Additional file 3: Figure S2. of DNA methylation and gene expression of HIF3A: cross-tissue validation and associations with BMI and insulin resistance

Correlation between HIF3A DNA methylation levels at CpG sites 1 to 4 in subcutaneous adipose tissue. (PDF 126 kb

Additional file 4: Table S2. of DNA methylation and gene expression of HIF3A: cross-tissue validation and associations with BMI and insulin resistance

Associations between HIF3A DNA methylation levels in blood and subcutaneous adipose tissue. (PDF 175 kb

Clinical characteristics of the FDR group (n = 124) stratified according to glucose tolerance status.

<p>Data are mean ± SD. Significant differences between NGT and IFG/IGT at *<i>P</i><0.05. **<i>P</i><0.001. Significant differences between NGT and T2D at ⁺<i>P</i><0.05, ⁺⁺<i>P</i><0.001. Significant differences between IFG/IGT and T2D at ^§<i>P</i><0.05, ^§§<i>P</i><0.001. All parameters except age and BMI were analyzed with unpaired non-parametric tests due to lack of normal distribution. Indices of insulin sensitivity and insulin secretion were calculated as described in subjects and methods. BMI, body mass index; CIR, corrected insulin response; HOMA-β, homeostatic model assessment of β-cell function; HOMA-IR, homeostatic model assessment of insulin resistance; IFG, impaired fasting glycemia; IGT, impaired glucose tolerance; NGT, normal glucose tolerance; OGTT, oral glucose tolerance test; T2D, type 2 diabetes.</p

CpG sites analyzed in the <i>PPARGC1A</i> promoter.

<p>The CpG sites investigated are marked with a perpendicular line.</p

Skeletal muscle gene expression of <i>PPARGC1A</i>.

<p>Participants are stratified according to glucose tolerance status (NGT, IFG/IGT, T2D). Data are mean±SE.</p

Correlation between average skeletal muscle DNA methylation and gene expression of <i>PPARGC1A</i>.

<p>Methylation is show in percentage and gene expression in arbitrary units (AU). β = 0.013 (−0.034;0.059), <i>P = </i>0.59, adjusted for age, gender, BMI, glucose tolerance and family pedigree. Unadjusted (Spearman’s correlation): ρ 0.22, <i>P</i> = 0.04.methylation at CpG site −260 in the <i>PPARGC1A</i> promoter was 0% in 98 individuals and 4–10% in 11 individuals (4 with T2D and 7 with NGT). The DNA methylation at CpG site −260 was not different among T2D (1.1±1.7) compared to NGT subjects (0.74±2.3), and there were no significant associations between DNA methylation and whole body insulin sensitivity, gene expression or any other clinical parameter (data not shown).</p

Global gene promoter DNA methylation in monozygotic twins.

<p>The DNA methylation was measured as the β-value ranging from 0 (unmethylated) to 1 (completely methylated) at 26,850 CpG sites located in the promoters of 14,279 genes. The plots are shown for a representative twin pair (#3). <b>A</b> Skeletal muscle (r = 0.95, <i>P</i><0.001). <b>B</b> SAT (r = 0.97, <i>P</i><0.001). <b>C</b> Comparison of DNA methylation in SAT and skeletal muscle from the non-diabetic twin.</p

Differentially methylated type 2 diabetes susceptibility genes.

<p>The microarray included in total 49 type 2 diabetes candidate genes represented by 136 probes. Each CpG site is identified with Illumina probe target ID. The CpG site location is given as the base pair distance to transcription start site (TSS) if available. Data are shown as mean±standard deviation. <i>P</i>_adj-values are corrected for multiple testing (136 tests).</p

Differentially methylated genes.

<p>The 20 CpG sites with the lowest <i>P</i>-values for the intra-pair methylation difference between type 2 diabetic and non-diabetic twins are shown for subcutaneous adipose tissue and skeletal muscle. The total number of differentially methylated CpG sites, without correction for multiple testing, was 1,458 in subcutaneous adipose tissue and 789 in skeletal muscle. Each CpG site is identified with Illumina probe target ID. The CpG site location is given as the base pair distance to transcription start site (TSS) if available. Data are shown as mean±standard deviation. <i>P</i>_adj-values are corrected for multiple testing (26,850 tests).</p

Intra-twin pair variation of DNA methylation in repetitive DNA sequences.

<p>The variation is given by the standard deviation (SD) of the absolute methylation differences between monozygotic twins in skeletal muscle. <b>A</b> SD of methylation differences on all repetitive versus all promoter CpG sites (r = −0.05, <i>P</i> = 0.9). <b>B</b> SD of methylation differences on LINE1 repetitive CpG sites versus absolute difference in BMI (r = 0.77, <i>P</i> = 0.007). <b>C</b> SD of methylation differences on LINE1 repetitive CpG sites versus absolute difference in 2-hour plasma glucose (r = 0.66, <i>P</i> = 0.03). <b>D</b> SD of methylation differences on LINE1 repetitive CpG sites versus absolute difference in glucose infusion rate (r = 0.52, <i>P</i> = 0.2).</p