Tissue-specific patterns of allelically-skewed DNA methylation

Marzi, S. and Meaburn, Emma L. and Dempster, E.L. and Lunnon, K. and Paya-Cano, J. and Smith, R. and Volta, M. and Troakes, C. and Schalkwyk, L.C. and Mill, J. (2016) Tissue-specific patterns of allelically-skewed DNA methylation. Epigenetics 11 (1), pp. 24-35. ISSN 1559-2294.

Abstract

While DNA methylation is usually thought to be symmetrical across both alleles, there are some notable exceptions. Genomic imprinting and X chromosome inactivation are two well-studied sources of allele-specific methylation (ASM), but recent research has indicated a more complex pattern in which genotypic variation can be associated with allelically-skewed DNA methylation in cis. Given the known heterogeneity of DNA methylation across tissues and cell types we explored inter- and intra-individual variation in ASM across several regions of the human brain and whole blood from multiple individuals. Consistent with previous studies, we find widespread ASM with >4% of the ~220,000 loci interrogated showing evidence of allelically-skewed DNA methylation. We identify ASM flanking known imprinted regions, and show that ASM sites are enriched in DNase I hypersensitivity sites and often located in an extended genomic context of intermediate DNA methylation. We also detect examples of genotype-driven ASM, some of which are also tissue-specific. These findings contribute to our understanding about the nature of differential DNA methylation across tissues and have important implications for genetic studies of complex disease. As a resource to the community, ASM patterns across each of the tissues studied are available in a searchable online database: http://epigenetics.essex.ac.uk/ASMBrainBlood.

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