ArticleGenome biology2020
Genome-wide identification of genes regulating DNA methylation using genetic anchors for causal inference.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 2 of them syntheses that pooled it.
What it found
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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.
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Who cites it
24 citing papers in PubMed, 2 syntheses or guidelines pooled it, 47 citations in OpenAlex.
- Genome-wide study of DNA methylation shows alterations in metabolic, inflammatory, and cholesterol pathways in ALS.Science translational medicine · 2022Pooled it
- Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology.Nature genetics · 2021Pooled it
- Epigenetic dysregulation in osteonecrosis of the femoral head: a critical review of DNA methylation, histone modifications, and clinical translation.Journal of orthopaedic surgery and research · 2026Review
- The genetic basis for DNA methylation variation across tissues and development.Nature communications · 2026Article
- Identification of SENP7 and UTF1/VENTX as new loci influencing clustered protocadherin methylation across blood and brain using a genome-wide association study.Molecular psychiatry · 2026Article
- Genetic regulation of sperm DNA methylation in cattle through meQTL mapping.BMC genomics · 2025Article
- Editing epigenetic age.Nature aging · 2025Article
- CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses.Science advances · 2024Article
- Epigenetic Contributions to Clinical Risk Prediction of Cardiovascular Disease.Circulation. Genomic and precision medicine · 2024Article
- Developmental Dyslexia: Insights from EEG-Based Findings and Molecular Signatures-A Pilot Study.Brain sciences · 2024Article
- Linking Prenatal Environmental Exposures to Lifetime Health with Epigenome-Wide Association Studies: State-of-the-Science Review and Future Recommendations.Environmental health perspectives · 2023Review
- Article
- Unlocking the secrets: the power of methylation-based cfDNA detection of tissue damage in organ systems.Clinical epigenetics · 2023Review
- The inactive X chromosome accumulates widespread epigenetic variability with age.Clinical epigenetics · 2023Article
- Genome-wide methylomic regulation of multiscale gene networks in Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2023Article
- Quantitative trait locus (xQTL) approaches identify risk genes and drug targets from human non-coding genomes.Human molecular genetics · 2022Review
- Local CpG density affects the trajectory and variance of age-associated DNA methylation changes.Genome biology · 2022Article
- Functional genomics analysis identifies T and NK cell activation as a driver of epigenetic clock progression.Genome biology · 2022Article
- Genetic variation influencing DNA methylation provides insights into molecular mechanisms regulating genomic function.Nature genetics · 2022Article
- Master Transcription Regulators and Transcription Factors Regulate Immune-Associated Differences Between Patients of African and European Ancestry With Colorectal Cancer.Gastro hep advances · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors at 7 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDNA methylation is a key epigenetic modification in human development and disease, yet there is limited understanding of its highly coordinated regulation. Here, we identify 818 genes that affect DNA methylation patterns in blood using large-scale population genomics data.
resultsBy employing genetic instruments as causal anchors, we establish directed associations between gene expression and distant DNA methylation levels, while ensuring specificity of the associations by correcting for linkage disequilibrium and pleiotropy among neighboring genes. The identified genes are enriched for transcription factors, of which many consistently increased or decreased DNA methylation levels at multiple CpG sites. In addition, we show that a substantial number of transcription factors affected DNA methylation at their experimentally determined binding sites. We also observe genes encoding proteins with heterogenous functions that have widespread effects on DNA methylation, e.g., NFKBIE, CDCA7(L), and NLRC5, and for several examples, we suggest plausible mechanisms underlying their effect on DNA methylation.
conclusionWe report hundreds of genes that affect DNA methylation and provide key insights in the principles underlying epigenetic regulation.
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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.