ArticleGenome biology2016
Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 123 papers, 1 of them a synthesis that pooled it.
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Who cites it
123 citing papers in PubMed, 1 synthesis or guideline pooled it, 219 citations in OpenAlex.
- Bibliometric analysis of evolutionary trends and hotspots of super-enhancers in cancer.Frontiers in pharmacology · 2023Pooled it
- Article
- Epigenetic biomarkers in inflammatory bowel diseases-computational challenges and opportunities.Journal of Crohn's & colitis · 2026Review
- DNMT1 loss leads to hypermethylation of a subset of late replicating domains by DNMT3A.PLoS genetics · 2026Article
- Epigenetic Gatekeeping of Intestinal Stem Cell Transformation.bioRxiv : the preprint server for biology · 2026Article
- Epigenetic profiling reveals key super-enhancer networks driving oncogenesis in HPV-positive HNSCC.iScience · 2025Article
- Comparison of current methods for genome-wide DNA methylation profiling.Epigenetics & chromatin · 2025Article
- Article
- Tracing regulatory element networks using epigenetic traits to identify key transcription factors: TENET R/Bioconductor package.Bioinformatics (Oxford, England) · 2025Article
- Insight into the role of DNA methylation in prognosis and treatment response prediction of gastrointestinal cancers.Epigenomics · 2025Review
- Heterogeneity in Cancer.Cancers · 2025Review
- DNA methylation in mammalian development and disease.Nature reviews. Genetics · 2025Review
- Targeting super-enhancers in liver cancer: from pathogenic mechanisms to clinical applications.Frontiers in pharmacology · 2025Review
- Super-enhancer DNA methylation in cancer: the mechanism of action and therapeutic directions.Frontiers in oncology · 2025Review
- Dissecting the Kaiso binding profile in clear renal cancer cells.Epigenetics & chromatin · 2024Article
- Deciphering the role of LOC124905135-related non-coding RNA cluster in human cancers: A comprehensive review.Heliyon · 2024Review
- Genome-wide methylation profiling reveals extracellular vesicle DNA as an ex vivo surrogate of cancer cell-derived DNA.Scientific reports · 2024Article
- Unraveling the key role of chromatin structure in cancer development through epigenetic landscape characterization of oral cancer.Molecular cancer · 2024Article
- Radiogenomic profiling of global DNA methylation associated with molecular phenotypes and immune features in glioma.BMC medicine · 2024Article
- Genome-wide screening and functional validation of methylation barriers near promoters.Nucleic acids research · 2024Article
63 more citing papers are in PubMed but not listed here.
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Authors and funding
20 authors at 7 institutions in 3 countries.
Funding
Abstract
backgroundOne of the hallmarks of cancer is the disruption of gene expression patterns. Many molecular lesions contribute to this phenotype, and the importance of aberrant DNA methylation profiles is increasingly recognized. Much of the research effort in this area has examined proximal promoter regions and epigenetic alterations at other loci are not well characterized.
resultsUsing whole genome bisulfite sequencing to examine uncharted regions of the epigenome, we identify a type of far-reaching DNA methylation alteration in cancer cells of the distal regulatory sequences described as super-enhancers. Human tumors undergo a shift in super-enhancer DNA methylation profiles that is associated with the transcriptional silencing or the overactivation of the corresponding target genes. Intriguingly, we observe locally active fractions of super-enhancers detectable through hypomethylated regions that suggest spatial variability within the large enhancer clusters. Functionally, the DNA methylomes obtained suggest that transcription factors contribute to this local activity of super-enhancers and that trans-acting factors modulate DNA methylation profiles with impact on transforming processes during carcinogenesis.
conclusionsWe develop an extensive catalogue of human DNA methylomes at base resolution to better understand the regulatory functions of DNA methylation beyond those of proximal promoter gene regions. CpG methylation status in normal cells points to locally active regulatory sites at super-enhancers, which are targeted by specific aberrant DNA methylation events in cancer, with putative effects on the expression of downstream genes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.