Fig. 4

Genes with altered expression are proportionally distributed across the genome. a Clustered heatmap of pair-wise correlation between RNA-seq gene expression profiles. We compare RNA-seq gene expression in our wild-type (WT) and TKO cells to RNA-seq data from a wide range of mouse tissues published by the ENCODE consortium. mESC mouse embryonic stem cell. b Volcano plot of statistical significance (-log10 p value) against fold change comparing RNA-seq gene expression between WT and H1 TKO mouse ES cells. Transcripts that are significantly differentially expressed between the two conditions are shown in red, whereas the genes in blue do not reach the threshold. c RNA-seq normalized expression values for a selection of transcripts previously reported to be down-regulated (Hox genes, left panel) and up-regulated (imprinted genes, right panel) in H1-depleted ES cells. d Percentages of differentially up- and down-regulated genes compared with the percentages of sites with a significant loss of DNA methylation in TKO ES cells and compared with all mouse genes. Percentages are calculated in groups of TADs ranked according to the number of overlapping sites that lose DNA methylation in TKOs. The ranking on the x-axis is such that the leftmost group contains the 20 % TADs with the lowest number of TKO hypomethylated sites and the rightmost group of TADs contains the highest number of such sites. e Percentages of differentially expressed genes compared with all genes in groups of TADs ranked according to the number of genes. The ranking on the x-axis is such that the rightmost group contains the 20 % TADs with the highest number of genes and the leftmost group of TADs contains the lowest number. The genomic sizes of the groups of TADs as a percentage of the total genomic size of all TADs is plotted as a reference. f Percentages of differentially up- and down-regulated genes compared with the percentages of sites with a significant increase in H3K4me1 enrichment in TKO ES cells and compared with all mouse genes. Percentages are calculated in groups of TADs ranked according to the number of overlapping sites that gain H3K4me1 in TKOs. The ranking on the x-axis is such that the leftmost group contains the 20 % TADs with the lowest and the rightmost group of TADs contains the highest number of these sites. g Percentages of differentially up- and down-regulated genes compared with the percentages of sites with a significant decrease in H3K4me1 enrichment in TKO ES cells and compared with all mouse genes. Percentages are calculated in groups of TADs ranked according to the number of overlapping sites that lose H3K4me1 in TKOs. The ranking on the x-axis is such that the leftmost group contains the 20 % TADs with the lowest and the rightmost group of TADs contains the highest number of these sites