Loss of Trm9 preferentially reduces expression of proteins from genes enriched with AGA and GAA codons, but not other codons.

<p>Groups of genes were identified, each with a significantly high use of one of 61 codons. Within each codon group, the number or percentage of significantly altered proteins and the ratio of down- to up-regulated proteins (D/U) were calculated. (<b>A</b>) Hierarchical clustering analysis of gene-specific codon usage patterns (Z-scores) for all yeast genes. Z-scores were calculated as the difference between the frequency of each codon used by each transcript and the genome average, divided by the standard deviation, with the scores indicating whether a transcript is over- or under-represented with a specific codon compared to the genome average. Over-represented codons are displayed in yellow and under-represented codons are displayed in blue. Codons showing no difference from the genome average are displayed in black. For clarity dendrograms are not displayed. Data are taken from (<b>B</b>) Plot of D/U <i>versus</i> the number of significantly down-regulated proteins in each group of proteins enriched with a given codon. The red dots represent data for the groups linked to the codons read by Trm9-modified tRNAs, while grey dots represent data for other codon groups. (<b>C</b>) To control for differences in group size, the ratio of down- to up-regulated (D/U) proteins was plotted as a function of the percentage of significantly down-regulated proteins in each group of proteins enriched with a given codon. The red lines indicate the overall percentage of significantly down-regulated proteins and the average D/U ratio in all proteins, respectively. (<b>D</b>) To account for codon biases other than AGA, proteins enriched with other codons (except for GAA) were removed from the AGA-enriched group, one codon at a time. Proteins from genes enriched with GAA were likewise removed from groups of proteins enriched in other codons. The values of the remaining proteins enriched with AGA were separately plotted in red dots, while the values of the remaining proteins enriched with other codons were plotted in grey dots. (<b>E</b>) Analysis similar to (<b>D</b>) repeated for proteins enriched with GAA.