ArticleEpigenetics & chromatin2019
Genome-wide allele-specific methylation is enriched at gene regulatory regions in a multi-generation pedigree from the Norfolk Island isolate.
Article in Epigenetics & chromatin, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 21 citations in OpenAlex.
- Genome-wide DNA methylation analysis in pigs using long-read sequencing unveils high-altitude adaptation and allele-specific regulation.BMC genomics · 2026Article
- Interplay of the Genetic Variants and Allele Specific Methylation in the Context of a Single Human Genome Study.International journal of molecular sciences · 2025Article
- Epigenetic networks coordinate DNA methylation across the genome.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
- Long-read RNA sequencing reveals allele-specific NbioRxiv : the preprint server for biology · 2024Article
- Investigating the potential of single-cell DNA methylation data to detect allele-specific methylation and imprinting.American journal of human genetics · 2024Article
- DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing.Nature communications · 2023Article
- Dynamics of Methylation of CpG Sites Associated With Systemic Lupus Erythematosus Subtypes in a Longitudinal Cohort.Arthritis & rheumatology (Hoboken, N.J.) · 2022Article
- A comparative methylome analysis reveals conservation and divergence of DNA methylation patterns and functions in vertebrates.BMC biology · 2022Article
- Identification of genetic variants influencing methylation in brain with pleiotropic effects on psychiatric disorders.Progress in neuro-psychopharmacology & biological psychiatry · 2022Article
- The nuclear periphery is a scaffold for tissue-specific enhancers.Nucleic acids research · 2021Article
- Genetic impacts on DNA methylation: research findings and future perspectives.Genome biology · 2021Review
- The conserved DNMT1-dependent methylation regions in human cells are vulnerable to neurotoxicant rotenone exposure.Epigenetics & chromatin · 2020Article
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundAllele-specific methylation (ASM) occurs when DNA methylation patterns exhibit asymmetry among alleles. ASM occurs at imprinted loci, but its presence elsewhere across the human genome is indicative of wider importance in terms of gene regulation and disease risk. Here, we studied ASM by focusing on blood-based DNA collected from 24 subjects comprising a 3-generation pedigree from the Norfolk Island genetic isolate. We applied a genome-wide bisulphite sequencing approach with a genotype-independent ASM calling method to map ASM across the genome. Regions of ASM were then tested for enrichment at gene regulatory regions using Genomic Association Test (GAT) tool.
resultsIn total, we identified 1.12 M CpGs of which 147,170 (13%) exhibited ASM (P ≤ 0.05). When including contiguous ASM signal spanning ≥ 2 CpGs, this condensed to 12,761 ASM regions (AMRs). These AMRs tagged 79% of known imprinting regions and most (98.1%) co-localised with known single nucleotide variants. Notably, miRNA and lncRNA showed a 3.3- and 1.8-fold enrichment of AMRs, respectively (P < 0.005). Also, the 5' UTR and start codons each showed a 3.5-fold enrichment of AMRs (P < 0.005). There was also enrichment of AMRs observed at subtelomeric regions of many chromosomes. Five out of 11 large AMRs localised to the protocadherin cluster on chromosome 5.
conclusionsThis study shows ASM extends far beyond genomic imprinting in humans and that gene regulatory regions are hotspots for ASM. Future studies of ASM in pedigrees should help to clarify transgenerational inheritance patterns in relation to genotype and disease phenotypes.
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