SynthesisOncotarget2012
On the presence and role of human gene-body DNA methylation.
Synthesis in Oncotarget, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 303 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
303 citing papers in PubMed, 1 synthesis or guideline pooled it, 542 citations in OpenAlex.
- Disease classification for whole-blood DNA methylation: Meta-analysis, missing values imputation, and XAI.GigaScience · 2022Pooled it
- Epigenetic Changes Associated With a Phenotypic Transition in Namibian Cheetahs.Molecular ecology · 2026Article
- Genome-wide DNA methylation profiling of triple-negative breast cancer uncovers epigenetic biomarkers of tumor identity and the immune microenvironment.NPJ breast cancer · 2026Article
- Characteristics, Epigenetics, and Management of Non-Infectious Preterm Birth-Sterile Intrauterine Inflammation and Idiopathic Preterm Birth.Life (Basel, Switzerland) · 2026Review
- Postoperative delirium in hip fracture patients linked to epigenetic alterations in inflammatory and immune pathways: a genome-wide DNA methylation study.Translational psychiatry · 2026Article
- Epigenome-wide DNA methylation patterns associated with disease activity in systemic lupus erythematosus.Scientific reports · 2026Article
- Acute Hyperinsulinemia during Hyperinsulinemic- Euglycemic Clamp Influences DNA Methylation and Gene Expression in Peripheral Blood Cells of Adult Men.Diabetes & metabolism journal · 2026Article
- Identification of circadian rhythm-related genes in colorectal cancer by integrating bioinformatics and multi-omics mendelian randomization.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Epigenetics and chromatin structure regulateeLife · 2026Article
- Epigenomic methylome landscape of promoters in vertebrate genomes.bioRxiv : the preprint server for biology · 2026Article
- Promoter Methylation-Expression Coupling of Gliogenesis Genes inInternational journal of molecular sciences · 2026Article
- Epigenetics and chromatin structure regulatebioRxiv : the preprint server for biology · 2026Article
- Epigenome-wide analysis identifies DNA methylation signatures associated with the infant pupillary light reflex, a candidate intermediate phenotype for autism.Scientific reports · 2026Article
- Helios expression in naive CD4+ T cells decreases from neonates to older adults.Clinical and experimental immunology · 2026Article
- Genome-wide analysis of strand-specific transcription and DNA methylation inFrontiers in microbiology · 2026Article
- Multidimensional regulatory mechanisms and translational potential of epigenetic networks in the rheumatoid arthritis disease course.Frontiers in immunology · 2026Review
- Epigenome-Wide Search for Distinctive Methylation Biomarkers of Endothelial and Leukocyte DNA.Epigenomes · 2025Article
- Cell-type-specific DNA methylation dynamics in the prenatal and postnatal human cortex.Cell genomics · 2025Article
- Epigenome-wide association study of perceived discrimination in the Multi-Ethnic Study of Atherosclerosis (MESA).Epigenetics · 2025Article
- Epigenetic motifs distinguishing endogenous from exogenous retroviral integrants.Journal of virology · 2025Article
243 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation of promoter sequences is a repressive epigenetic mark that down-regulates gene expression. However, DNA methylation is more prevalent within gene-bodies than seen for promoters, and gene-body methylation has been observed to be positively correlated with gene expression levels. This paradox remains unexplained, and accordingly the role of DNA methylation in gene-bodies is poorly understood. We addressed the presence and role of human gene-body DNA methylation using a meta-analysis of human genome-wide methylation, expression and chromatin data sets. Methylation is associated with transcribed regions as genic sequences have higher levels of methylation than intergenic or promoter sequences. We also find that the relationship between gene-body DNA methylation and expression levels is non-monotonic and bell-shaped. Mid-level expressed genes have the highest levels of gene-body methylation, whereas the most lowly and highly expressed sets of genes both have low levels of methylation. While gene-body methylation can be seen to efficiently repress the initiation of intragenic transcription, the vast majority of methylated sites within genes are not associated with intragenic promoters. In fact, highly expressed genes initiate the most intragenic transcription inconsistent with the previously held notion that gene-body methylation serves to repress spurious intragenic transcription to allow for efficient transcriptional elongation. These observations lead us to propose a model to explain the presence of human gene-body methylation. This model holds that the repression of intragenic transcription by gene-body methylation is largely epiphenomenal, and suggests that gene-body methylation levels are predominantly shaped via the accessibility of the DNA to methylating enzyme complexes.
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What OpenQuestion holds
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.