Fig. 3
eIF4A-dependent mRNAs are not enriched in G-quadruplexes. a A scatter plot depicting the log-fold change in expression between hippuristanol and control, in the polysomal and sub-polysomal fractions, for all 16,868 genes in the MCF7-specific transcriptome. A negative log-fold change indicates reduced expression following hippuristanol treatment and vice versa. The plot is color coded by those mRNAs identified as either eIF4A-dependent (4A-dep) (728), eIF4A-independent (4A-indep) (4587), or eIF4A-antidependent (4A-antidep) (78) or those that were not assigned to each category (see the “Methods” section). b–e Density plots, showing 5′UTR length, C content, G content, and G4NN scores (see the “Methods” section) for 4A-dep and 4A-indep mRNAs. For those mRNAs which we were able to determine the UTR boundaries (see the “Methods” section), the most abundant transcript per gene was selected. An equal group size of 4A-indep mRNAs was created by selecting the mRNAs with the lowest posterior probability, i.e., those which with most confidence are 4A-indep. This resulted in 441 mRNAs per group. P values and 95% confidence intervals were calculated using an un-paired, two-sided Wilcoxon test. f A diagrammatic representation of a (GGC)4 sequence folded into a G-quadruplex, with the cytosine residues highlighted in yellow, indicating their accessibility to DMS. g Normalized average reactivity of all (GGC)4 and (GCC)4 motifs within 5′UTRs. One motif per 5′UTR was randomly selected, which resulted in 91 (GGC)4 and 54 (GCC)4 motifs. The reactivity of the motif was normalized by subtracting the average reactivity for the corresponding 5′UTR. P values and 95% confidence intervals were calculated using an un-paired, two-sided Wilcoxon test. h Normalized average Δ reactivity of the (GGC)4 and (GCC)4 motifs from panel G. The Δ reactivity of the motif was normalized by subtracting the average Δ reactivity for the corresponding 5′UTR. P values and 95% confidence intervals were calculated using an un-paired, two-sided Wilcoxon test. i, j Normalized Δ reactivity of (GGC)4 and (GCC)4 motifs, compared between 4A-dep and an equal-sized group of 4A-indep mRNAs. There are 16 (GGC)4 and 15 (GCC)4 motifs in each group. P values and 95% confidence intervals were calculated using an un-paired, two-sided Wilcoxon test