Figure 3
The periodic signal varies with expression level and specificity, and H3K56 acetylation. (a) We divided 4,372 genes into two groups (low expression (LE) and high expression (HE)) according to their median expression level across 72 tissues. The boxplots show the distribution of the magnitude of the 10-bp periodic signal for 5,000 bootstrap iterations on 1,000 randomly selected TSSs in each group (see Materials and methods). The 10-bp periodic signal is stronger in the low expression group than in the high expression group. (b) The same set of genes were divided into three groups according to their tissue specificity (low, medium and high tissue specificity) and the same bootstrap analysis was performed. (c) The distribution of the normalized H3K56ac enrichment (log2 ratio) for the 6,518 TSSs that possess an H3K56ac sequence tag (see Materials and methods) is shown. The TSSs were divided into three groups of equal size with, respectively, low (L, blue) medium (M, green) and high (H, orange) H3K56ac enrichment ratios. (d) The three groups of H3K56ac enrichment are associated with different strengths of the periodic RR/YY signal. A randomization test shows that increased H3K56 acetylation levels is significantly correlated with increased 10-bp periodic signal (Wilcoxon rank sum test, one sided: L versus M P-value = 2.2 × 10-16; M versus H P-value = 3.8 × 10-07; L versus H P-value = 2.2 × 10-16).