Additional file 2: Figure S4. of Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

Characteristics of nucleocyclic TSSs in the blastulae. a. Representative TSSs in blastulae are clustered into three groups according to nucleosome positioning consistency (autocorrelation) downstream of the TSSs. The upper left box shows the number of TSSs in each group. A running average over 21-bp window is shown. b. Distribution of gene expression (TSS capture frequencies) in log scale. Capture frequencies for the nucleocyclic TSSs in Group 1 is significantly higher than that of non-nucleocyclic TSSs in Group 2 or 3 (p = 1.9 x 10-5). c. Average incidence of nucleobase A, T, C and G at positions within 500 bp from representative TSSs in Groups 1, 2 and 3. A running average over 41-bp window is shown. The small histogram in each graph shows the significance of asymmetry of each rate in individual group. The arrows suggest that the A, C, and G incidences around the first nucleosome dyads and linkers downstream of nucleocyclic TSSs significantly differ from those incidences around nucleosomes in the entire genome in Figure S4d. d. Around nucleosome dyads in the entire genome, the A/T (C/G, respectively) incidences around linkers are smaller (greater) than those around dyads, while this tendency is less pronounced around first dyads downstream of TSSs. Indeed, the difference in the tendency is significant; namely, p < 10-6 for any of A, C, G, and T by one-tailed Wilcoxon’s ranksum test (Materials and Methods). A running average over 41-bp window is shown. (PDF 821 kb