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Fig. 6 | BMC Biology

Fig. 6

From: Bivalent promoter hypermethylation in cancer is linked to the H327me3/H3K4me3 ratio in embryonic stem cells

Fig. 6

DNA Hypermethylation of hiBiv in cancer. a Normal and cancer H3K27me3 ChIPseq (n = 1) heatmap profiles. Bottom: average profiles of heatmap data. b Violin plots of absolute DNA methylation (WGBS) levels genome-wide in the indicated samples for hiBiv and loBiv. Replicates: HMEC (n = 10), HCC1954 (n = 15), MCF7 (n = 1), colon (n = 3), tumour (n = 3). c Venn diagram of genes frequently methylated in cancer and genes associated with human hiBiv and loBiv. F. E = fold-enrichment over random gene selection. d Kernel density plots of differential methylation at human hiBiv and loBiv. e RNAseq boxplots for normal and cancer samples in the indicated clusters. Replicates: HMEC (n = 3), HCC1954 (n = 4), MCF7 (n = 3), colon (n = 18), tumour (n = 18). f Pan-Cancer Atlas Infinium 450K DNA methylation data derived from breast and gastrointestinal tissues. Upper: mean gene promoter unclustered methylation heatmaps; lower: histogram distribution of promoter associated individual CpG methylation and inset boxplots with Fisher’s exact test. Breast dataset: controls (n = 86), patients (n = 780); colon dataset: controls (n = 33), patients (n = 291). g Violin plots of absolute DNA methylation (WGBS) levels, adjacent to TSS, in the indicated samples for hiBiv and loBiv. h Violin plots of WGBS absolute DNA methylation levels, at CGI shores, in the indicated samples for hiBiv and loBiv. Replicates (g, h): WT-C57Bl/6 J (n = 1), Kdm2b−/− (n = 1), WT-J1 (n = 1), Eed−/− (n = 1), Ring1b (n = 1) and DKO (n = 1). See Additional file Table S3 for replicate metrics

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