Figure 4

O/E sites and TATA-boxes are enriched near rat, human, dog and cow OR TSSs. In all panels, the black lines represent data for the 314 mouse OR promoters (i.e., the same data as shown in Figure 1). Colored lines represent putative orthologous promoter regions (determined using UCSC's liftOver utility) from rat (gray), human (red), dog (dark blue) and cow (green). In panels B and C, solid lines represent matrix matches exceeding MatInspector's default score threshold ("opt"), and dotted lines represent matches found using a less stringent score threshold ("opt-0.1"). Panel A shows that orthologous promoters from all four placental mammals examined exhibit the same reduction in repeat content and characteristic fluctuation in GC content near the predicted TSS. Panel B shows that O/E sites are enriched upstream of orthologous promoters in placental mammals, and panel C shows that TATA-boxes are enriched upstream of orthologous TSSs. As in Figure 1, coverage is calculated as the proportion of promoter sequences containing a predicted O/E (or VTBP) binding site at each base-pair, averaged over 20-bp windows, sliding along promoters 1 bp at a time.