Obligatory and facilitative allelic variation in the DNA methylome within common disease-associated loci

• DOI: 10.1038/s41467-017-01586-1
• Publication Date: 2017-12-27T11:38:31Z
• Authors: Christopher G. Bell; Fei Gao; Wei Yuan; Leonie Roos; Richard J. Acton; Yudong Xia; Jordana Bell; Kirsten Ward; Massimo Mangino; Pirro G. Hysi; Jun Wang; Timothy D. Spector
• Keywords: 0301 basic medicine; 570; Genome, Human; Science; Q; 610; Genetic Variation; High-Throughput Nucleotide Sequencing; DNA Methylation; Polymorphism, Single Nucleotide; Article; Epigenesis, Genetic; 03 medical and health sciences; Haplotypes; Risk Factors; MD Multidisciplinary; Humans; CpG Islands; Disease; Genetic Predisposition to Disease; Alleles; Genome-Wide Association Study

AbstractIntegrating epigenetic data with genome-wide association study (GWAS) results can reveal disease mechanisms. The genome sequence itself also shapes the epigenome, with CpG density and transcription factor binding sites (TFBSs) strongly encoding the DNA methylome. Therefore, genetic polymorphism impacts on the observed epigenome. Furthermore, large genetic variants alter epigenetic signal dosage. Here, we identify DNA methylation variability between GWAS-SNP risk and non-risk haplotypes. In three subsets comprising 3128 MeDIP-seq peripheral-blood DNA methylomes, we find 7173 consistent and functionally enriched Differentially Methylated Regions. 36.8% can be attributed to common non-SNP genetic variants. CpG-SNPs, as well as facilitative TFBS-motifs, are also enriched. Highlighting their functional potential, CpG-SNPs strongly associate with allele-specific DNase-I hypersensitivity sites. Our results demonstrate strong DNA methylation allelic differences driven by obligatory or facilitative genetic effects, with potential direct or regional disease-related repercussions. These allelic variations require disentangling from pure tissue-specific modifications, may influence array studies, and imply underestimated population variability in current reference epigenomes.