Liu CF, Lefebvre V | title = The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis | journal = Nucleic Acids Research | volume = 43 | issue = 17 | pages = 8183–203 | date = September 2015 | pmid = 26150426 | pmc = 4787819 | doi = 10.1093/nar/gkv688 }}{{cite journal | vauthors = Ohba S, He X, Hojo H, McMahon AP | title = Distinct Transcriptional Programs Underlie Sox9 Regulation of the Mammalian Chondrocyte | journal = Cell Reports | volume = 12 | issue = 2 | pages = 229–43 | date = July 2015 | pmid = 26146088 | pmc = 4504750 | doi = 10.1016/j.celrep.2015.06.013 }}{{cite journal | vauthors = Kaikkonen MU, Niskanen H, Romanoski CE, Kansanen E, Kivelä AM, Laitalainen J, Heinz S, Benner C, Glass CK, Ylä-Herttuala S | title = Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization | journal = Nucleic Acids Research | volume = 42 | issue = 20 | pages = 12570–84 | date = November 2014 | pmid = 25352550 | pmc = 4227755 | doi = 10.1093/nar/gku1036 }}{{cite journal | vauthors = Gosselin D, Link VM, Romanoski CE, Fonseca GJ, Eichenfield DZ, Spann NJ, Stender JD, Chun HB, Garner H, Geissmann F, Glass CK | title = Environment drives selection and function of enhancers controlling tissue-specific macrophage identities | journal = Cell | volume = 159 | issue = 6 | pages = 1327–40 | date = December 2014 | pmid = 25480297 | pmc = 4364385 | doi = 10.1016/j.cell.2014.11.023 }}{{cite journal | vauthors = Sun J, Rockowitz S, Xie Q, Ashery-Padan R, Zheng D, Cvekl A | title = Identification of in vivo DNA-binding mechanisms of Pax6 and reconstruction of Pax6-dependent gene regulatory networks during forebrain and lens development | journal = Nucleic Acids Research | volume = 43 | issue = 14 | pages = 6827–46 | date = August 2015 | pmid = 26138486 | pmc = 4538810 | doi = 10.1093/nar/gkv589 }}

The enhancers comprising super-enhancers share the functions of enhancers, including binding transcription factor proteins, looping to target genes, and activating transcription. Three notable traits of enhancers comprising super-enhancers are their clustering in genomic proximity, their exceptional signal of transcription-regulating proteins, and their high frequency of physical interaction with each other. Perturbing the DNA of enhancers comprising super-enhancers showed a range of effects on the expression of cell identity genes, suggesting a complex relationship between the constituent enhancers. Super-enhancers separated by tens of megabases cluster in three-dimensions inside the nucleus of mouse embryonic stem cells.{{cite journal | vauthors = Beagrie RA, Scialdone A, Schueler M, Kraemer DC, Chotalia M, Xie SQ, Barbieri M, de Santiago I, Lavitas LM, Branco MR, Fraser J, Dostie J, Game L, Dillon N, Edwards PA, Nicodemi M, Pombo A | title = Complex multi-enhancer contacts captured by Genome Architecture Mapping (GAM)| journal = Nature | volume = 543 | pages = 519–524 | date = March 2017 | issue = 7646| pmid = 28273065 | pmc = 5366070 | doi = 10.1038/nature21411 | bibcode = 2017Natur.543..519B}}{{cite journal | vauthors = Quinodoz SA, Ollikainen N, Tabak B, Palla A, Schmidt JM, Detmar E, Lai MM, Shishkin AA, Bhat P, Takei Y, Trinh V, Aznauryan E, Russell P, Cheng C, Jovanovic M, Chow A, Cai L, McDonel P, Garber M, Guttman M | title = Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus| journal = Cell | volume = 174 | pages = 744–757 | date = June 2018 | issue = 3| pmid = 29887377 | doi = 10.1016/j.cell.2018.05.024 | pmc=6548320}}

High levels of many transcription factors and co-factors are seen at super-enhancers (e.g., CDK7, BRD4, and Mediator).

This high concentration of transcription-regulating proteins suggests why their target genes tend to be more highly expressed than other classes of genes. However, housekeeping genes tend to be more highly expressed than super-enhancer—associated genes.

Super-enhancers may have evolved at key cell identity genes to render the transcription of these genes responsive to an array of external cues. The enhancers comprising a super-enhancer can each be responsive to different signals, which allows the transcription of a single gene to be regulated by multiple signaling pathways. Pathways seen to regulate their target genes using super-enhancers include Wnt, TGFb, LIF, BDNF, and NOTCH.{{cite journal | vauthors = Joo JY, Schaukowitch K, Farbiak L, Kilaru G, Kim TK | title = Stimulus-specific combinatorial functionality of neuronal c-fos enhancers | journal = Nature Neuroscience | volume = 19 | issue = 1 | pages = 75–83 | date = January 2016 | pmid = 26595656 | pmc = 4696896 | doi = 10.1038/nn.4170 }}{{cite journal | vauthors = Herranz D, Ambesi-Impiombato A, Palomero T, Schnell SA, Belver L, Wendorff AA, Xu L, Castillo-Martin M, Llobet-Navás D, Cordon-Cardo C, Clappier E, Soulier J, Ferrando AA | title = A NOTCH1-driven MYC enhancer promotes T cell development, transformation and acute lymphoblastic leukemia | journal = Nature Medicine | volume = 20 | issue = 10 | pages = 1130–7 | date = October 2014 | pmid = 25194570 | pmc = 4192073 | doi = 10.1038/nm.3665 }}{{cite journal | vauthors = Wang H, Zang C, Taing L, Arnett KL, Wong YJ, Pear WS, Blacklow SC, Liu XS, Aster JC | title = NOTCH1-RBPJ complexes drive target gene expression through dynamic interactions with superenhancers | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 111 | issue = 2 | pages = 705–10 | date = January 2014 | pmid = 24374627 | pmc = 3896193 | doi = 10.1073/pnas.1315023111 | bibcode = 2014PNAS..111..705W | doi-access = free }}{{cite journal | vauthors = Yashiro-Ohtani Y, Wang H, Zang C, Arnett KL, Bailis W, Ho Y, Knoechel B, Lanauze C, Louis L, Forsyth KS, Chen S, Chung Y, Schug J, Blobel GA, Liebhaber SA, Bernstein BE, Blacklow SC, Liu XS, Aster JC, Pear WS | display-authors = 6 | title = Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 111 | issue = 46 | pages = E4946-53 | date = November 2014 | pmid = 25369933 | pmc = 4246292 | doi = 10.1073/pnas.1407079111 | bibcode = 2014PNAS..111E4946Y | doi-access = free }} The constituent enhancers of super-enhancers physically interact with each other and their target genes over a long range sequence-wise.{{cite journal | vauthors = Hnisz D, Weintraub AS, Day DS, Valton AL, Bak RO, Li CH, Goldmann J, Lajoie BR, Fan ZP, Sigova AA, Reddy J, Borges-Rivera D, Lee TI, Jaenisch R, Porteus MH, Dekker J, Young RA | title = Activation of proto-oncogenes by disruption of chromosome neighborhoods | journal = Science | volume = 351 | issue = 6280 | pages = 1454–8 | date = March 2016 | pmid = 26940867 | doi = 10.1126/science.aad9024 | pmc=4884612| bibcode = 2016Sci...351.1454H }}

Super-enhancers that control the expression of major cell surface receptors with a crucial role in the function of a given cell lineage have also been defined. This is notably the case for B-lymphocytes, the survival, the activation and the differentiation of which rely on the expression of membrane-form immunoglobulins (Ig). The Ig heavy chain locus super-enhancer is a very large (25kb) cis-regulatory region, including multiple enhancers and controlling several major modifications of the locus (notably somatic hypermutation, class-switch recombination and locus suicide recombination).

Mutations in super-enhancers have been noted in various diseases, including cancers, type 1 diabetes, Alzheimer’s disease, lupus, rheumatoid arthritis, multiple sclerosis, systemic scleroderma, primary biliary cirrhosis, Crohn’s disease, Graves disease, vitiligo, and atrial fibrillation.{{cite journal | vauthors = Mansour MR, Abraham BJ, Anders L, Berezovskaya A, Gutierrez A, Durbin AD, Etchin J, Lawton L, Sallan SE, Silverman LB, Loh ML, Hunger SP, Sanda T, Young RA, Look AT | title = Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element | journal = Science | volume = 346 | issue = 6215 | pages = 1373–7 | date = December 2014 | pmid = 25394790 | pmc = 4720521 | doi = 10.1126/science.1259037 }}{{cite journal | vauthors = Cavalli G, Hayashi M, Jin Y, Yorgov D, Santorico SA, Holcomb C, Rastrou M, Erlich H, Tengesdal IW, Dagna L, Neff CP, Palmer BE, Spritz RA, Dinarello CA | title = MHC class II super-enhancer increases surface expression of HLA-DR and HLA-DQ and affects cytokine production in autoimmune vitiligo | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 113 | issue = 5 | pages = 1363–8 | date = February 2016 | pmid = 26787888 | doi = 10.1073/pnas.1523482113 | pmc = 4747741 | bibcode = 2016PNAS..113.1363C | doi-access = free }}{{cite journal | vauthors = Farh KK, Marson A, Zhu J, Kleinewietfeld M, Housley WJ, Beik S, Shoresh N, Whitton H, Ryan RJ, Shishkin AA, Hatan M, Carrasco-Alfonso MJ, Mayer D, Luckey CJ, Patsopoulos NA, De Jager PL, Kuchroo VK, Epstein CB, Daly MJ, Hafler DA, Bernstein BE | title = Genetic and epigenetic fine mapping of causal autoimmune disease variants | journal = Nature | volume = 518 | issue = 7539 | pages = 337–43 | date = February 2015 | pmid = 25363779 | pmc = 4336207 | doi = 10.1038/nature13835 | bibcode = 2015Natur.518..337F }}{{cite journal | vauthors = Weinstein JS, Lezon-Geyda K, Maksimova Y, Craft S, Zhang Y, Su M, Schulz VP, Craft J, Gallagher PG | title = Global transcriptome analysis and enhancer landscape of human primary T follicular helper and T effector lymphocytes | journal = Blood | volume = 124 | issue = 25 | pages = 3719–29 | date = December 2014 | pmid = 25331115 | pmc = 4263981 | doi = 10.1182/blood-2014-06-582700 }}{{cite journal | vauthors = Oldridge DA, Wood AC, Weichert-Leahey N, Crimmins I, Sussman R, Winter C, McDaniel LD, Diamond M, Hart LS, Zhu S, Durbin AD, Abraham BJ, Anders L, Tian L, Zhang S, Wei JS, Khan J, Bramlett K, Rahman N, Capasso M, Iolascon A, Gerhard DS, Guidry Auvil JM, Young RA, Hakonarson H, Diskin SJ, Look AT, Maris JM | display-authors = 6 | title = Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism | journal = Nature | volume = 528 | issue = 7582 | pages = 418–21 | date = December 2015 | pmid = 26560027 | pmc = 4775078 | doi = 10.1038/nature15540 | bibcode = 2015Natur.528..418O }} A similar enrichment in disease-associated sequence variation has also been observed for stretch enhancers.

Super-enhancers may play important roles in the misregulation of gene expression in cancer. During tumor development, tumor cells acquire super-enhancers at key oncogenes, which drive higher levels of transcription of these genes than in healthy cells.{{cite journal | vauthors = Affer M, Chesi M, Chen WD, Keats JJ, Demchenko YN, Tamizhmani K, Garbitt VM, Riggs DL, Brents LA, Roschke AV, Van Wier S, Fonseca R, Bergsagel PL, Kuehl WM | title = Promiscuous MYC locus rearrangements hijack enhancers but mostly super-enhancers to dysregulate MYC expression in multiple myeloma | journal = Leukemia | volume = 28 | issue = 8 | pages = 1725–35 | date = August 2014 | pmid = 24518206 | pmc = 4126852 | doi = 10.1038/leu.2014.70 }}{{cite journal | vauthors = Drier Y, Cotton MJ, Williamson KE, Gillespie SM, Ryan RJ, Kluk MJ, Carey CD, Rodig SJ, Sholl LM, Afrogheh AH, Faquin WC, Queimado L, Qi J, Wick MJ, El-Naggar AK, Bradner JE, Moskaluk CA, Aster JC, Knoechel B, Bernstein BE | display-authors = 6 | title = An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma | journal = Nature Genetics | volume = 48 | issue = 3 | pages = 265–72 | date = March 2016 | pmid = 26829750 | doi = 10.1038/ng.3502 | pmc = 4767593 }}{{cite journal | vauthors = Northcott PA, Lee C, Zichner T, Stütz AM, Erkek S, Kawauchi D, Shih DJ, Hovestadt V, Zapatka M, Sturm D, Jones DT, Kool M, Remke M, Cavalli FM, Zuyderduyn S, Bader GD, VandenBerg S, Esparza LA, Ryzhova M, Wang W, Wittmann A, Stark S, Sieber L, Seker-Cin H, Linke L, Kratochwil F, Jäger N, Buchhalter I, Imbusch CD, Zipprich G, Raeder B, Schmidt S, Diessl N, Wolf S, Wiemann S, Brors B, Lawerenz C, Eils J, Warnatz HJ, Risch T, Yaspo ML, Weber UD, Bartholomae CC, von Kalle C, Turányi E, Hauser P, Sanden E, Darabi A, Siesjö P, Sterba J, Zitterbart K, Sumerauer D, van Sluis P, Versteeg R, Volckmann R, Koster J, Schuhmann MU, Ebinger M, Grimes HL, Robinson GW, Gajjar A, Mynarek M, von Hoff K, Rutkowski S, Pietsch T, Scheurlen W, Felsberg J, Reifenberger G, Kulozik AE, von Deimling A, Witt O, Eils R, Gilbertson RJ, Korshunov A, Taylor MD, Lichter P, Korbel JO, Wechsler-Reya RJ, Pfizer SM | display-authors = 6 | title = Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma | journal = Nature | volume = 511 | issue = 7510 | pages = 428–34 | date = July 2014 | pmid = 25043047 | pmc = 4201514 | doi = 10.1038/nature13379 | bibcode = 2014Natur.511..428N }}{{cite journal | vauthors = Walker BA, Wardell CP, Brioli A, Boyle E, Kaiser MF, Begum DB, Dahir NB, Johnson DC, Ross FM, Davies FE, Morgan GJ | title = Translocations at 8q24 juxtapose MYC with genes that harbor superenhancers resulting in overexpression and poor prognosis in myeloma patients | journal = Blood Cancer Journal | volume = 4 | pages = e191 | date = 14 March 2014 | issue = 3 | pmid = 24632883 | pmc = 3972699 | doi = 10.1038/bcj.2014.13 }}{{cite journal | vauthors = Gröschel S, Sanders MA, Hoogenboezem R, de Wit E, Bouwman BA, Erpelinck C, van der Velden VH, Havermans M, Avellino R, van Lom K, Rombouts EJ, van Duin M, Döhner K, Beverloo HB, Bradner JE, Döhner H, Löwenberg B, Valk PJ, Bindels EM, de Laat W, Delwel R | display-authors = 6 | title = A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukemia | journal = Cell | volume = 157 | issue = 2 | pages = 369–81 | date = April 2014 | pmid = 24703711 | doi = 10.1016/j.cell.2014.02.019 | doi-access = free }}{{cite journal | vauthors = Shi J, Whyte WA, Zepeda-Mendoza CJ, Milazzo JP, Shen C, Roe JS, Minder JL, Mercan F, Wang E, Eckersley-Maslin MA, Campbell AE, Kawaoka S, Shareef S, Zhu Z, Kendall J, Muhar M, Haslinger C, Yu M, Roeder RG, Wigler MH, Blobel GA, Zuber J, Spector DL, Young RA, Vakoc CR | display-authors = 6 | title = Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation | journal = Genes & Development | volume = 27 | issue = 24 | pages = 2648–62 | date = December 2013 | pmid = 24285714 | pmc = 3877755 | doi = 10.1101/gad.232710.113 }}{{cite journal | vauthors = Kennedy AL, Vallurupalli M, Chen L, Crompton B, Cowley G, Vazquez F, Weir BA, Tsherniak A, Parasuraman S, Kim S, Alexe G, Stegmaier K | title = Functional, chemical genomic, and super-enhancer screening identify sensitivity to cyclin D1/CDK4 pathway inhibition in Ewing sarcoma | journal = Oncotarget | volume = 6 | issue = 30 | pages = 30178–93 | date = October 2015 | pmid = 26337082 | pmc = 4745789 | doi = 10.18632/oncotarget.4903 }}{{cite journal | vauthors = Tomazou EM, Sheffield NC, Schmidl C, Schuster M, Schönegger A, Datlinger P, Kubicek S, Bock C, Kovar H | title = Epigenome mapping reveals distinct modes of gene regulation and widespread enhancer reprogramming by the oncogenic fusion protein EWS-FLI1 | journal = Cell Reports | volume = 10 | issue = 7 | pages = 1082–95 | date = February 2015 | pmid = 25704812 | pmc = 4542316 | doi = 10.1016/j.celrep.2015.01.042 }}{{cite journal | vauthors = Nabet B, Ó Broin P, Reyes JM, Shieh K, Lin CY, Will CM, Popovic R, Ezponda T, Bradner JE, Golden AA, Licht JD | title = Deregulation of the Ras-Erk Signaling Axis Modulates the Enhancer Landscape | journal = Cell Reports | volume = 12 | issue = 8 | pages = 1300–13 | date = August 2015 | pmid = 26279576 | doi = 10.1016/j.celrep.2015.06.078 | pmc = 4551578 | doi-access = free }}{{cite journal | vauthors = Zhang X, Choi PS, Francis JM, Imielinski M, Watanabe H, Cherniack AD, Meyerson M | title = Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers | journal = Nature Genetics | volume = 48 | issue = 2 | pages = 176–82 | date = February 2016 | pmid = 26656844 | pmc = 4857881 | doi = 10.1038/ng.3470 }} Altered super-enhancer function is also induced by mutations of chromatin regulators.{{cite journal | vauthors = Hodges HC, Stanton BZ, Cermakova K, Chang CY, Miller EL, Kirkland JG, Ku WL, Veverka V, Zhao K, Crabtree GR | title = Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers | journal = Nature Structural & Molecular Biology | volume = 25 | issue = 1 | pages = 61–72 | date = January 2018 | pmid = 29323272 | doi = 10.1038/s41594-017-0007-3 | pmc = 5909405 }} Acquired super-enhancers may thus be biomarkers that could be useful for diagnosis and therapeutic intervention.

Proteins enriched at super-enhancers include the targets of small molecules that target transcription-regulating proteins and have been deployed against cancers.{{cite journal | vauthors = Porcher C | title = Toward a BETter grasp of acetyl-lysine readers | journal = Blood | volume = 125 | issue = 18 | pages = 2739–41 | date = April 2015 | pmid = 25931578 | doi = 10.1182/blood-2015-03-630830 | doi-access = free }} For instance, super-enhancers rely on exceptional amounts of CDK7, and, in cancer, multiple papers report the loss of expression of their target genes when cells are treated with the CDK7 inhibitor THZ1.{{cite journal | vauthors = Wang Y, Zhang T, Kwiatkowski N, Abraham BJ, Lee TI, Xie S, Yuzugullu H, Von T, Li H, Lin Z, Stover DG, Lim E, Wang ZC, Iglehart JD, Young RA, Gray NS, Zhao JJ | title = CDK7-dependent transcriptional addiction in triple-negative breast cancer | journal = Cell | volume = 163 | issue = 1 | pages = 174–86 | date = September 2015 | pmid = 26406377 | doi = 10.1016/j.cell.2015.08.063 | pmc = 4583659 | doi-access = free }} Similarly, super-enhancers are enriched in the target of the JQ1 small molecule, BRD4, so treatment with JQ1 causes exceptional losses in expression for super-enhancer—associated genes.

Super-enhancers have been most commonly identified by locating genomic regions that are highly enriched in ChIP-Seq signal. ChIP-Seq experiments targeting master transcription factors and co-factors like Mediator or BRD4 have been used, but the most frequently used is H3K27ac-marked nucleosomes.{{cite journal | vauthors = Wei Y, Zhang S, Shang S, Zhang B, Li S, Wang X, Wang F, Su J, Wu Q, Liu H, Zhang Y | title = SEA: a super-enhancer archive | journal = Nucleic Acids Research | volume = 44 | issue = D1 | pages = D172-9 | date = January 2016 | pmid = 26578594 | pmc = 4702879 | doi = 10.1093/nar/gkv1243 }}{{cite journal | vauthors = Khan A, Zhang X | title = dbSUPER: a database of super-enhancers in mouse and human genome | journal = Nucleic Acids Research | volume = 44 | issue = D1 | pages = D164-71 | date = January 2016 | pmid = 26438538 | pmc = 4702767 | doi = 10.1093/nar/gkv1002 }}{{cite journal | vauthors = Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA, Boyer LA, Young RA, Jaenisch R | title = Histone H3K27ac separates active from poised enhancers and predicts developmental state | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 107 | issue = 50 | pages = 21931–6 | date = December 2010 | pmid = 21106759 | pmc = 3003124 | doi = 10.1073/pnas.1016071107 | doi-access = free }} The program “ROSE” (Rank Ordering of Super-Enhancers) is commonly used to identify super-enhancers from ChIP-Seq data. This program stitches together previously identified enhancer regions and ranks these stitched enhancers by their ChIP-Seq signal. The stitching distance selected to combine multiple individual enhancers into larger domains can vary. Because some markers of enhancer activity also are enriched in promoters, regions within promoters of genes can be disregarded. ROSE separates super-enhancers from typical enhancers by their exceptional enrichment in a mark of enhancer activity. Homer is another tool that can identify super-enhancers.{{cite journal | vauthors = Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK | title = Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities | journal = Molecular Cell | volume = 38 | issue = 4 | pages = 576–89 | date = May 2010 | pmid = 20513432 | pmc = 2898526 | doi = 10.1016/j.molcel.2010.05.004 }}

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Category:Gene expression