Differential DNA methylation of microRNAs within promoters, intergenic and intragenic regions of type 2 diabetic, pre-diabetic and non-diabetic individuals

Accumulating evidence supports the role of epigenetic modifications, and in particular DNA methylation and non-coding RNAs in the pathophysiology of type 2 diabetes. Alterations in methylation patterns within promoter regions are linked with aberrant transcription and pathological gene expression; however the role of methylation within non-promoter regions is not yet fully elucidated. We performed whole genome methylated DNA immunoprecipitation sequencing (MeDIP-Seq) in peripheral-blood-derived DNA from age–gender–body mass index (BMI)–ethnicity matched type 2 diabetic, pre-diabetic and non-diabetic individuals. The density of methylation normalized to the average length of the promoter, intergenic and intragenic regions and to CpG count was 3.17, 9.80 and 0.09 for the promoter, intergenic and intragenic regions, respectively. Methylation within these regions varied according to glucose tolerance status and was associated with hypermethylation rather than hypomethylation. MicroRNA–DNA methylation peaks accounted for 4.8% of the total number of peaks detected. Differential DNA methylation of these microRNA peaks was observed during dysglycemia, with the promoter, intergenic and intragenic regions accounting for 2%, 95% and 3% respectively, of the differentially methylated microRNA peaks. Genome-wide DNA methylation varied according to glucose tolerance. Methylation within non-promoter regions accounted for the majority of differentially methylated peaks identified, thus highlighting the importance of DNA methylation within these non-promoter regions in the pathogenesis of type 2 diabetes. This study suggests that DNA methylation within intergenic regions is a mechanism regulating microRNAs, another increasingly important epigenetic factor, during type 2 diabetes. •Genome-wide DNA methylation varied according to glucose tolerance.•DNA methylation was greatest in non-promoter regions.•MicroRNA peaks accounted for ~5% of the total number of methylated peaks detected.•DNA methylation within intergenic regions is a mechanism regulating microRNAs.