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Population-specificity of human DNA methylation

ABSTRACT: Ethnic differences in human DNA methylation have been shown for a number of CpG sites, but the genome-wide patterns and extent of these differences are unknown. In addition, whether the genetic control of polymorphic DNA methylation is population-specific has not been investigated. Here we measure DNA methylation near the transcription start sites of over 14,000 genes in 180 cell lines derived from one African and one European population. We find population-specific patterns of DNA methylation at over a third of all genes. Furthermore, although the methylation at over a thousand CpG sites is heritable, these heritabilities are also distinctly different between populations, suggesting extensive divergence in the genetic control of DNA methylation. In support of this, genetic mapping of DNA methylation reveals that there is also little overlap in genetic associations between populations. This population-specificity is supported by the patterns of DNA methylation in several hundred brain samples, suggesting it holds in vivo and across tissues. These results suggest that DNA methylation is highly divergent between populations, and that this divergence may be due in large part to complex epistasis or gene x environment interactions. Genomic DNA from 180 lymphoblastoid cell lines were bisulphite converted and hybridized, along with 8 additional technical replicates, to the Illumina Infinium HumanMethylation27 Beadchip v1.2 for genome-wide DNA methylation profiling. The cell lines were derived from two HapMap populations: 'CEPH (Utah residents with ancestry from northern and western Europe)' (CEU) and 'Yoruba in Ibadan, Nigeria' (YRI).

ORGANISM(S): Homo sapiens

SUBMITTER: Michael Kobor

PROVIDER: E-GEOD-27146 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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