Fig. 4

eIF4A-dependent mRNAs become more structured than eIF4A-independent mRNAs at the 3′ end of the 5′UTR. a–c Violin plots for the average Δ reactivity in the 5′UTR, CDS, and 3′UTR for eIF4A-dependent (4A-dep) and independent transcripts (4A-indep). Transcripts were filtered by coverage and 5′ end coverage and the most abundant transcript per gene was selected, resulting in 192 4A-dep mRNAs. To ensure equal group sizes, of the 663 4A-indep transcripts, the 192 transcripts with the lowest posterior probability were selected, i.e., the 192 mRNAs that with greatest confidence are 4A-indep. Violin plots include boxplots, with the mean denoted by a dot. P values and 95% confidence intervals were calculated using an un-paired, two-sided Wilcoxon test. d Binned Δ reactivity for all 4A-dep (blue) and 4A-indep (orange) mRNAs across the length of the UTRs (25 bins) and coding sequence (50 bins). Negative values indicate increased structure following hippuristanol treatment, whereas positive values indicate decreased structure. Only those mRNAs from panels a–c whose 5′UTR, CDS, and 3′UTR are at least 100 nt were included, resulting in 147 4A-dep mRNAs and an equal group size of 4A-indep mRNAs