Fig. 2

Identification of two classes of bivalent promoters. a Boxplots showing H3K27me3 levels in parental wild-type ES quintiles of 1-kb tiled regions (left) and log2-fold changes in H3K27me3 in the indicated quintiles (right). b Average plots of DNA methylation (WGBS) in wild-type mESC (n = 1) across gene promoters defined as bivalent, HK27me3-only or H3K4me3-only. c Heatmap of H3K27me3 and H3K4me3 ChIPseq (n = 1) in bivalent, H3K27me3 only and H3K4me3 only regions defined in wild-type mESC. Bottom: average profiles of heatmap data. d k-means (k = 2) clustering of histone modifications (n = 1) over bivalent regions in shown in 2c. Bottom: average profiles of heatmap data. Boxplot of mean ChIPseq signal ratios for H3K27me3 and H3K4me3 over hiBiv and loBiv regions. Student’s t test used to compare two groups of ratios. e ChIPseq heatmap of indicated chromatin-associated factors over hiBiv and loBiv (n = 1). Bottom: average profiles of heatmap data. f Left: wild-type mESC expression (RNAseq, n = 3) of hiBiv and loBiv associated genes compared to all genes; right: log2-fold expression changes between TKO and wild-type mESC (RNAseq, n = 3) of hiBiv, loBiv associated genes compared to all genes. g ChIPseq heatmap of indicated RPII forms (n = 1) over hiBiv and loBiv. Bottom: average profiles of heatmap data. h Log2-fold expression changes between activin-induced differentiation and wild-type mESC (RNAseq, n = 2) of hiBiv, loBiv associated genes compared to all genes. See Additional file Table S3 for replicate metrics