Figure 3.

Promoter iiDMRs anti-correlate with H2A.Z changes and are preferentially found at genes expressed at low levels. (A) Anti-correlation between inter-individual DNA methylation (for only >5% methylation differences) and H2A.Z differences in CD14+ cells. Data are shown as mean and 95% credible intervals. (B) Inter-individual promoter epiallelic differences are not correlated with gene expression differences. For each bin of inter-individual DNA methylation differences we calculated the ratio of log transformed RNA-seq reads (FPKM) in the first individual of each comparison respect to the other. Data are represented as 95% credible intervals on the mean. The left panel shows the correlations using DNA methylation data only, the middle panel uses those epialleles in which DNA methylation and H2AZ are anti-correlated, and the right panel looks at epiallelic variation at CpG shores (as defined in the Illumina450K array annotation file). (C) iiDMRs are predominantly found at genes expressed at low levels. Shown is the distribution RNA-seq reads (expressed as FPKM) for iiDMRs and non-iiDMRs. In all cases the curves corresponding to DMRs are shifted to the left compared to non-DMRs showing that DMRs occur preferentially at genes expressed at low levels. For all cases 31/32 and 21/22 plots correspond to MZ twin comparisons; 31/21, 31/11 and 11/22 correspond to unrelated individuals comparisons. (D) Promoter iiDMRs occur preferentially at regions depleted for H3K4me3 and enriched for H3K27me3 (K4lo/K27hi) or depleted for both these marks (K4lo/K27lo) in human embryonic stem (hES) cells. hES cell H3K4me3 and H3K27me3 ChIP-seq data are from [24]. The dashed line in each plot refers to the overall iiDMR fraction against the whole dataset. (E) Illumina450K probes were ranked by methylation-ageing correlation using data from [20], and the 500 most- age-associated probes were taken as aDMRs, while 500 randomly selected probes from the remainder of the dataset were taken as controls. For each set, we collected absolute methylation differences from each of the five possible pairings of individuals in this study, and plot 95% credible intervals on the mean.

Gemma et al. Genome Biology 2013 14:R43   doi:10.1186/gb-2013-14-5-r43
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