Figure 3

Heatmap analysis with k-means clustering. By combining H3K27me3, H3K9me3, H3K4me3, H3K4me2, H3K36me3 and MES-4 (the histone H3K36 methyltransferase) ChIP-chip signals, as in Figure 2a, the Cistrome heatmap tool separates the ± 1-kbp regions for all of the C. elegans TSSs into five clusters using k-means clustering. From top to bottom, the clusters are as follows: (1) about 3,000 TSSs related to active genes have high H3K4me3 upstream of the TSSs and high H3K36me3 downstream of the TSSs; (2) about 2,000 TTSs have slightly lower H3K4me3 levels downstream of the TSSs and no significant K36me3 enrichment; (3) about 2,000 TSSs have high H3K27me3 and H3K9me3 related to inactive genes; (4) about 2,500 TTSs with low H3K27me3, moderate H3K4me3 and high H3K36me3 enrichment around the TTS related to genes in operons; and (5) about 10,000 TTSs have no strong marks.