Fig. 3.

The RNA structures that control translation rates. a The most folded window controls translation more strongly than less folded windows. The correlation between log₁₀ translation rates (TR) and single windows within mRNA 5′ regions is shown. Six windows were selected based on the rank of their free energy: “min,” “10%,” “25%,” “75%,” “90%,” and “max,” where “min” is the most folded (smallest free energy) and “max” is the least folded. The values plotted are the R² coefficients of determination expressed as a percent of the R² coefficient for the “min” window. The window length was the optimum for each species: S. cerevisiae, 35; Arabidopsis, 40; and M. musculus, 55; H. sapiens, 60; and S. pombe, 25. b Number of nucleotide pairs describe the regulatory potential of the most folded window. The number of paired nucleotides was calculated in the most folded (min) window of each gene for the longest contiguous stem without mismatches or single nucleotide bulges (contig stem, light blue), the longest stem (max stem, mid blue), and for all pairs within the window, including those not in the longest stem (all, dark blue). The Pearson correlation coefficients between each of these three measures and log₁₀ translation rates are plotted on the y-axis for the five example datasets. The lengths of the most folded widows are also given. For all but S. pombe, the correlation coefficients are more negative for measures that include more nucleotide pairs. The primary data are provided in Additional file 6