Fig. 2

Characterization of altered nucleosome distributions in KDM5B-depleted ES cells. Schema of + 1 nucleosomes relative to transcriptional start sites (TSS) shifted a downstream or b upstream. c Average density profiles of nucleosomes around TSS of genes with + 1 nucleosomes shifted downstream (shift distance: 10–50, 51–100, 101–150, 151–200 bp). Note the altered nucleosome densities and asynchronous array of nucleosomes in KDM5B-depleted ES cells. d Two-dimensional (2D) occupancy plot of nucleosomes around TSS of genes with + 1 nucleosomes shifted downstream in KDM5B-depleted ES cells. Plot2DO [31] was used to show relative nucleosome occupancy and fragment length in a heatmap matrix. Average profile of nucleosome occupancy is shown above the heatmap plot. X-axis: position relative to center of nucleosome; y-axis: fragment length (bp). e Average profiles of nucleosomes around TSS of genes with + 1 nucleosomes shifted upstream in KDM5B-depleted ES cells. f Two-dimensional (2D) occupancy plot of nucleosomes around TSS of genes with + 1 nucleosomes shifted upstream in KDM5B-depleted and control ES cells