The incidence of diabetes is increasing worldwide, with the most prevalent form being type 2 diabetes. Two fundamental processes contribute to the development of type 2 diabetes: insulin resistance in target organs and insufficient insulin secretion from the pancreatic beta-cells. The aim of this thesis was to explore the role of DNA methylation and common genetic variation on glucose metabolism and the pathogenesis of type 2 diabetes.

Reduced oxidative capacity of the mitochondria in skeletal muscle has been suggested to play a role in insulin resistance and type 2 diabetes. In studies I and II, we investigated the regulation of COX7A1 and ATP5O, which encode two subunits of the mitochondrial respiratory chain. We found that genetic variation and age were associated with skeletal muscle mRNA expression in both studies. mRNA levels were also positively correlated with the expression of the transcriptional co-activator PPARGC1A and insulin-stimulated glucose uptake, i.e., elderly individuals had reduced mRNA expression levels and reduced in vivo glucose uptake. Additionally, DNA methylation of the COX7A1 promoter was increased in elderly individuals concordant with the decrease in COX7A1 mRNA expression, suggesting a role for genetic, epigenetic and non-genetic factors in gene regulation.

In study III, we investigated a common genetic variant in MTNR1B that has previously been found to be associated with increased risk of type 2 diabetes, increased fasting plasma glucose and impaired insulin secretion in populations of European ancestry. We aimed to replicate these findings in a type 2 diabetes case-control cohort of Han Chinese ancestry. We confirmed the association between rs10830963 and both the risk of type 2 diabetes and increased fasting plasma glucose levels, suggesting a relatively ancient origin for this variant.

In study IV, common genetic variants that introduce or remove potential DNA methylation sites were selected based on their association with the risk of type 2 diabetes and changes in gene expression in blood. These genetic variants were analysed together with the level of DNA methylation and gene expression in human skeletal muscle, adipose tissue, blood and pancreatic islets. We found that 18 of the 19 sites that we analysed were associated with a difference in DNA methylation related to genotype, and for 11 of these sites this finding was consistent in all four tissues. Additionally, our data suggested a tissue-specific pattern of DNA methylation. Our results confirm an interaction between genetic and epigenetic mechanisms, which introduces a new level of complexity to our knowledge of gene regulation in type 2 diabetes.

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