Fig. 6

Characterization of H3K4me3, RNAPII and expression of genes with altered nucleosome distributions. a–d Boxplots of a, b H3K4me3 (log2) and c, d RNAPII (log2) densities at regions with shifted + 1 and − 1 nucleosomes relative to TSS regions in shLuc and shKdm5b ES cells. Shift distance (bp). e RNA-Seq expression analysis. Percentage of upregulated or downregulated differentially expressed (DE) genes with uniform nucleosome placement (0-bp shift) or shifted + 1 or − 1 nucleosomes (10–200-bp shift) relative to TSS in KDM5B-depleted ES cells. f Percentage of upregulated or downregulated DE genes, bound by KDM5B, with uniform or shifted nucleosome placement relative to TSS in KDM5B-depleted ES cells