ArticleBMC genomics2018
An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers, 5 of them syntheses that pooled it.
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Who cites it
37 citing papers in PubMed, 5 syntheses or guidelines pooled it, 54 citations in OpenAlex.
- Epigenome-wide meta-analysis of BMI in nine cohorts: Examining the utility of epigenetically predicted BMI.American journal of human genetics · 2023Pooled it
- Cord blood epigenome-wide meta-analysis in six European-based child cohorts identifies signatures linked to rapid weight growth.BMC medicine · 2023Pooled it
- Epigenome-wide meta-analysis identifies DNA methylation biomarkers associated with diabetic kidney disease.Nature communications · 2022Pooled it
- Meta-analyses identify DNA methylation associated with kidney function and damage.Nature communications · 2021Pooled it
- Epigenome-wide association study of diet quality in the Women's Health Initiative and TwinsUK cohort.International journal of epidemiology · 2021Pooled it
- Expression quantitative trait methylation across multiple cancer types with functional and therapeutic characterization using Onco-eQTM.NAR genomics and bioinformatics · 2026Article
- Genome-wide DNA methylation analysis revealed epigenetic mechanism underlying end-stage renal disease.Nature communications · 2026Article
- Blood DNA methylation markers are associated with diabetic kidney disease progression in type 1 diabetes.Diabetologia · 2026Article
- Brain DNA Methylation Atlas of AppAging cell · 2025Article
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- Using Callus as an Ex Vivo System for Chromatin Analysis.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Epigenetic landscape of 5-hydroxymethylcytosine and associations with gene expression in placenta.Epigenetics · 2024Article
- Lack of SMARCB1 expression characterizes a subset of human and murine peripheral T-cell lymphomas.Nature communications · 2024Article
- Torch-eCpG: a fast and scalable eQTM mapper for thousands of molecular phenotypes with graphical processing units.BMC bioinformatics · 2024Article
- Genome-wide methylomic regulation of multiscale gene networks in Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2023Article
- Modulating epigenetic modifications for cancer therapy (Review).Oncology reports · 2023Review
- Gastrointestinal Symptom Cluster is Associated With Epigenetic Regulation of Lymphotoxin Beta in Oncology Patients Receiving Chemotherapy.Biological research for nursing · 2023Article
- Large-scale integration of DNA methylation and gene expression array platforms identifies bothEpigenetics · 2022Article
- Clonal hematopoiesis of indeterminate potential, DNA methylation, and risk for coronary artery disease.Nature communications · 2022Article
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundGene expression can be influenced by DNA methylation 1) distally, at regulatory elements such as enhancers, as well as 2) proximally, at promoters. Our current understanding of the influence of distal DNA methylation changes on gene expression patterns is incomplete. Here, we characterize genome-wide methylation and expression patterns for ~ 13 k genes to explore how DNA methylation interacts with gene expression, throughout the genome.
resultsWe used a linear mixed model framework to assess the correlation of DNA methylation at ~ 400 k CpGs with gene expression changes at ~ 13 k transcripts in two independent datasets from human blood cells. Among CpGs at which methylation significantly associates with transcription (eCpGs), > 50% are distal (> 50 kb) or trans (different chromosome) to the correlated gene. Many eCpG-transcript pairs are consistent between studies and ~ 90% of neighboring eCpGs associate with the same gene, within studies. We find that enhancers (P < 5e-18) and microRNA genes (P = 9e-3) are overrepresented among trans eCpGs, and insulators and long intergenic non-coding RNAs are enriched among cis and distal eCpGs. Intragenic-eCpG-transcript correlations are negative in 60-70% of occurrences and are enriched for annotated gene promoters and enhancers (P < 0.002), highlighting the importance of intragenic regulation. Gene Ontology analysis indicates that trans eCpGs are enriched for transcription factor genes and chromatin modifiers, suggesting that some trans eCpGs represent the influence of gene networks and higher-order transcriptional control.
conclusionsThis work sheds new light on the interplay between epigenetic changes and gene expression, and provides useful data for mining biologically-relevant results from epigenome-wide association studies.
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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.