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Bivalent Regions of Cytosine Methylation and H3K27 Acetylation Suggest an Active Role for DNA Methylation at Enhancers

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Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells

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The emerging role of super enhancer-derived noncoding RNAs in human cancer

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Stress-induced RNA–chromatin interactions promote endothelial dysfunction

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Cornelia de Lange syndrome: from molecular diagnosis to therapeutic approach

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Overexpression of the cohesin-core subunit SMC1A contributes to colorectal cancer development

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Mechanisms of Enhancer-Promoter Interactions in Higher Eukaryotes

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The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops

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A genetic disorder reveals a hematopoietic stem cell regulatory network co-opted in leukemia

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Genetic Dissection of a Super Enhancer Controlling the Nppa-Nppb Cluster in the Heart

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Hippo-YAP signaling controls lineage differentiation of mouse embryonic stem cells through modulating the formation of super-enhancers

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Positive Regulation of Estrogen Receptor Alpha in Breast Tumorigenesis

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Batf-mediated Epigenetic Control of Effector CD8+ T Cell Differentiation

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The multifaceted roles of cohesin in cancer

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Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer

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High-resolution genome topology of human retina uncovers super enhancer-promoter interactions at tissue-specific and multifactorial disease loci

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A model of active transcription hubs that unifies the roles of active promoters and enhancers

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Super-Enhancers, Phase-Separated Condensates, and 3D Genome Organization in Cancer

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Condensins and cohesins – one of these things is not like the other!

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Dynamic CpG methylation delineates subregions within super-enhancers selectively decommissioned at the exit from naive pluripotency

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Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions

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Super-enhancers complexes zoom in transcription in cancer

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Bidirectional epigenetic editing reveals hierarchies in gene regulation

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Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9

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A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer

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The sirtuin-associated human senescence program converges on the activation of placenta-specific gene PAPPA.

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Mapping the evolving landscape of super-enhancers during cell differentiation

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Phase Separation and Transcription Regulation: Are Super-Enhancers and Locus Control Regions Primary Sites of Transcription Complex Assembly?

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Fra-1 regulates its target genes via binding to remote enhancers without exerting major control on chromatin architecture in triple negative breast cancers

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An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo

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Loop competition and extrusion model predicts CTCF interaction specificity

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Identification of a modular super-enhancer in murine retinal development

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Nuclear compartmentalization, dynamics, and function of regulatory DNA sequences

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CRISPRi links COVID-19 GWAS loci to LZTFL1 and RAVER1

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PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and RNA polymerase pause release at select gene targets

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Primordial super-enhancers: heat shock-induced chromatin organization in yeast

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Integrative analysis of liver-specific non-coding regulatory SNPs associated with the risk of coronary artery disease

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Regulation of Transcription Factor NF-κB in Its Natural Habitat: The Nucleus

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The 3D Genome as a Target for Anticancer Therapy

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Multiple mechanisms regulate H3 acetylation of enhancers in response to thyroid hormone

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The androgen receptor is a therapeutic target in desmoplastic small round cell sarcoma

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Cohesin-mediated 3D contacts tune enhancer-promoter regulationPreprint

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Super-enhancers and novel therapeutic targets in colorectal cancer

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Progressing super-enhancer landscape during mammary differentiation controls tissue-specific gene regulation

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Single-cell chromatin accessibility identifies enhancer networks driving gene expression during spinal cord development in mouse

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Super-Enhancers and CTCF in Early Embryonic Cell Fate Decisions

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Dysregulated Transcriptional Control in Prostate Cancer

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Multimodal regulatory elements within a hormone-specific super enhancer control a heterogeneous transcriptional response

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Broad H3K4me3 domains: Maintaining cellular identity and their implication in super‐enhancer hijacking

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Spatial promoter–enhancer hubs in cancer: organization, regulation, and function

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The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance

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Super enhancers—Functional cores under the 3D genome

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Dynamic 3D genome reorganization during development and metabolic stress of the porcine liver

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H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactionsPreprint

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Applications of single-cell genomics and computational strategies to study common disease and population-level variationPreprint

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Impact of 3D genome organization, guided by cohesin and CTCF looping, on sex-biased chromatin interactions and gene expression in mouse liver

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Distinct IL‐1α‐responsive enhancers promote acute and coordinated changes in chromatin topology in a hierarchical manner

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A set of accessible enhancers enables the initial response of breast cancer cells to physiological progestin concentrations

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HDAC4 influences the DNA damage response and counteracts senescence by assembling with HDAC1/HDAC2 to control H2BK120 acetylation and homology-directed repair

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Clinical Efficacy of a Novel Therapeutic Principle, Anakoinosis

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Understanding the function of regulatory DNA interactions in the interpretation of non-coding GWAS variants

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Characterization of a functional endothelial super-enhancer that regulates ADAMTS18 and angiogenesis

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Chromatin Rewiring by Mismatch Repair Protein MSH2 Alters Cell Adhesion Pathways and Sensitivity to BET Inhibition in Gastric Cancer

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Enhanced transcriptional heterogeneity mediated by NF-κB super-enhancers

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Analysis of super-enhancer using machine learning and its application to medical biology

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Super-Enhancers and Their Parts: From Prediction Efforts to Pathognomonic Status

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Unraveling three-dimensional chromatin structural dynamics during spermatogonial differentiation

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Activity-by-Contact model of enhancer specificity from thousands of CRISPR perturbationsPreprint

Fulco, C. P., Nasser, J., Jones, T. R., Munson, G., Bergman, D. T., Subramanian, V., Grossman, S. R., Anyoha, R., Patwardhan, T. A., Nguyen, T. H., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/529990 · Cited by 21 · see citing works

Super-enhancers require a combination of classical enhancers and novel facilitator elements to drive high levels of gene expressionPreprint

Blayney, J., Francis, H. S., Camellato, B. R., MITCHELL, L. A., Stolper, R. J., Boeke, J. D., Higgs, D. R., & Kassouf, M. T. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.20.496856 · Cited by 21 · see citing works

Genome-wide chromatin contacts of super-enhancer-associated lncRNA identify LINC01013 as a regulator of fibrosis in the aortic valve

Chignon, A., Argaud, D., Boulanger, M.-C., Mkannez, G., Bon-Baret, V., Li, Z.-L., Thériault, S., Bossé, Y., & Mathieu, P. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010010 · Cited by 17 · see citing works

A distant global control region is essential for normal expression of anterior HOXA genes during mouse and human craniofacial development

Wilderman, A. S., D’haene, E., Baetens, M., Yankee, T. N., Winchester, E. W., Glidden, N. C., Roets, E., Dorpe, J. V., Janssens, S., Miller, D. E., et al. (2024) · Nature Communications · doi:10.1038/s41467-023-44506-2 · Cited by 21 · see citing works

The SNP of rs6854845 suppresses transcription via the DNA looping structure alteration of super-enhancer in colon cells

Cong, Z., Li, Q., Yang, Y., Guo, X., Cui, L., & You, T. (2019) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2019.04.190 · Cited by 20 · see citing works

NR2F2 Orphan Nuclear Receptor is Involved in Estrogen Receptor Alpha-Mediated Transcriptional Regulation in Luminal A Breast Cancer Cells

Erdős, E., & Bálint, B. L. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21061910 · Cited by 19 · see citing works

Integrated high-throughput analysis identifies super enhancers associated with chemoresistance in SCLC

Bao, J., Li, M., Liang, S., Yang, Y., Wu, J., Zou, Q., Fang, S., Chen, S., & Guo, L. (2019) · BMC Medical Genomics · doi:10.1186/s12920-019-0520-9 · Cited by 19 · see citing works

The structural and functional roles of CTCF in the regulation of cell type-specific and human disease-associated super-enhancers

Shin, H. Y. (2018) · Genes & Genomics · doi:10.1007/s13258-018-0768-z · Cited by 17 · see citing works

Dissecting Tissue-Specific Super-Enhancers by Integrating Genome-Wide Analyses and CRISPR/Cas9 Genome Editing

Yoo, K. H., Hennighausen, L. G., & Shin, H. Y. (2018) · Journal of Mammary Gland Biology and Neoplasia · doi:10.1007/s10911-018-9417-z · Cited by 18 · see citing works

Disruption of Broad Epigenetic Domains in PDAC Cells by HAT Inhibitors

Gerrard, D., Boyd, J. R., Stein, G., Jin, V. X., & Frietze, S. E. (2019) · Epigenomes · doi:10.3390/epigenomes3020011 · Cited by 19 · see citing works

CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions

Stuart, W. D., Guo, M., Fink-Baldauf, I. M., Coleman, A. M., Clancy, J. P., Mall, M. A., Lim, F. Y., Brewington, J. J., & Maeda, Y. (2020) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqaa036 · Cited by 16 · see citing works

Molecular basis for SOX2-dependent regulation of super-enhancer activity

Yoo, W., Song, Y. W., Kim, J., Ahn, J., Kim, J., Shin, Y., Ryu, J., & Kim, K. K. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad908 · Cited by 16 · see citing works

Single-cell 3D genome imaging shows super-enhancer hubs are rare, nonspecific, and neither necessary nor sufficient for transcriptional bursting

Le, D. J., Hafner, A., Venkatesh, A. R., Udomlumleart, T., Gaddam, S., Novačić, A., Wang, K., & Boettiger, A. N. (2026) · Cell Genomics · doi:10.1016/j.xgen.2026.101331 · Cited by 1 · see citing works

Bioinformatics Pipelines for Identification of Super-Enhancers and 3D Chromatin Contacts

Sakashita, A., Takeuchi, C., Maezawa, S., & Namekawa, S. H. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2724-2_9 · Cited by 3 · see citing works

Specialised super-enhancer networks in stem cells and neuronsPreprint

Harabula, I., Speakman, L., Musella, F., Fiorillo, L., Zea-Redondo, L., Kukalev, A., Beagrie, R. A., Morris, K. J., Fernandes, L., Irastorza-Azcárate, I., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.08.13.670083

Super-enhancers in immune system regulation: mechanisms, pathological reprogramming, and therapeutic opportunities

Lai, X., Li, C., Tang, X., Luo, X., Wu, F., Liang, Y., Huang, B., & Li, H. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1652398 · Cited by 4 · see citing works

Super-enhancers in transcriptional regulation and genome organization

Wang, X., Cairns, M. J., & Yan, J. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1038 · Cited by 154 · see citing works