Differential TE transcripts in eIF3dKD and eIF3eKD show negative correlation with the UTR length and uORF content while they positively correlate with GC content of their 3’ UTRs and coding sequences (CDS).
(A) Bar plot showing the Spearman correlation between the observed ΔTE values for all genes with assigned adjusted p-values in each knock-down and different mRNA features (5’ and 3’ UTR length or GC content, uORF content in 5’ UTR). *** = P < 10-20, ** = P < 10-10, * = P < 0.005. (B-C) Box and whisker plots comparing UTR lengths or GC content (in UTRs or CDS) among mRNAs with TE significantly increased (red, upregulated), decreased (blue, downregulated), or unchanged (white) in eIF3dKD (B) and eIF3eKD (C); *** = Padj < 10-10, ** = Padj < 10-5, * = Padj < 0.05, color indicates comparison set. (D) Same as in (B-C) but for the number of AUG-initiated uORFs in 5’ UTRs in the eIF3d, eIF3e and eIF3h knock-downs. Outliers are not shown for better clarity. (E) Histogram of the frequency of AUG-initiated uORFs per 5’ UTR in all transcripts listed in the uORFdb database that were assigned a p-value in this study (n=11450), for downregulated translation only DTEGs in eIF3dKD (n=1027) and for downregulated translation only DTEGs in eIF3eKD (n=618). (F) Venn diagram summarizing the main results of this study. Groups of significant DTEGs identified in given knock-downs (encircled – color-coded) are indicated by a blue arrow for downregulated or an orange arrow for upregulated. Results confirmed by western blotting are shown in bold. Ribosomal proteins were placed on the borderline between eIF3dKD and eIF3eKD because they were identified as eIF3eKD “unique upregulated” DTEGs, but their protein levels were elevated in both eIF3eKD and eIF3dKD, as shown by western blotting. The “MAPK/ERK signaling” is shown in bold italics because it is an independent phenomenon that could be detected only by western blotting.