Fig. 6

Impact of promoter DNA methylation on gene expression in vertebrates. a Boxplots showing gene expression scores (rpkm) depending on the level of promoter DNA methylation for genes with LCP, ICP or HCP promoters in each species. b Boxplots of promoter DNA methylation scores in fibroblasts for the previously identified list of germline genes upregulated in Dnmt3a/3b double knockout embryos (termed 'gg dko' genes). For the species other than mouse, orthologs of mouse 'gg dko' genes are shown. c Enrichment of 'gg dko' orthologs among genes with methylated CG-rich promoters in fibroblasts for each species. The graph shows the associated adjusted p-values (-log10) calculated by hypergeometric tests. d Boxplots of the fold change (FC) of gene expression of 'gg dko' orthologs compared to all genes after 5-azadC treatment in fibroblasts. e Enrichment of 'gg dko' orthologs among genes upregulated by 5-azadC in each species. The graph shows adjusted p-values (-log10) calculated by hypergeometric tests. f Table showing germline genes upregulated by 5-azadC in at least 3 vertebrate species. The stringent mode corresponds to genes with a methylated promoter in control condition (> 50%), a fold change upon 5-azadC treatment > 3 and an adjusted p-value < 0.01. The lenient mode corresponds to less stringent cut-offs on promoter DNA methylation (> 25%) or fold change upon 5-azadC treatment (> 2). Genes in white did not pass the previous criteria. g RT-qPCR quantification of the expression of the DAZL gene in dermal fibroblasts treated with 5-azadC for 72h compared to untreated fibroblasts (NT). The expression was normalized to two housekeeping genes (Gusb and Mrpl32) (mean ± SEM, n=3 independent experiments). In the boxplots, the line indicates the median, the box limits indicate the upper and lower quartiles, and the whiskers extend to 1.5 IQR from the quartiles in a, d or to the data extremes in b