Figure 2

KDM5B regulates H3K4 methylation at gene body regions. Knockdown of Kdm5b transcripts results in altered H3K4 methylation profiles at promoters and enhancers and within gene body regions. (A) Heat map density of ChIP-Seq data at refseq genes sorted according to their absolute expression in ES cells. shKdm5b ES cells exhibit increased H3K4me3/2 methylation in gene body regions and decreased H3K4me3/2/1 methylation at promoter regions. (B) Correlation between changes in gene body histone methylation and expression level. Log2 fold change normalized tag density ratios (shKdm5b/shLuc) of H3K4me3, H3K4me2, and H3K4me1 at all refseq genes, which were sorted into four groups based on their absolute expression level in ES cells (red line, highest 25% expressed; green line, lowest 25% expressed). (C) Scatter plot of gene body densities of H3K4me3/2/1 in shLuc and shKdm5b ES cells. (D) UCSC genome browser examples of altered profiles of H3K4me3/2 within gene bodies of pluripotency-related genes such as Lsd1 and Nr5a2 in shKdm5b ES cells.