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Fig. 1 | Genome Biology

Fig. 1

From: Local compartment changes and regulatory landscape alterations in histone H1-depleted cells

Fig. 1

Clustered DNA methylation changes in histone H1-depleted ES cells. a Circos plot showing the genome-wide distribution of hypomethylated (in blue) and hypermethylated (in red) loci along the linear sequence of chromosome 1 in H1 TKO compared with wild-type ES cells, based on the HELP-tagging assay. Inner tracks show local density of respective loci. b Histogram of number of genomic windows (fixed size, 20 kb, non-overlapping) that contain at least five randomly chosen sites out of the complete set of roughly one million assayable sites in the HELP-tagging assay. The counts in the histogram sum to the total number of random draws, i.e., 1000. The arrow indicates the observed number (103) of genomic windows that contain at least five differentially methylated sites, which is significantly more than expected by chance. c Percentages of genes compared with the percentages of DNA methylated sites in wild-type (WT) ES cells in groups of TADs ranked according to the number of overlapping genes (gene content). The ranking on the x-axis is such that the leftmost bin contains the 20 % TADs with the lowest number of genes and the rightmost bin TADs with the highest number of genes. The genomic sizes of the groups of TADs as a percentage of the total genomic size of all TADs is plotted as a reference. d Ratios of both the percentage of hypermethylated or hypomethylated sites in TKO cells over the percentage of DNA methylated sites in WT ES cells in the same groups of TADs as defined before (Fig. 1d). The ratio thus measures the amount of enrichment or depletion of hyper- and hypomethylation in TKO cells in each bin. e Spatial distribution of genomic sites where either hypo- or hypermethylation is observed in H1-depleted cells. We analyzed the location of differentially methylated sites with respect to different types of chromatin defined by the ChromHMM algorithm (based on a large collection of mouse ES cell ChIP-Seq data from the ENCODE consortium). For comparison, we include the same distribution for a random selection of sites where DNA methylation status was determined in the HELP-tagging experiment

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