Figure 4.

Distribution of mean methylation according to genomic feature (A) or CpG density relative to CpG islands (B). Classes B1, B2 and B3 correspond to hypomethylated, intermediate and hypermethylated probes in blood with E1, E2 and E3, the equivalent categories in eye tissue. Mean methylation was calculated as the average methylation level across each individual probe within a specific dataset used for the blood-eye comparison shown. The percentage of total probes is displayed. (A) The majority of probes are located in gene bodies or intergenic regions and show hyper- or intermediate methylation in both eye and blood. In contrast, a larger proportion of probes in the 5’UTR, 1^st Exon or TSS regions are hypomethylated in both blood and eye tissues. (B) As anticipated, the majority of CpG island-associated probes are hypomethylated in blood and eye tissue, whereas CpG island Shores, Shelves and Open Sea are more highly methylated in both tissues. Data are shown for (i) all probes, (ii) probes showing inter-individual variation in blood, (iii–v) blood variable probes highly correlated with RPE/choroid, optic nerve or retina. and (vi) PC13-specific probes (all on the X-axis). The latter are primarily located within 200 bp of gene transcription start sites in CpG island regions.