Although DNA methylation at CGIs is relatively conserved across tissues, intragenic CGIs are dramatically over-represented and promoter CGIs under-represented in the most tissue-variable CGIs. (a) Average DNA methylation values calculated by MEDIPS from MeDIP-seq data for all annotated gene features: CGIs (yellow), CGI shores (blue), gene promoters (red) and CDSs (green). DNA methylation is lower in promoter CGIs compared to intragenic, 3' UTR and intergenic CGIs. CGI shores are characterized by higher DNA methylation than CGIs, with less location-dependent variation. Promoter DNA methylation shows a strong inverse correlation with GC density, with LCPs showing a higher average level of DNA methylation than CDSs. Error bars represent standard error of the mean. (b) Although TS-DMRs are distributed across all feature types, there are marked differences in the between-tissue correlation of DNA methylation across each of the broad feature categories we examined, with CGIs being more correlated across cortex, cerebellum and blood than CGI shores or CDSs. (c, d) There is a highly significant enrichment of intragenic CGIs (P = 2 × 10-102) in analyses of CGI DMRs differentiating blood, cortex and cerebellum (c), and an even more dramatic enrichment (P = 1 × 10-246) in comparisons between cortex and cerebellum (d). EXP, expected; OBS, observed.
Davies et al. Genome Biology 2012 13:R43 doi:10.1186/gb-2012-13-6-r43