Loss of Trm9 selectively reduces expression of proteins from genes with high usage of AGA and GAA codons.

<p>(<b>A</b>) Proportion of down-regulated proteins in AGA-enriched proteins <i>versus</i> non-enriched proteins. The histogram shows the distribution of proportion of down-regulated proteins of the non-enriched proteins obtained by 100,000 random samplings. The position of AGA-enriched proteins is indicated by an arrow, with the p-values indicating the chance that a random sampling has a ratio no less than that of the AGA-enriched group. (<b>B</b>) Proportion of down-regulated proteins of GAA-enriched proteins <i>versus</i> non-enriched proteins, as described above. (<b>C</b>) The D/U ratio of AGA-enriched proteins <i>versus</i> non-enriched proteins. (<b>D</b>) The D/U ratio of GAA-enriched proteins <i>versus</i> non-enriched proteins. (<b>E</b>) Correlation between AGA or (<b>F</b>) GAA codon usage and changes in expression of all proteins in <i>trm9</i>Δ cells. Spearman rank correlation coefficient (rs) and p-value are shown. (<b>G, H</b>) To further assess codon usage among significantly up- and down-regulated proteins, proteins were divided into seven bins based on AGA (<b>G</b>) or GAA (<b>H</b>) codon frequency (number per 1000 codons; bins of 0–10,10–20, <i>etc</i>.), and the average codon frequency in each bin was plotted relative to the ratio of down- to up-regulated proteins (D/U ratio for significantly altered proteins) calculated for each binned group.