Extended Data Fig. 5: Co-occupancy analysis of H3K4me3 and H3K27me3 in mESCs.
a, Track view displaying H3K4me3 and H3K27me3 signals at three different representative loci in mESC. b, Bivalency score at the promoter regions (TSS ± 3 kb) of genes. H3K4me3 and H3K27me3 signals were normalized using RPKM. 2,706 reported bivalent genes were colored with red. Bulk H3K4me3, H3K27me3 ChIP-seq and bulk RNA-seq data were downloaded from GSM1000124, GSM1000089 and GSM723776, respectively. c-d, Dimensionality reduction for visualizing both 6,993 single cells and 350 pseudosingle cells of mESCs colored by clusters (c) and pseudotime (d) ordered by RNA profiles. e, The pseudotemporal dynamics of H3K4me3, H3K27me3, RNA, and bivalency scores of representative pluripotency genes. f, UMAP plot showing bivalency scores (up) and gene expression (down) in 350 pseudosingle cells of mESCs. Notably, bivalent genes are typically silenced or expressed at a very low level in mESCs.
