Fig. 2

Altered genomic regulatory landscape in H1 TKO cells. a Clustered heatmap of fraction of overlap of enriched regions (peaks) in ChIP-sequencing experiments. We compare our ChIP-seq data for the histone modifications H3K4me1, H3K4me3, H3K27me3, and H3K9me3 in wild-type (WT) and TKO cells to ChIP-seq data for these marks published by the ENCODE consortium in another mouse ES cell line. b Heatmap of DNase-seq coverage in triplicate experiments in WT and H1 TKO cells. Genome-wide statistical analysis of differences in DNase-seq coverage between WT and TKO cells revealed 2123 sites (top) with a gain and 2043 sites (bottom) with a loss of DNaseI hypersensitivity in TKO cells, respectively. The rows of the heatmap correspond to these ~4000 sites, ordered by log-fold change in coverage, with a random collection of unaltered DNaseI hypersensitive sites in between. c Venn diagrams that contain counts of sites that gain (left) or lose (right) enrichment of the histone marks H3K4me1 and H3K4me3 and their overlap with the 2123 newly formed DHSs in TKO cells. d Heatmaps of ChIP-seq enrichment for histone marks H3K4me1 and H3K4me3 in WT and H1 TKO cells. Profiles represent averages over duplicate experiments. Genomic sites represented by rows in the heatmap are sites where significant changes in H3K4me3 enrichment are observed. Rows are ranked by the magnitude of that change from top to bottom in descending order of increase in H3K4me3 enrichment in TKO cells. e Scatter plot of changes in H3K4me1 enrichment and DNA methylation at sites where significant changes in both are observed