ArticlePLoS genetics2018
A survey of inter-individual variation in DNA methylation identifies environmentally responsive co-regulated networks of epigenetic variation in the human genome.
Article in PLoS genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers, 1 of them a synthesis that pooled it.
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Who cites it
37 citing papers in PubMed, 1 synthesis or guideline pooled it, 78 citations in OpenAlex.
- Exposure to arsenic at different life-stages and DNA methylation meta-analysis in buccal cells and leukocytes.Environmental health : a global access science source · 2021Pooled it
- Whole-genome DNA methylation analysis reveals distinct subtype characteristics in epithelial ovarian cancer.Cancer gene therapy · 2026Article
- Systematic investigation of interindividual variation of DNA methylation in human whole blood.Genome biology · 2026Article
- Genetic impacts on within-pair DNA methylation variance in monozygotic twins capture gene-environment interactions and cell-type effects.Genome biology · 2026Article
- RAMEN: Dissecting individual, additive and interactive gene-environment contributions to DNA methylome variability in cord blood.Genome biology · 2025Article
- Nonlethal, Epigenetic Age Estimation in a Freshwater Sportfish, Florida Bass (Ecology and evolution · 2025Article
- Epigenome-wide association study of BMI and waist-to-hip ratio and their associations with dietary patterns in Korean adults.Scientific reports · 2025Article
- Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes.Genome research · 2025Article
- Methylmap: visualization of modified nucleotides for large cohort sizes.BMC bioinformatics · 2025Article
- Unravelling the link between neurodevelopmental disorders and short tandem CGG-repeat expansions.Emerging topics in life sciences · 2023Review
- Rare genetic variants underlie outlying levels of DNA methylation and gene-expression.Human molecular genetics · 2023Article
- Epigenomic signatures reveal mechanistic clues and predictive markers for autism spectrum disorder.Molecular psychiatry · 2023Review
- Updates to data versions and analytic methods influence the reproducibility of results from epigenome-wide association studies.Epigenetics · 2022Article
- Tissue- and ethnicity-independent hypervariable DNA methylation states show evidence of establishment in the early human embryo.Nucleic acids research · 2022Article
- Pollution induces epigenetic effects that are stably transmitted across multiple generations.Evolution letters · 2022Article
- Cell-type-specific epigenomic variations associated withNAR genomics and bioinformatics · 2022Article
- Global DNA Methylation in Dental Implant Failure Due to Peri-Implantitis: An Exploratory Clinical Pilot Study.International journal of environmental research and public health · 2022Article
- JAK/STAT Signaling: Molecular Targets, Therapeutic Opportunities, and Limitations of Targeted Inhibitions in Solid Malignancies.Frontiers in pharmacology · 2022Review
- Genetic and in utero environmental contributions to DNA methylation variation in placenta.Human molecular genetics · 2021Article
- Revisiting genetic artifacts on DNA methylation microarrays exposes novel biological implications.Genome biology · 2021Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
While population studies have resulted in detailed maps of genetic variation in humans, to date there are few robust maps of epigenetic variation. We identified sites containing clusters of CpGs with high inter-individual epigenetic variation, termed Variably Methylated Regions (VMRs) in five purified cell types. We observed that VMRs occur preferentially at enhancers and 3' UTRs. While the majority of VMRs have high heritability, a subset of VMRs within the genome show highly correlated variation in trans, forming co-regulated networks that have low heritability, differ between cell types and are enriched for specific transcription factor binding sites and biological pathways of functional relevance to each tissue. For example, in T cells we defined a network of 95 co-regulated VMRs enriched for genes with roles in T-cell activation; in fibroblasts a network of 34 co-regulated VMRs comprising all four HOX gene clusters enriched for control of tissue growth; and in neurons a network of 18 VMRs enriched for roles in synaptic signaling. By culturing genetically-identical fibroblasts under varying environmental conditions, we experimentally demonstrated that some VMR networks are responsive to the environment, with methylation levels at these loci changing in a coordinated fashion in trans dependent on cellular growth. Intriguingly these environmentally-responsive VMRs showed a strong enrichment for imprinted loci (p<10-80), suggesting that these are particularly sensitive to environmental conditions. Our study provides a detailed map of common epigenetic variation in the human genome, showing that both genetic and environmental causes underlie this variation.
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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.