Fig. 4
Translation is shifted towards rG4-containing 5′-UTRs in DHX36- and DHX9-depleted cells. rG4s mark the 5′-UTR of DHX36- and DHX9-dependent mRNAs. Are reported the 5′-UTR length-normalized (a) rG4 and (b) dsRNA secondary structures predicted folding energies of the TEdown – RPFdistup and TEup – RPFdispdown groups compared to background transcripts (see main text for description of the different sets of transcripts). c Most enriched motif in the 5′-UTR of the TEdown – RPFdistup group (P < 2.2 × 10−16, Fisher exact test). The same motif was found depleted in the 5′-UTR of TEup – RPFdispdown group (P = 2.4 × 10−2, Fisher exact test). d rG4 and e dsRNA secondary structures predicted folding energies of the TEdown – RPFdistup top motif in the background or TEdown – RPFdistup transcripts. Sequences corresponding to the identified motif ± 10 nt were considered to reflect the influence of 5′-UTR base composition on local predicted structures. f Ribosome distribution normalized by mRNA signal, describing local translation efficiency, of the TEdown group (903 transcripts with combined Q value ≤ 0.05) in control (black), DHX36 (red), and DHX9 (green) depleted cells. The plots show changes in 5′-UTR translation upon depletion of the helicases. Ribosome footprint, mRNA signal coverages, and transcript length are normalized; dotted lines indicate annotated translation start and stop sites. g Predicted rG4 structure folding energies of detected high ORFscore uORFs in control (gray) or DHX36 (red) and DHX9 (green) depleted cells. The background set (black) represents uORFs with negative ORFscore in control cells. Data are means ± s.e.m.; P values were assessed using one-tailed Mann–Whitney nonparametric tests. ns: non significant, *P < 0.05, **P < 0.01. h rG4 structure potential downstream the start codons of DHX36- and DHX9-dependent. The cartoon above the plot depicts a “queue” of ribosomes stretching back to the uORF initiator codon. Folding energies were calculated per position using a sliding window of 35 nt and the lines represent the average of the values over 10 nt. Filled points are the identified local minima. The dotted lines represent the size of 80S ribosomes (40 nt) phased downstream the start codon. The cartoon above the plot depicts a “queue” of ribosomes stretching back to the uORF initiator codon