Read-through motifs are avoided in highly expressed genes.

“TGACA” and “TGACT” (stop codon underlined) are two previously identified sequence motifs conducive to stop-codon read-through. A total of 6,572 yeast genes and 11,895 fruit fly genes are considered. (A-D) Yeast (A-B) and fruit fly (C-D) genes with and without the read-through motifs show significantly different expression levels. The distribution of gene expression level is shown in a box plot, where the lower and upper edges of a box represent the first (qu1) and third quartiles (qu3), respectively, the horizontal line inside the box indicates the median (md), the whiskers extend to the most extreme values inside inner fences, md±1.5(qu3-qu1), and the circles represent values outside the inner fences (outliers). P-values are based on Mann-Whitney U tests. (E-H) Observed and expected motif frequencies in yeast (E-F) and fruit fly (G-H) genes of low, medium, and high expressions. Genes are ranked by expression levels and then divided into three bins of equal numbers of genes. Each bar shows the observed motif frequency, with the error bar representing the standard deviation based on 1,000 bootstrap samples of genes within the bin. Each dot shows the motif frequency expected from the observed frequencies of the three components (stop codon and each of the following two nucleotides) of the motif in the bin. We shuffled motif components among genes in the same bin 10,000 times, and the P-value above each dot shows the probability that the number of motifs observed upon a shuffle is equal to or smaller than the number in the actual genes. (I-K) Frequencies of the stop codon TGA (I), C following the stop codon (J), and A/T at the next position (K) in yeast (grey bars) and fruit fly (white bars) genes of low, medium, and high expressions. Error bars show standard deviations based on 1,000 bootstrap samples of genes within the bin. Note that the Y-axis does not start from 0 in (I)-(K).