Super-enhancers in the control of cell identity and disease
Open accessAbstract
Super-enhancers are large clusters of transcriptional enhancers that drive expression of genes that define cell identity. Improved understanding of the roles that super-enhancers play in biology would be afforded by knowing the constellation of factors that constitute these domains and by identifying super-enhancers across the spectrum of human cell types. We describe here the population of transcription factors, cofactors, chromatin regulators, and transcription apparatus occupying super-enhancers in embryonic stem cells and evidence that super-enhancers are highly transcribed. We produce a catalog of super-enhancers in a broad range of human cell types and find that super-enhancers associate with genes that control and define the biology of these cells. Interestingly, disease-associated variation is especially enriched in the super-enhancers of disease-relevant cell types. Furthermore, we find that cancer cells generate super-enhancers at oncogenes and other genes important in tumor pathogenesis. Thus, super-enhancers play key roles in human cell identity in health and in disease.
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In mammals, cellular identity is established prenatally and maintained by H3K27ac-enriched super-enhancers.
“In mammals, cellular identity is established prenatally and maintained by H3K27ac-enriched super-enhancers (Hnisz et al., 2013; Whyte et al., 2013).”
From Loss of epigenetic information as a cause of mammalian aging (2023) · cites this paper as Hnisz et al., 2013
The Results section, “Super-enhancers in many cell types” (page unavailable), says super-enhancers drive genes that control and define cell identity and identifies H3K27ac as a useful mark for finding them. The paper does not say that mammalian cellular identity is established prenatally or demonstrate that H3K27ac-enriched super-enhancers maintain it thereafter. (LLM, conf=0.88)
Experimental — accuracy not yet measuredThe level of H3K27ac is not skewed in a similar manner towards Bim -117 and Atp1b3 -35, indicating that these regions are not super-enhancers.
“The level of the active enhancer chromatin mark, H3K27ac, is not skewed in a similar manner towards these two locations, indicating that these regions are not super-enhancers”
From The transcriptional cofactor TRIM33 prevents apoptosis in B lymphoblastic leukemia by deactivating a single enhancer (2015) · cites this paper as Hnisz et al., 2013
The Results section, “Super-enhancers in many cell types” (page unavailable), supports using H3K27ac to identify super-enhancers. It does not report H3K27ac levels at Bim -117 or Atp1b3 -35, so it cannot verify the conclusion about those specific regions. (LLM, conf=0.87)
Experimental — accuracy not yet measuredSuper-enhancers commonly drive high-level expression of tissue-specific genes, including miRNA genes, with evolutionarily conserved cell type-specific function.
“Super-enhancers commonly drive high-level expression of tissue-specific genes, including miRNA genes, with evolutionarily conserved cell type-specific function11–13.”
From Gain-of-function mutation of microRNA-140 in human skeletal dysplasia (2019) · cites this paper as [13]
The Results section reports that super-enhancers drive high-level expression of associated genes, and the Discussion says those genes tend to have cell type-specific expression and include miRNAs. Our copy does not establish that their cell type-specific function is evolutionarily conserved (pages not provided). (LLM, conf=0.86)
Experimental — accuracy not yet measuredSEs in both HCC and TAN are associated with GO terms related to metabolic genes (e.g. CYP3A4, SLC38A4, IGFBP1).
“SEs in both HCC and TAN were associated with GO terms related to metabolic genes (e.g. CYP3A4, SLC38A4, and IGFBP1) (Fig. 2c)20,21,58.”
From Multi-omic analysis of hepatocellular carcinoma reveals aberrant cis-regulatory changes and dysregulated retrotransposons with prognostic potential (2025) · cites this paper as [20]
In Results, ‘Super-enhancers in many cell types,’ the paper reports that Gene Ontology analysis links super-enhancer-associated genes to cell- and tissue-defining biological processes. It does not report this GO finding for both HCC and tumor-adjacent normal tissue (TAN), or identify metabolic terms or the three named genes in that comparison. The copy provides section labels but no page numbers. (LLM, conf=0.79)
Experimental — accuracy not yet measuredSuper-enhancers, which are clusters of several enhancers, play a key role in activating genes that define cell identity.
“Clusters of multiple enhancers, referred to as super enhancers, are particularly important in driving the expression of cell identity genes (6).”
From Brain cell type–specific enhancer–promoter interactome maps and disease <b>-</b> risk association (2019) · cites this paper as [6]
Many Hep-IDCONNECT TFs, including NR1H3 and THRB, do not display typically used features to define hepatocyte identity TFs such as hepatocyte-specific expression and association with super-enhancers.
“Many Hep‐IDCONNECT TFs, including NR1H3 and THRB, do not display typically used features to define hepatocyte identity TFs such as hepatocyte‐specific expression and association with super‐enhancers (Hnisz et al, 2013; Dubois et al, 2020a; Table EV3).”
From An extended transcription factor regulatory network controls hepatocyte identity (2023) · cites this paper as Hnisz et al, 2013
Some enhancers reside in clusters of a handful to even hundreds ('super enhancers'), whereas many are solo.
“Some enhancers reside in clusters of a handful116 to even hundreds (‘super enhancers’76,117), whereas many are solo.”
From Towards a comprehensive catalogue of validated and target-linked human enhancers (2020) · cites this paper as [117]
Liver-restricted TFs (C/EBPα/β, HNF1A, HNF4A), pioneering TFs (CEBPα/β, FOXA2, FOXA3), and Wnt-signaling TFs (TCF7) bind at individual GPC3 constituent enhancers.
“we detected binding of liver-restricted TFs (C/EBPα/β, HNF1A, and HNF4A), pioneering TFs (CEBPα/β, FOXA2, and FOXA3), and Wnt-signaling TFs (TCF7) at individual constituent enhancers (Fig. 3b)20,21.”
From Multi-omic analysis of hepatocellular carcinoma reveals aberrant cis-regulatory changes and dysregulated retrotransposons with prognostic potential (2025) · cites this paper as [20]
The Results section ('Transcription factors in ESCs'; page unavailable) reports transcription-factor enrichment at ESC super-enhancers, including the Wnt-pathway factor Tcf3, but not binding at GPC3 enhancers. Searches for GPC3 and the named liver, pioneer, and Wnt-signaling factors found no passage addressing the specific binding claim. (LLM, conf=0.76)
Experimental — accuracy not yet measuredH3K27M participates in the formation of super enhancer-like elements.
“suggesting that H3K27M participates in the formation of super enhancer-like elements purported to play a key role in cancer14.”
From Therapeutic targeting of polycomb and BET bromodomain proteins in diffuse intrinsic pontine gliomas (2017) · cites this paper as [14]
The majority of disease-associated non-coding variation occurs in the vicinity of enhancers and thus likely impacts these enhancers' target genes.
“This mystery, which we will call the enhancer-gene specificity conundrum, is important to solve because the majority of disease-associated non-coding variation occurs in the vicinity of enhancers and thus likely impacts these enhancers’ target genes (Ernst et al., 2011; Farh et al., 2015; Hnisz et al., 2013; Maurano et al., 2012).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Hnisz et al., 2013
Tens of thousands of non-coding genetic variants have been linked with various human diseases and traits in genome-wide association studies (GWAS), and the majority of these variants occur in enhancers.
“Tens of thousands of non-coding genetic variants have been linked with various human diseases and traits in genome-wide association studies (GWAS), and the majority of these variants occur in enhancers (Ernst et al., 2011; Farh et al., 2015; Hnisz et al., 2013; Maurano et al., 2012).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Hnisz et al., 2013
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Partitioning heritability by functional annotation using genome-wide association summary statistics
ReproGen Consortium, Finucane, H. K., Schizophrenia Working Group of the Psychiatric Genomics Consortium, The RACI Consortium, Bulik-Sullivan, B., Gusev, A., Trynka, G., Reshef, Y., Loh, P.-R., Anttila, V., et al. (2015) · Nature Genetics · doi:10.1038/ng.3404 · Cited by 2,604 · see citing works
Coactivator condensation at super-enhancers links phase separation and gene control
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Long non-coding RNAs: definitions, functions, challenges and recommendations
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Genetic and epigenetic fine mapping of causal autoimmune disease variants
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Cohesin Loss Eliminates All Loop Domains
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A Phase Separation Model for Transcriptional Control
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Self-citationTOX transcriptionally and epigenetically programs CD8+ T cell exhaustion
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Association analysis identifies 65 new breast cancer risk loci
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Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin
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An environment-dependent transcriptional network specifies human microglia identity
Gosselin, D., Skola, D., Coufal, N. G., Holtman, I. R., Schlachetzki, J. C. M., Sajti, E., Jaeger, B. N., O’Connor, C., Fitzpatrick, C., Pasillas, M. P., et al. (2017) · Science · doi:10.1126/science.aal3222 · Cited by 1,220 · see citing works
Transcriptional Addiction in Cancer
Bradner, J. E., Hnisz, D., & Young, R. A. (2017) · Cell · doi:10.1016/j.cell.2016.12.013 · Cited by 1,188 · see citing works
Self-citationRegulatory T Cells and Human Disease
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Activation of proto-oncogenes by disruption of chromosome neighborhoods
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“Active oncogenes are often associated with super-enhancers (17, 18), and we found that 13 of the 27 active T-ALL Pathogenesis Genes associated with super-enhancers (Fig.”
BackgroundSelf-citationThe selection and function of cell type-specific enhancers
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Kinase inhibitors: the road ahead
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Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes
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Self-citationEver-Changing Landscapes: Transcriptional Enhancers in Development and Evolution
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The Mediator complex: a central integrator of transcription
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Discovery of a selective catalytic p300/CBP inhibitor that targets lineage-specific tumours
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Getting up to speed with transcription elongation by RNA polymerase II
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A compendium of chromatin contact maps reveals spatially active regions in the human genome
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The Mechanisms behind the Therapeutic Activity of BET Bromodomain Inhibition
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Liquid-Liquid Phase Separation in Disease.
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Targeting transcription regulation in cancer with a covalent CDK7 inhibitor
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Self-citationContextual determinants of TGFβ action in development, immunity and cancer
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Brain cell type–specific enhancer–promoter interactome maps and disease <b>-</b> risk association
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An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element
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CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells
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Long Noncoding RNAs in Cardiovascular Diseases
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Structural variation in the 3D genome
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Liquid–liquid phase separation in human health and diseases
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BRD4 and Cancer: going beyond transcriptional regulation
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Enhancers as non-coding RNA transcription units: recent insights and future perspectives
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Human body epigenome maps reveal noncanonical DNA methylation variation
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Pol II phosphorylation regulates a switch between transcriptional and splicing condensates
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Self-citationFunctional annotation of native enhancers with a Cas9–histone demethylase fusion
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RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer
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Loss of epigenetic information as a cause of mammalian aging
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Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma
Northcott, P. A., Lee, C., Zichner, T., Stütz, A. M., Erkek, S., Kawauchi, D., Shih, D. J. H., Hovestadt, V., Zapatka, M., Sturm, D., et al. (2014) · Nature · doi:10.1038/nature13379 · Cited by 642 · see citing works
CDK7 Inhibition Suppresses Super-Enhancer-Linked Oncogenic Transcription in MYCN-Driven Cancer
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Self-citationResponse and resistance to BET bromodomain inhibitors in triple-negative breast cancer
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Self-citationNF-κB Directs Dynamic Super Enhancer Formation in Inflammation and Atherogenesis
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Epigenetics and epigenomics in diabetic kidney disease and metabolic memory
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Transcription regulation by the Mediator complex
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Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology
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Genome-wide analysis identifies NR4A1 as a key mediator of T cell dysfunction
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Mechanisms of Jak/STAT Signaling in Immunity and Disease
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Neuroblastoma is composed of two super-enhancer-associated differentiation states
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Glioma epigenetics: From subclassification to novel treatment options
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Absence of a simple code: how transcription factors read the genome
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Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits
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H3K4me3 breadth is linked to cell identity and transcriptional consistency
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A DNA Hypomethylation Signature Predicts Antitumor Activity of LSD1 Inhibitors in SCLC
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Epigenetic control of CD8+ T cell differentiation
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Partitioning of cancer therapeutics in nuclear condensates
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Self-citationParkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression
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Heterogeneity of neuroblastoma cell identity defined by transcriptional circuitries
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Looping Back to Leap Forward: Transcription Enters a New Era
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Transcription factor trapping by RNA in gene regulatory elements
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Self-citationOverview of Histone Modification
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Cancer epigenetics: Moving forward
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Therapeutic targeting of polycomb and BET bromodomain proteins in diffuse intrinsic pontine gliomas
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CDK7-Dependent Transcriptional Addiction in Triple-Negative Breast Cancer
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Self-citationBET Proteins as Targets for Anticancer Treatment
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Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers
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Self-citationRole of non-coding sequence variants in cancer
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RNA Exosome-Regulated Long Non-Coding RNA Transcription Controls Super-Enhancer Activity
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Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas
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Editing the epigenome: technologies for programmable transcription and epigenetic modulation
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MYC Deregulation in Primary Human Cancers
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Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler
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The 3D genome in transcriptional regulation and pluripotency
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Liquid–liquid phase separation drives cellular function and dysfunction in cancer
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Targeting Transcriptional Addictions in Small Cell Lung Cancer with a Covalent CDK7 Inhibitor
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Self-citationThe Nature of Embryonic Stem Cells
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- Authors
- Hnisz, D., Abraham, B. J., Lee, T. I., Lau, A., Saint-André, V., Sigova, A. A., Hoke, H. A., & Young, R. A.
- Affiliations
- Whitehead Institute for Biomedical Research (US)
- Corresponding author
- Young, Richard A.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2013-11
- Volume
- 155
- Issue
- 4
- Pages
- 934-947
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3841062
- OpenAlex
- W2004966039
- Cited by
- 3,662
- References
- 164
- Citations by year
- 2026: 182 · 2025: 294 · 2024: 332 · 2023: 321 · 2022: 360 · 2021: 406 · 2020: 331 · 2019: 315 · 2018: 291 · 2017: 259 · 2016: 232 · 2015: 215 · 2014: 110 · 2013: 5
- FWCI
- 83.97
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- HAL (submittedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-nd)
- PMC
- Funders
- University of California
- National Institutes of Health (CA146445, HG002668, CA109901, P30AG10161, R01AG36042, R01AG17917, RC2AG36547)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- super-enhancers, enhancers, cell identity, transcription factors, chromatin regulators, embryonic stem cells, oncogenes, cancer, enhancer transcription, human cell types
- MeSH terms
- Animals, Chromatin, Enhancer Elements, Genetic, Humans, Neoplasms, RNA Polymerase II, Transcription Factors, Transcription, Genetic, Polymorphism, Single Nucleotide, Embryonic Stem Cells
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