ArticleGenome biology2014
The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 270 papers, 7 of them syntheses that pooled it.
What it found
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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.
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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.
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Who cites it
270 citing papers in PubMed, 7 syntheses or guidelines pooled it, 465 citations in OpenAlex.
- Integrating genome-wide and epigenome-wide associations for antipsychotic induced extrapyramidal side effects.Psychopharmacology · 2026Pooled it
- Pooled it
- RNAAgeCalc: A multi-tissue transcriptional age calculator.PloS one · 2020Pooled it
- Human Dermal Fibroblast: A Promising Cellular Model to Study Biological Mechanisms of Major Depression and Antidepressant Drug Response.Current neuropharmacology · 2020Pooled it
- A DNA methylation biomarker of alcohol consumption.Molecular psychiatry · 2018Pooled it
- Genetically defined elevated homocysteine levels do not result in widespread changes of DNA methylation in leukocytes.PloS one · 2017Pooled it
- Breastfeeding effects on DNA methylation in the offspring: A systematic literature review.PloS one · 2017Pooled it
- Impact of a diet and activity health promotion intervention on regional patterns of DNA methylation.Clinical epigenetics · 2019Trial
- Co-occurring expression and methylation QTLs allow detection of common causal variants and shared biological mechanisms.Nature communications · 2018Trial
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- Integration of DNA methylation and gene expression analysis in Gephyrocapsa huxleyi provides insight into genes related to calcification.G3 (Bethesda, Md.) · 2026Article
- Dissecting epigenetic heterogeneity in single-cell DNA methylomes with a unified framework.Nature communications · 2026Article
- Whole-Genome Bisulfite Sequencing Identifies Blood-Based DNA Methylation Biomarker for Hepatocellular Carcinoma.Molecular carcinogenesis · 2026Article
- How epigenetic clocks tick: Unpacking the black box by deciphering biological pathways and transcriptomic signatures of accelerated aging.Research square · 2026Article
- Setd1a Loss-of-function Disrupts Epigenetic Regulation of Ribosomal Genes via Altered DNA Methylation.Schizophrenia bulletin · 2026Article
- Differential DNA-methylation of synaptic genes in CSF and blood in schizophrenia.Schizophrenia (Heidelberg, Germany) · 2026Article
- Astrocyte epigenetics in development, aging, and neurodegeneration: a DNA methylation perspective.Frontiers in molecular neuroscience · 2026Review
- Brain DNA Methylation Atlas of AppAging cell · 2025Article
210 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
6 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundDNA methylation plays an essential role in the regulation of gene expression. While its presence near the transcription start site of a gene has been associated with reduced expression, the variation in methylation levels across individuals, its environmental or genetic causes, and its association with gene expression remain poorly understood.
resultsWe report the joint analysis of sequence variants, gene expression and DNA methylation in primary fibroblast samples derived from a set of 62 unrelated individuals. Approximately 2% of the most variable CpG sites are mappable in cis to sequence variation, usually within 5 kb. Via eQTL analysis with microarray data combined with mapping of allelic expression regions, we obtained a set of 2,770 regions mappable in cis to sequence variation. In 9.5% of these expressed regions, an associated SNP was also a methylation QTL. Methylation and gene expression are often correlated without direct discernible involvement of sequence variation, but not always in the expected direction of negative for promoter CpGs and positive for gene-body CpGs. Population-level correlation between methylation and expression is strongest in a subset of developmentally significant genes, including all four HOX clusters. The presence and sign of this correlation are best predicted using specific chromatin marks rather than position of the CpG site with respect to the gene.
conclusionsOur results indicate a wide variety of relationships between gene expression, DNA methylation and sequence variation in untransformed adult human fibroblasts, with considerable involvement of chromatin features and some discernible involvement of sequence variation.
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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.