Figure 5

ChIP-chip analysis of multiple histone marks at the promoters of repressed genes. Plotted in the heatmap are -log10 P-values corresponding to ChIP-chip signal intensities of H3K4me3, H3K27me3, H3K9me2, and H4K20me3 at the promoters of 80 genes as measured in SW480 versus normal colon mucosa. The heatmap reveals two main classes of genes. Most repressed genes designated as K4-independent retain H3K4me3 (blue color) and gain repressive histone marks, including H3K27me3 and H4K20me3, which move from mostly red in normal to blue in the tumor. In contrast, most repressed genes designated as K4-dependent show loss of H3K4me3 (with H3K4me3 going from blue in tumor to red in SW480) and have not acquired any other repressive marks (with the other marks displayed as red in both the normal and tumor). In addition, the majority of genes within K4-dependent lack a CpG island (***no CpG island), while all K4-independent genes have a CpG island.