Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome
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In diploid mammalian genomes, parental alleles can exhibit different methylation patterns (allele-specific DNA methylation, ASM), which have been documented in a small number of cases except for the imprinted regions and X chromosomes in females. We carried out a chromosome-wide survey of ASM across 16 human pluripotent and adult cell lines using Illumina bisulfite sequencing. We applied the principle of linkage disequilibrium (LD) analysis to characterize the correlation of methylation between adjacent CpG sites on single DNA molecules, and also investigated the correlation between CpG methylation and single nucleotide polymorphisms (SNPs). We observed ASM on 23% approximately 37% heterozygous SNPs in any given cell line. ASM is often cell-type-specific. Furthermore, we found that a significant fraction (38%-88%) of ASM regions is dependent on the presence of heterozygous SNPs in CpG dinucleotides that disrupt their methylation potential. This study identified distinct types of ASM across many cell types and suggests a potential role for CpG-SNP in connecting genetic variation with the epigenome.
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DNA methylation has been shown to frequently occur in an allele-specific manner.
“DNA methylation has been shown to frequently occur in an allele-specific manner (He et al., 2015;Meaburn, Schalkwyk, & Mill, 2010;Shoemaker, Deng, Wang, & Zhang, 2010).”
From The applied implications of epigenetics in anxiety, affective and stress-related disorders - A review and synthesis on psychosocial stress, psychotherapy and prevention (2020) · cites this paper as Shoemaker, Deng, Wang, & Zhang, 2010
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- Authors
- Shoemaker, R., Deng, J., Wang, W., & Zhang, K.
- Affiliations
- University of California San Diego (US)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2010-04-23
- Volume
- 20
- Issue
- 7
- Pages
- 883-889
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC2892089
- OpenAlex
- W2155471840
- Cited by
- 380
- References
- 25
- Citations by year
- 2026: 7 · 2025: 15 · 2024: 13 · 2023: 14 · 2022: 22 · 2021: 17 · 2020: 16 · 2019: 23 · 2018: 29 · 2017: 33 · 2016: 31 · 2015: 43 · 2014: 33 · 2013: 25 · 2012: 30
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Institutes of Health
- University of California, San Diego
- National Institute on Drug Abuse (R01DA025779)
- National Institute of General Medical Sciences (R01GM072856)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Syndromes and Imprinting
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- allele-specific methylation, DNA methylation, heterozygous SNPs, linkage disequilibrium, cell type-specific methylation, epigenome, genetic variation, human genome
- MeSH terms
- Adult, Alleles, Base Sequence, Cell Line, DNA Mutational Analysis, Female, Gene Frequency, Humans, Linkage Disequilibrium, Genome, Human, CpG Islands, DNA Methylation, Polymorphism, Single Nucleotide
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