ArticleBMC medical genomics2016
Frequent hypermethylation of orphan CpG islands with enhancer activity in cancer.
Article in BMC medical genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Profiling the immune epigenome across global cattle breeds.Genome biology · 2023Article
- DNA Methylation Analysis Reveals Distinct Patterns in Satellite Cell-Derived Myogenic Progenitor Cells of Subjects with Spastic Cerebral Palsy.Journal of personalized medicine · 2022Article
- Prognostic and therapeutic prediction by screening signature combinations from transcriptome-methylome interactions in oral squamous cell carcinoma.Scientific reports · 2022Article
- Association of DNA methylation and genetic variations of theBiomedical reports · 2022Article
- A bipartite element with allele-specific functions safeguards DNA methylation imprints at the Dlk1-Dio3 locus.Developmental cell · 2021Article
- Super Enhancer Profiles Identify Key Cell Identity Genes During Differentiation From Embryonic Stem Cells to Trophoblast Stem Cells Super Enhencers in Trophoblast Differentiation.Frontiers in genetics · 2021Article
- Simplified MethylRAD Sequencing to Detect Changes in DNA Methylation at Enhancer Elements in Differentiating Embryonic Stem Cells.Epigenomes · 2020Article
- Review
- DNA hypermethylation in disease: mechanisms and clinical relevance.Epigenetics · 2019Review
- Functional and topographic effects on DNA methylation in IDH1/2 mutant cancers.Scientific reports · 2019Article
- Review
- Differential Methylation inInternational journal of molecular sciences · 2019Article
- Continuous Developmental and Early Life Trichloroethylene Exposure Promoted DNA Methylation Alterations in Polycomb Protein Binding Sites in Effector/Memory CD4Frontiers in immunology · 2019Article
- DNA methylation of TOMM40-APOE-APOC2 in Alzheimer's disease.Journal of human genetics · 2018Article
- Orphan CpG islands define a novel class of highly active enhancers.Epigenetics · 2017Article
- Methylation of kruppel-like factor 2 (KLF2) associates with its expression and non-small cell lung cancer progression.American journal of translational research · 2017Article
- Regulation of glutamate transport and neuroinflammation in a term newborn rat model of hypoxic-ischaemic brain injury.Brain and neuroscience advancesArticle
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCpG islands (CGIs) are interspersed DNA sequences that have unusually high CpG ratios and GC contents. CGIs are typically located in the promoter of protein-coding genes. They normally lack DNA methylation but become hypermethylated and induce repression of associated genes in cancer. However, the biological functions of non-promoter CGIs (orphan CGIs) largely remain unclear.
resultsHere, we identify orphan CGIs that do not map to the promoter of any protein-coding or non-coding transcripts but possess chromatin and transcriptional marks that reflect enhancer activity (termed eCGIs). They exhibit three-dimensional chromatin looping toward multiple target genes with high affinity. Intriguingly, transcription regulators were frequently associated with such CGI-containing enhancers. Remarkably, our analyses in cell lines and clinical tissues showed that eCGIs have more dynamic DNA methylation changes in cancer relative to promoter CGIs. The observed eCGI hypermethylation was accompanied by a loss of enhancer marks and transcriptional inactivation of the target genes.
conclusionOur results suggest that eCGIs may constitute a distinct class of enhancers and perform a more instrumental role in tumorigenesis than typical CGIs in gene promoters.
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