Fig. 2 |. Globally, mRNA intrinsic structure is not a main driver of translation.

a, Schematic representation of the two models that might explain the observed anticorrelation between translation efficiency and RNA structure in CDS regions in vivo. In the first model, preexisting CDS RNA structures guide translation (top; this is not supported by our analysis). In a second model, translating ribosomes are responsible for the unfolding of CDS RNA structures (bottom; consistent with our analysis). b, Cumulative distributions of global CDS RNA accessibility in vitro at 2 hpf, displaying no difference among mRNAs with different translation efficiency. Transcripts (n = 2,526) were binned into quintiles according to their translation efficiency. P value was computed with a one-sided Mann–Whitney U test. Although P was < 0.05, we considered this change nonsignificant, given the magnitude of the change and the large sample size; this conclusion is further supported by the scatter-plot analysis in Supplementary Fig. 2c. c, Scatter plot between in vivo and in vitro CDS accessibility at 2 hpf. In vivo, the accessibility was higher for highly translated mRNAs (red dots) and lower for weakly translated mRNAs (blue dots). d, Schematic view of the two models in which RNA structure at the AUG initiation codon is either the cause (top) or the result (bottom) of mRNA translation. e, Correlation between translation efficiency and the structure at AUG regions (n = 2,360), for both in vitro (left) and in vivo (right) conditions. Spearman correlation coefficients (ρ) and the corresponding asymptotic P values are shown.