Fig. 3

DNA demethylation at promoter CGIs alters the pattern and level of histone modification. A Heatmaps showing DNA methylation profiles at promoter CGIs and flanked regions of demethylation group genes and unchanged group genes in DKO cells (left panels) and WT HCT116 cells (right panels). DNAm, DNA methylation. B The stacked bar plot showing proportion of bivalent and non-bivalent genes in demethylation group and unchanged group. C The stacked bar plot showing proportion of up-regulated (DKO Up), down-regulated (DKO Down) and not significantly (NS) changed genes in demethylation and unchanged groups (left panels), as well as in bivalent and non-bivalent genes groups (right panels). D, F, H Heatmaps showing enrichment of H3K4me1, H3K4me3 and H3K27me3 at promoter CGIs and flanked regions of each group of genes in WT and DKO HCT116 cells. E, G, I Quantification of D, F, H by average plots. (D-I bivalent demeth: group of bivalent genes with demethylated promoter CGIs; non-biv demeth: group of non-bivalent genes with demethylated promoter CGIs; bivalent unchan: group of bivalent genes with unchanged promoter CGIs; non-biv unchan: group of non-bivalent genes with unchanged promoter CGIs.) J Average plot showing the distribution pattern and level of H3K4me1 (left) and H3K4me3 (right) at promoter CGIs and flanked regions of bivalent and non-bivalent genes in NCM460 and LSD1 OE cells. K Average plot showing the distribution pattern and level of DNA methylation at promoter CGIs and flanked regions of 4 groups of genes in NCM460 and LSD1 OE cells. common: group of genes with H3K4me1 peaks in both NCM460 and LSD1 OE cells (n = 1,011); LSD1 OE specific H3K4me1: group of genes with H3K4me1 peaks only in LSD1 OE cells (n = 233); NCM 460 specific H3K4me1: group of genes with H3K4me1 peaks only in NCM 460 cells (n = 1,141); other: other genes (n = 12,585).