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. 2019 Jan 30;47(5):2216–2228. doi: 10.1093/nar/gkz033

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© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 7. — Occurrence and position of non-optimal/optimal codon stretches in yeast mRNAs and their impact on translation. (A) The frequency of stretches of 10 consecutive codons with extremely low CSC values (≤–1.28) (red line) across the mRNA sequence. Neutral stretches (0.05 ≥ CSC ≥ –0.05, black line) and optimal stretches of CSCs (≥1.28) (blue line) were used as the control groups. Dunn's multiple test comparisons; **** ≤–1.28 versus neutral (0.05 to –0.05), **** ≤–1.28 versus ≥1.28 and **** ≥1.28 versus neutral (0.05 to –0.05). See details of the statistical analysis in Supplementary Table S7A. (B) mRNA sequences containing a 10-codon stretch with CSC values ≤–1.28 were aligned according to the position of the non-optimal stretch from the start codon. The heatmap depicts the sum of the CSC values in a ten-codon window. Panel (C) shows the mRNA half-lives (11) of the genes presented in panel 7B. (D) The average ribosome footprint density of the genes presented in panel 7C from the stretch of non-optimal codons (position 0). The number of reads at each position was normalized to the total number of reads in a 500-nucleotide window before and after the stretch. Genes with optimal stretches of CSC (≥1.28) (blue line) were used as the control group. The right y-axis represents the adjusted p-value (green area) calculated for each nucleotide position by multiple t-tests using the Holm-Sidak method. (E) The mRNA half-life values (11) were plotted according to the position of the non-optimal codon stretch (CSC ≤ –1.28) from the ATG. No correlation was found between the non-optimal codon position and the mRNA half-life. (F) The half-life (11) of the gene categories used in panels A and D. Kruskal–Wallis test, ****<0.0001, *0.017.