Fig. 3

H3K27me3-H3K4me1 transition influences tissue-specific gene expression. A Heatmaps showing patterns of H3K4me1, H3K4me3 and H3K27me3 of each tissue-specific bivalent genes at promoter CGIs and their shores in hESCs and lung. Lung: tissue-specific bivalent genes of lung; Liver: tissue-specific bivalent genes of liver; Pancreas: tissue-specific bivalent genes of pancreas; Spleen: tissue-specific bivalent genes of spleen; All Other: all the other tissues without lung. Each line represents a single CpG island. B Boxplots showing differences of H3K4me1, H3K4me3 and H3K27me3 between hESC and lung of each tissue-specific bivalent genes at promoter CGIs. Lung: tissue-specific bivalent genes of lung; Liver: tissue-specific bivalent genes of liver; Pancreas: tissue-specific bivalent genes of pancreas; Spleen: tissue-specific bivalent genes of spleen; All Other: all the other tissues without lung. Significance was examined with t-test, *p value < 0.05, **p value < 0.01, ****p value < 0.0001, ns: not significantly. C IGV browser track showing the H3K27me3-H3K4me1 transition from hESCs to lung at bivalent promoter CGIs. Lung tissue-specific bivalent gene (FOXF2) undergoes lower unimodal enrichment of H3K4me1 than non-lung tissue-specific bivalent genes (PTF1A and DEPDC7). D Heatmaps showing patterns of H3K4me1 and H3K27ac at enhancers of each tissue-specific bivalent genes in hESCs and lung, respectively. Lung: tissue-specific bivalent genes of lung; Liver: tissue-specific bivalent genes of liver; Pancreas: tissue-specific bivalent genes of pancreas; Spleen: tissue-specific bivalent genes of spleen; All Other: all the other tissues without lung. Each line represents a single enhancer. E Boxplots showing levels of H3K4me1 and H3K27ac at enhancers of each tissue-specific bivalent genes in hESCs and lung, respectively. Lung: tissue-specific bivalent genes of lung; Liver: tissue-specific bivalent genes of liver; Pancreas: tissue-specific bivalent genes of pancreas; Spleen: tissue-specific bivalent genes of spleen; All Other: all the other tissues without lung. Significance was examined with t-test, *p value < 0.05, ****p value < 0.0001, ns not significantly. F Forest plot showing association between the differences of the level of enhancer H3K4me1, enhancer H3K27ac, CGI H3K4me1, CGI H3K4me3 and CGI H3K27me3 between hESC and lung and tissue specificity. G Boxplot showing interaction score between promoter and enhancer of lung tissue-specific and all other tissue (lung not included)-specific bivalent genes in lung. Significance was examined with Wilcoxon rank-sum test, ****p value < 0.0001