DNA methylation differences between CPA (n = 8) and control (n = 12) groups in anti-inflammatory cytokines IL-4 and IL-10 loci in T cells.

<p>Expanded views from the UCSC genome browser of IL-4 (<b>A</b>) and IL-10 (<b>B</b>) loci located on chromosomes 5 and 1 are depicted (top panel). In both panels, the first track shows the average MeDIP probe log2-fold differences (scale top panel: −0.4 to 0.4, botom panel: −1.0 to 1.0) between chronic physical aggressive (CPA) and control groups are shown for T cells. In black are probes that are more methylated and in gray are those that are less methylated in the CPA group. Highlighted in blue are regions significantly differentially methylated between the groups in T cells for IL-4 (<b>A</b>) and IL-10 (<b>B</b>). The second track shows Pearson’s correlation coefficient (scale top panel: −0.4 to 0.4, botom panel: −0.7 to 0.7) calculated between the MeDIP microarray probe intensities and the plasma IL-4 (<b>A</b>) and IL-10 (<b>B</b>) levels obtained from the same subject (n = 20). In red are probes whose methylation levels correlate positively with the cytokine level in plasma and in green are those that correlated negatively. In the top panel, the last track shows the average methylation level for all the subjects in T cells for IL-4 (<b>A</b>) and IL-10 (<b>B</b>) estimated from the microarray data. The bottom panel shows differentially methylated regions located within known Th2 LCRs where the CPA group is found significantly less methylated than the control group in the IL-4 locus (<b>A</b>) and significantly more methylated in the IL-10 locus (<b>B</b>). For the first differentially methylated region in IL-4, an overall positive correlation between methylation and IL-4 level in plasma is observed but did not reach significance after correcting for multiple testing (<b>A</b>, bottom panel). In the region more methylated in the CPA group of the IL-10 locus (<b>B</b>, bottom panel), the overall correlation with IL-10 level in plasma is negative although not significant after corrections for multiple testing. The regulatory elements from ENCODE identified in these regions (see methods) are shown in the additional tracks. First, shown with black lines, is the location of individual CpG sites. Second, is the location of DNase hypersensitive clusters where black indicate strong signal and grey a weaker signal from ChIP-seq data in 24 cell lines. Third is the location of transcription factors (TF) identified from ChIP-seq data in 24 cell lines where black indicate a strong and grey weaker signal occupancy. The letter next to the TF boxes identified the cell line where it was found enriched (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071691#pone.0071691.s008" target="_blank">Table S1</a> for the full legend). The last tracks, identified the level of enrichment of three histone marks determined from ChIP-seq assay, histone 3 lysine 4 tri- and mono-methylation as well as histone 3 lysine 27 acetylation in two cell lines, GM12878 (pink) and K562 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071691#pone.0071691-Armario1" target="_blank">[106]</a>.