Figure 4. Epigenetic changes in HCT116-DKO cells.

A. Clustering analysis of epigenetic changes on chr19 in HCT116-DKO cells in comparison to HCT116-WT cells. Each vertical line represents one gene. Green, red and black colors represent low, high and average occupation by epigenetic marks, respectively, in comparison to the average signal along the chromosome. Similarly, gene expression is indicated by green, red and black color showing low, high and average expression level, respectively, in comparison to average transcription levels on chr19. For expression changes, red, green and black colors represent activation, repression and no change of transcription activity, respectively, in HCT116-DKO cells in comparison to HCT116-WT cells. Abbreviations WT and DKO are for HCT116-WT and HCT116-DKO cells, respectively. B. Interrelation between genome-wide expression changes in HCT116-DKO cells in comparison to HCT116-WT cells and gene body CpG density (R = -0.02, p  =  0.03). Red color indicates ZNF genes. C. Representative epigenetic profiles of activated ZNF genes in HCT116-DKO and silent state of these genes in HCT116-WT cells. Direction of transcription and gene coordinates on chromosome 19 are indicated. The boxes span promoters of genes that become demethylated and reactivated in DKO cells as indicated by appearance of the H3K36me3 mark in their gene bodies. D. Composite profile of H3K36me3-associated genes in HCT116-DKO and in HCT116-WT cells. The profile was created for genes with gene bodies covered by H3K36me3 and DNA methylation with at least 20% of gene body length covered in HCT116-WT cells. Each gene body was divided into 20 bins and the 5 kb upstream of the TSS and 5 kb downstream of the 3' gene end were divided into 10 bins. The average signal for each single bin is indicated. E. H3K36me3 is not lost in regions with extensive loss of DNA methylation in gene bodies. Despite of loss of DNA methylation (blue tracks) in gene bodies, the H3K36 profile (black tracks) is almost unaltered.