Figure 3: Functional characterization of genes driven by bivalent promoters.

(a) Distribution of the seven TSS classes in High CpG content promoters (HCPs). (b) GO-term enrichment of the seven classes for GO:0032502 (developmental process), GO:0008152 (metabolic process) and GO:0002376 (immune system process). Shown are the calculated log₂ fold enrichment in the respective terms indicated by the colour (see colour key). Top, for all genes; bottom for genes annotated to be bivalent by BGDB²⁹. Stars indicate statistical significance: (***) P value <0.0001, (**) P value <0.001 and (*) P value <0.05 (Two-sided Fisher’s exact test). (c) Boxplots of DNA methylation levels contingent on the seven promoter classes. (***) P value <2.2e−16 (Wilcoxon signed-rank test). (d) Top, enrichment/depletion analysis of BGDB bivalent genes in the seven classes. Stars indicate statistical significance as in b; bottom, percentage of TSS in the different classes. Dark bars denote TSS overlapping with the BGDB bivalent genes; fair bars denote the genomic distribution. (e) Boxplots of gene expression for the different classes. Dark coloured, gene expression measured in the sample used for (re)ChIP; fair coloured, gene expression average over five independent central memory T-cell samples²⁸.