Figure 6

A combined regulation of protein biosynthesis genes by promoter and 3' UTR motifs. (a) A schematic depiction of the regulation of typical ribosomal biogenesis and assembly genes and of rRNA transcription and processing genes. While many protein biosynthesis genes (predominantly ribosomal genes) are regulated by Rap1 in their promoters, and most rRNA transcription and processing genes are regulated by the combined Pac-RRPE cassette, these two types of genes are suggested here to share a stability-associated motif in their 3' UTR, namely M24. (b) Combinogram analysis [18] of the protein biosynthesis genes in the condition of environmental response to peroxide stress [61]. We gathered all genes annotated with protein biosynthesis by the SGD [32] and partitioned them into four disjoint sets: genes containing only RAP1, only M24, both of them and neither of them. The motif presence is marked by a plus symbol in the second panel. The first panel presents a dendrogram built using the correlation coefficients between the mean expression profiles of each of the four sets. We also present, for each set, its EC score [18,31], in a bar diagram. All four EC scores had a p-value < 0.05. The number of genes in each set is also given, for which we had expression profiles in the presented condition. Finally, in the fourth panel, we show the expression profiles of the genes in each set in blue, and their mean profile in black. The genes on the far right of the fourth panel, which contain only M24 in their 3' UTRs, but not Rap1 in their promoter, exhibit a significantly more coherent behavior than the background set (genes containing neither of the two motifs) and their profiles show a sharper decrease in the beginning of the experiment.