Figure 5

Regulation of gene expression at the level of TE and mRNA abundance. A) Genome-wide plot of the change in TE versus the change in mRNA between slBF and PCF, expressed as log2 ratios. B-D) Examples of genes where changes in protein production are mediated by different mechanisms. Panel B, regulation primarily by changes in mRNA abundance; Panel C, regulation primarily by changes in TE, and Panel D, regulation in which changes in both mRNA and TE contribute strongly. The histograms show the median log2-normalized fold change in read counts for ribosome footprint, mRNA and the TE. In the histograms, magenta tones are used for genes up-regulated in slBF while green tones are used for those up-regulated in PCF. The Artemis view from PCF3 (green) and slBF3 (magenta) are shown for each gene, with ribosome footprint being the dark color and mRNA being the light color. Similar changes were seen for cBF versus PCF. The genes depicted in this figure had negligible multi-mapping reads. The bars at the edge of the graphs indicate the relative scaling of ribosome profiling and mRNA read counts in the two stages. The SL reads (black in PCF, blue in slBF) are not to scale. The scale bar below the first panel represents 500 nt, used for all images).