ArticleGenome biology2017
Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 56 papers.
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56 citing papers in PubMed, 97 citations in OpenAlex.
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- A novel high-dimensional model for identifying regional DNA methylation QTLs.Biostatistics (Oxford, England) · 2025Article
- DNA methylation of food sensitization in a French-Canadian population.Clinical epigenetics · 2025Article
- Peripheral DNA Methylation of Cortisol- and Serotonin-Related Genes Predicts Hippocampal Volume in a Pediatric Population.Biological psychiatry global open science · 2025Article
- DNA methylation biomarkers of intellectual/developmental disability across the lifespan.Journal of neurodevelopmental disorders · 2025Review
- Identifying Differential Methylation in Cancer Epigenetics via a Bayesian Functional Regression Model.Biomolecules · 2024Article
- Intercontinental insights into autism spectrum disorder: a synthesis of environmental influences and DNA methylation.Environmental epigenetics · 2024Review
- Direct haplotype-resolved 5-base HiFi sequencing for genome-wide profiling of hypermethylation outliers in a rare disease cohort.Nature communications · 2023Article
- Epigenomic signatures reveal mechanistic clues and predictive markers for autism spectrum disorder.Molecular psychiatry · 2023Review
- Sperm DNA methylome abnormalities occur both pre- and post-treatment in men with Hodgkin disease and testicular cancer.Clinical epigenetics · 2023Article
- An integrative framework and recommendations for the study of DNA methylation in the context of race and ethnicity.Discover social science and health · 2023Review
- DNA methylation QTL mapping across diverse human tissues provides molecular links between genetic variation and complex traits.Nature genetics · 2023Article
- Using epigenomics to understand cellular responses to environmental influences in diseases.PLoS genetics · 2023Review
- Alpha-synuclein overexpression induces epigenomic dysregulation of glutamate signaling and locomotor pathways.Human molecular genetics · 2022Article
- Differentially methylated CpGs in response to growth hormone administration in children with idiopathic short stature.Clinical epigenetics · 2022Article
- DNA methylation and single-nucleotide polymorphisms in DDX58 are associated with hand, foot and mouth disease caused by enterovirus 71.PLoS neglected tropical diseases · 2022Article
- A new approach to decode DNA methylome and genomic variants simultaneously from double strand bisulfite sequencing.Briefings in bioinformatics · 2021Article
- Article
Corrections and comments
- Erratum issued
Authors and funding
33 authors at 12 institutions in 4 countries.
Funding
Abstract
backgroundThe functional impact of genetic variation has been extensively surveyed, revealing that genetic changes correlated to phenotypes lie mostly in non-coding genomic regions. Studies have linked allele-specific genetic changes to gene expression, DNA methylation, and histone marks but these investigations have only been carried out in a limited set of samples.
resultsWe describe a large-scale coordinated study of allelic and non-allelic effects on DNA methylation, histone mark deposition, and gene expression, detecting the interrelations between epigenetic and functional features at unprecedented resolution. We use information from whole genome and targeted bisulfite sequencing from 910 samples to perform genotype-dependent analyses of allele-specific methylation (ASM) and non-allelic methylation (mQTL). In addition, we introduce a novel genotype-independent test to detect methylation imbalance between chromosomes. Of the ~2.2 million CpGs tested for ASM, mQTL, and genotype-independent effects, we identify ~32% as being genetically regulated (ASM or mQTL) and ~14% as being putatively epigenetically regulated. We also show that epigenetically driven effects are strongly enriched in repressed regions and near transcription start sites, whereas the genetically regulated CpGs are enriched in enhancers. Known imprinted regions are enriched among epigenetically regulated loci, but we also observe several novel genomic regions (e.g., HOX genes) as being epigenetically regulated. Finally, we use our ASM datasets for functional interpretation of disease-associated loci and show the advantage of utilizing naïve T cells for understanding autoimmune diseases.
conclusionsOur rich catalogue of haploid methylomes across multiple tissues will allow validation of epigenome association studies and exploration of new biological models for allelic exclusion in the human genome.
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