Figure 1

KDM5B occupies active genes, pluripotency regulators, and bivalent genes in ES cells. KDM5B is associated with transcriptional start sites (TSSs) and gene body regions of highly expressed genes in ES cells. (A) ChIP-Seq tag density of KDM5B binding at TSS normalized by input (log2 scale) of all refseq genes sorted into quartiles based on their mRNA expression level in ES cells. (B) ChIP-Seq tag densities of KDM5B and H3K4me3 around TSSs in ES cells. KDM5B binding profiles are similar to H3K4me3 marks near TSS regions, while KDM5B occupancy is enriched more in gene body regions relative to H3K4me3. (C) Scatter plot of the ratio of relative tag densities of KDM5B and H3K4me3 in promoter versus gene body regions. (D) RNA polymerase II and MLL4 are also enriched at TSS regions. (E) KDM5B occupies promoters of pluripotency-related genes in ES cells (Pou5f1/Oct4, Sox2, and Nanog). ChIP-Seq binding profiles of KDM5B, H3K4me3, RNA polymerase II, and Mll4 at core pluripotency genes. (F) Venn diagrams showing the co-occupancy of KDM5B and H3K4me3 (left panel), H3K27me3 (middle panel), and both modifications (right panel) at promoter regions. (G) Example of KDM5B binding at promoters marked with H3K4me3 and H3K27me3 (for example, HoxA cluster). (H) Correlation matrix of KDM5B binding with an assortment of TFs and epigenetic modifiers that are highly expressed in ES cells. Hierarchical clustering heat map generated by evaluating pair-wise affinities at promoters between ChIP-Seq datasets generated from this study (KDM5B, H3K4me3, RNAPII) and from published datasets [3, 35–39]. AutoSOME [40] was used to generate pair-wise affinity values. (I) Venn diagrams showing co-occupancy of KDM5B, OCT4, SOX2, and NANOG at promoter regions.