Fig. 6.

Differentially reactive windows gain in structure in 4A-dep 5′UTRs more than in 4A-indep 5′UTRs. a Violin and density scatter plots depicting the average reactivity under control and hippuristanol conditions within all 27,396 windows identified by dStruct with an FDR less than 0.25. There are 1467 windows in the 5′UTRs, 372 windows overlapping the 5′UTR/CDS junction, 19,269 windows in the CDS, 331 windows overlapping the CDS/3′UTR junction and 5957 windows in the 3′UTR. Violin plots include boxplots, with the mean denoted by a dot. P values and 95% confidence intervals were calculated using a paired, two-sided Wilcoxon test. b Violin plots depicting the Δ reactivities of all windows in 4A-dep and 4A-indep mRNAs. There are 87 and 379 windows in 4A-dep and 4A-indep 5′UTRs respectively, 37 and 125 in 4A-dep and 4A-indep 5′UTR/CDS junctions respectively, 292 and 1508 in 4A-dep and 4A-indep CDSs respectively, 19 and 115 in 4A-dep and 4A-indep CDS/3′UTR junctions respectively and 183 and 924 in 4A-dep and 4A-indep 3′UTRs respectively. P values and 95% confidence intervals were calculated using an un-paired, two-sided Wilcoxon test. c, d Binned average Δ reactivity of c all dStruct windows and d all windows in 4A-dep and 4A-indep mRNAs. Shaded area in c represents 95% confidence limits for the difference in means between control and hippuristanol mRNAs within each bin, calculated by a paired two-sided t test. e, f Average Δ reactivity for each nucleotide either side of e the 5′UTR/CDS junction and f the CDS/3′UTR junction, for all windows spanning these junctions in 4A-dep and 4A-indep mRNAs