Supplementary Figure 12: Promoter architecture in stable and developmentally regulated genes.
From: Absence of canonical marks of active chromatin in developmentally regulated genes
Conservation of core promoter sequence. (a) Distribution of PhastCons scores derived from 12 Drosophila species in the promoter sequence (defined as 200 bp upstream of the TSS) of stable and regulated genes. Promoters of regulated genes show stronger sequence conservation than those of stable genes: average PhastCons score of 0.27 in regulated genes and 0.17 in stable genes (P < 2.2 × 10−16). The bottom and top of the boxes are the first and third quartiles, and the line within is the median. The whiskers denote the interval within 1.5 times the IQR from the median. Outliers are plotted as dots. (b) Conservation of transcription factor binding motifs. We identified the predicted binding motifs for transcription factors that have a PhastCons score greater than 0.95 in the promoter sequence of stable and variable genes. Box plots show the distribution of the number of conserved motifs only for promoters that contain at least one prediction (P = 2.217 × 10−6). P values were computed using Wilcoxon test (one-sided).
