Fig. 1

Profiling of nucleosome distributions in KDM5B-depleted ES cells. a–c Average profile of nucleosome density relative to a transcriptional start sites (TSS), b DNase I hypersensitive sites, and c CTCF-bound regions in KDM5B-depleted and control ES cells. d Density plot of nucleosome fragment length (bp) in control (shLuc) and KDM5B-depleted ES cells. e, f Density plot of nucleosome variance for e + 1 nucleosomes (red) or − 1 nucleosomes (blue; relative to TSS) and at f active (red; RPKM > 1) and inactive (blue; RPKM < 1) genes (x-axis: nucleosome variance (bp); y-axis: nucleosome density). g Heatmap of nucleosome variance (shift distance in bp) around + 1 nucleosomes and − 1 nucleosomes with respect to TSSs in KDM5B-depleted ES cells. h Density plot of nucleosome-to-nucleosome distance nearby active gene promoters (left), and at + 1 or − 1 variant nucleosomes (middle, right). i Heatmap of nucleosome densities in shLuc and shKdm5b ES cells sorted by distance between + 1 and + 2 nucleosomes (relative to TSS; left) and between + 1 and + 3 nucleosomes (right). Note the disorganized nucleosome array in KDM5B-depleted ES cells relative to control ES cells. j UCSC genome browser view of shLuc and shKdm5b MNase-Seq and MNase-Seq position difference in KDM5B-depleted and control ES cells. For MNase-Seq positional difference, if nucleosome occupancy is greater in shKdm5b ES cells relative to shLuc ES cells, the value is − log10 P-value, else, it is log10 P-value. Green line depicts TSS. k Percentage of KDM5B-bound (gray) and unbound (black) nucleosomes 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