ArticleNucleic acids research2017
Body-hypomethylated human genes harbor extensive intragenic transcriptional activity and are prone to cancer-associated dysregulation.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 41 citations in OpenAlex.
- PTPRN2 hypomethylation and PHB2-associated miR-153-3p maturation define dual epigenetic features linked to symptom variability in Myalgic encephalomyelitis.Journal of translational medicine · 2026Article
- XIST expression and hypermethylation of the X chromosome in males with systemic lupus erythematosus.Frontiers in immunology · 2026Article
- Oncogenic role of PMEPA1 and its association with immune exhaustion and TGF-β activation in HCC.JHEP reports : innovation in hepatology · 2024Article
- Epigenetics Research in Evolutionary Biology: Perspectives on Timescales and Mechanisms.Molecular biology and evolution · 2024Review
- DNA methylation differences between the female and male X chromosomes in human brain.bioRxiv : the preprint server for biology · 2024Article
- Investigation of the Proteasome 26S Subunit, ATPase Family Genes as Potential Prognostic Biomarkers and Therapeutic Targets for Hepatocellular Carcinoma.Cancer management and research · 2024Article
- New insights about endometriosis-associated ovarian cancer: pathogenesis, risk factors, prediction and diagnosis and treatment.Frontiers in oncology · 2024Review
- DNA Methylation Dynamics During Esophageal Epithelial Regeneration Following Repair with Acellular Silk Fibroin Grafts in Rat.Advanced biology · 2023Article
- Impact of chronic benzene poisoning on aberrant mitochondrial DNA methylation: A prospective observational study.Frontiers in public health · 2023Observational
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- Comparative DNA Methylome of Phytoplasma Associated Retrograde Metamorphosis in Sesame (Biology · 2022Article
- Alternative Splicing, Epigenetic Modifications and Cancer: A Dangerous Triangle, or a Hopeful One?Cancers · 2022Review
- Whole-Genome DNA Methylation Sequencing Reveals Epigenetic Changes in Myelodysplastic Syndromes.Frontiers in oncology · 2022Article
- Adenosine Kinase on Deoxyribonucleic Acid Methylation: Adenosine Receptor-Independent Pathway inFrontiers in pharmacology · 2022Review
- Genome-wide variation in DNA methylation linked to developmental stage and chromosomal suppression of recombination in white-throated sparrows.Molecular ecology · 2021Article
- Genome-Wide Open Chromatin Methylome Profiles in Colorectal Cancer.Biomolecules · 2020Article
- Differentially methylated gene patterns between age-matched sarcopenic and non-sarcopenic women.Journal of cachexia, sarcopenia and muscle · 2019Article
- DNA Analysis by Restriction Enzyme (DARE) enables concurrent genomic and epigenomic characterization of single cells.Nucleic acids research · 2019Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Genomic DNA methylation maps (methylomes) encode genetic and environmental effects as stable chemical modifications of DNA. Variations in DNA methylation, especially in regulatory regions such as promoters and enhancers, are known to affect numerous downstream processes. In contrast, most transcription units (gene bodies) in the human genome are thought to be heavily methylated. However, epigenetic reprogramming in cancer often involves gene body hypomethylation with consequences on gene expression. In this study, we focus on the relatively unexplored phenomenon that some gene bodies are devoid of DNA methylation under normal conditions. Utilizing nucleotide-resolution methylomes of diverse samples, we show that nearly 2000 human genes are commonly hypomethylated. Remarkably, these genes occupy highly specialized genomic, epigenomic, evolutionary and functional niches in our genomes. For example, hypomethylated genes tend to be short yet encode significantly more transcripts than expected based upon their lengths, include many genes involved in nucleosome and chromatin formation, and are extensively and significantly enriched for histone-tail modifications and transcription factor binding with particular relevance for cis-regulation. Furthermore, they are significantly more prone to cancer-associated hypomethylation and mutation. Consequently, gene body hypomethylation represents an additional layer of epigenetic regulatory complexity, with implications on cancer-associated epigenetic reprogramming.
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Registered trials
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.