The impact of sex, age, and genetic ancestry on DNA methylation across tissues

Abstract

Background: Understanding the consequences of individual DNA methylation variation is crucial for the study of human biology and disease. However, the collective impact of demographic traits on DNA methylation and subsequent gene expression across human tissues remains unexplored. Here, we quantify the contributions of sex, age, genetic ancestry, and BMI on DNA methylation variation across 9 human tissues and 424 individuals from the Genotype-Tissue Expression project. Results: We observe that inter-individual DNA methylation variation is higher than inter-individual gene expression variation. We show that genetic ancestry and age have a greater impact on DNA methylation than does sex, with aging effects being more widespread but less pronounced. On average, less than 10% of the gene expression variation in sex, age, and ancestry is mediated by DNA methylation differences, with ancestry showing the largest percentage of mediation. We show that DNA methylation differences between populations accumulate at regions with outlier DNA methylation profiles (high/lowly methylated) and are largely under genetic control. The female genome is predominantly hypermethylated across tissues, likely driven by the polycomb repressive complex. Ultimately, we demonstrate how aging increases DNA methylation levels at targets of the polycomb repressive complex in most tissues except the gonads. Conclusions: Overall, our multi-individual and multi-tissue analysis provides a comprehensive characterization of the main drivers of human DNA methylation variation under healthy conditions, laying the foundations for clinical studies considering demographic perspectives.