PreprintCited by 384Epigenetics and DNA MethylationGenetic Syndromes and ImprintingGenomics and Chromatin Dynamics

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Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome

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Shoemaker, Robert, Deng, Jie, Wang, Wei, Zhang, Kun·2010·Genome Research

DOI 10.1101/gr.104695.109PMC PMC2892089

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Abstract

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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Authors: Shoemaker, R., Deng, J., Wang, W., & Zhang, K.
Affiliations: University of California San Diego (US)
ORCID: Deng, Jie
Wang, Wei
Zhang, Kun
Venue: Genome Research
Publisher: Cold Spring Harbor Laboratory
Published: 2010-04-23
Volume: 20
Issue: 7
Pages: 883-889
ISSN: 1088-9051 (ISSN-L)
DOI: 10.1101/gr.104695.109
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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Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome

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