Distribution of H3K4me relative to genes. (a) Distribution of H3K4me at the 5' and 3' ends of genes. 'Isolated' genes are divided into four groups according to their length (see text for details). Genes belonging to each length group were aligned at the transcription start sites, and the percentage of genes containing H3K4me in their promoters or 5' ends is determined at 200-bp intervals (left y-axis). Similarly, genes belonging to each length group were aligned at the end of transcribed regions, and the percentage of genes containing H3K4me in their 3' ends or downstream flanking regions is determined at 200-bp intervals (right y-axis). The first and last 500 bp, 1 kb, 1.5 kb and 2 kb are shown for genes that are 1 to 2 kb, 2 to 3 kb, 3 to 4 kb and >4 kb in length, respectively. (b) Distribution of H3K4me across genes. Each gene (thick horizontal bar) was divided into 20 intervals (5% each interval), and the 1-kb regions upstream and downstream of each gene (thin horizontal bars) were divided into 50-bp intervals. The percentage of genes with H3K27me3 in each interval was graphed (y-axis). (c) Relationship between gene length and H3K4me. Genes are divided into eight categories according to the combination of H3K4me (see text for details), and the percentage of genes within each length group that are associated with a particular combination of H3K4me is shown (y-axis). (d) Length distribution of genes associated with different combinations of H3K4me. X-axis: gene length in kb (200 bp per bin); y-axis: the percentage of genes associated with a particular combination of H3K4me that are of the corresponding length. A small number of genes longer than 8 kb are not shown.