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Open Access Highly Accessed Research

Contribution of genetic variation to transgenerational inheritance of DNA methylation

Allan F McRae12*, Joseph E Powell12, Anjali K Henders3, Lisa Bowdler3, Gibran Hemani12, Sonia Shah12, Jodie N Painter3, Nicholas G Martin3, Peter M Visscher12 and Grant W Montgomery3

Author Affiliations

1 The Queensland Brain Institute, University of Queensland, Brisbane, Australia

2 University of Queensland Diamantina Institute, University of Queensland, Translational Research Institute (TRI), Brisbane, Australia

3 QIMR Berghofer Medical Research Institute, Brisbane, Australia

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Genome Biology 2014, 15:R73  doi:10.1186/gb-2014-15-5-r73

Published: 29 May 2014

Abstract

Background

Despite the important role DNA methylation plays in transcriptional regulation, the transgenerational inheritance of DNA methylation is not well understood. The genetic heritability of DNA methylation has been estimated using twin pairs, although concern has been expressed whether the underlying assumption of equal common environmental effects are applicable due to intrauterine differences between monozygotic and dizygotic twins. We estimate the heritability of DNA methylation on peripheral blood leukocytes using Illumina HumanMethylation450 array using a family based sample of 614 people from 117 families, allowing comparison both within and across generations.

Results

The correlations from the various available relative pairs indicate that on average the similarity in DNA methylation between relatives is predominantly due to genetic effects with any common environmental or zygotic effects being limited. The average heritability of DNA methylation measured at probes with no known SNPs is estimated as 0.187. The ten most heritable methylation probes were investigated with a genome-wide association study, all showing highly statistically significant cis mQTLs. Further investigation of one of these cis mQTL, found in the MHC region of chromosome 6, showed the most significantly associated SNP was also associated with over 200 other DNA methylation probes in this region and the gene expression level of 9 genes.

Conclusions

The majority of transgenerational similarity in DNA methylation is attributable to genetic effects, and approximately 20% of individual differences in DNA methylation in the population are caused by DNA sequence variation that is not located within CpG sites.