ArticleNature genetics2024
The correlation between CpG methylation and gene expression is driven by sequence variants.
Article in Nature genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Article
- Silencing of optogenetic and chemogenetic transgenes in human iPSCs involves promoter methylation and methylation-independent mechanisms.Epigenetics · 2026Article
- DNA methylation variability provides a complementary epigenetic signature of aging heterogeneity: Findings from the Canadian Longitudinal Study on Aging and the Baltimore Longitudinal Study of Aging.bioRxiv : the preprint server for biology · 2026Article
- Decoding the sequence determinants of locus-specific DNA methylation across human tissues.Nature communications · 2026Article
- Epigenetic blind spots - the role of DNA methylation dynamics in stem cell-based models of embryogenesis.FEBS letters · 2026Article
- Nanopore sequencing identifies parent-of-origin specific age-associated methylation changes at imprinted loci in the human genome.Nature communications · 2026Article
- Monoallelic Gene Expression: Stochastic or Clonal? From Detection to Mechanisms and Clinical Significance.International journal of molecular sciences · 2026Review
- Integrative bioinformatics and experimental analysis identify S100A10 as a diagnostic and prognostic biomarker in pancreatic adenocarcinoma.Translational cancer research · 2026Article
- nanoASM: Long-Read Allele-Specific DNA Methylation Profiling Enables Functional Annotation of Regulatory Noncoding Variants in Human Prostate Tissues.bioRxiv : the preprint server for biology · 2026Article
- Epigenetic conditioning improves sequence-based modeling of gene regulation across cell types and alleles.bioRxiv : the preprint server for biology · 2026Article
- Long-read sequencing technologies and bioinformatics: a new perspective for decoding DNA methylation modifications.Journal of translational medicine · 2026Review
- Epigenetic landscapes in human pancreatic islets reveal distinct drivers for adaptation to age and type 2 diabetes.Nature communications · 2026Article
- The gene-like promoter and transcription of LTR retrotransposons.bioRxiv : the preprint server for biology · 2026Article
- The genetic basis for DNA methylation variation across tissues and development.Nature communications · 2026Article
- Methylation array signals are predictive of chronological age without bisulfite conversion.GeroScience · 2026Article
- Epigenetic adaptation of beta cells across lifespan and disease.Nature metabolism · 2026Article
- From chromosomal protein disorder to chromatin phase separation.Epigenetics & chromatin · 2026Review
- The involvement of TNFRSF25 in age-related hearing loss.Human genetics · 2026Article
- Dysregulation of neurodevelopmental regulatory networks in Anorexia Nervosa: an integrated multi-layered omics analysis.Frontiers in cell and developmental biology · 2026Article
- Genome-wide association study identifiesiScience · 2025Article
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Authors and funding
32 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene promoter and enhancer sequences are bound by transcription factors and are depleted of methylated CpG sites (cytosines preceding guanines in DNA). The absence of methylated CpGs in these sequences typically correlates with increased gene expression, indicating a regulatory role for methylation. We used nanopore sequencing to determine haplotype-specific methylation rates of 15.3 million CpG units in 7,179 whole-blood genomes. We identified 189,178 methylation depleted sequences where three or more proximal CpGs were unmethylated on at least one haplotype. A total of 77,789 methylation depleted sequences (~41%) associated with 80,503 cis-acting sequence variants, which we termed allele-specific methylation quantitative trait loci (ASM-QTLs). RNA sequencing of 896 samples from the same blood draws used to perform nanopore sequencing showed that the ASM-QTL, that is, DNA sequence variability, drives most of the correlation found between gene expression and CpG methylation. ASM-QTLs were enriched 40.2-fold (95% confidence interval 32.2, 49.9) among sequence variants associating with hematological traits, demonstrating that ASM-QTLs are important functional units in the noncoding genome.
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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 Socratic graph.