Fig. 2: DHX36 binding induces mRNA structural loss and gained accessibility.

A The workflow for analyzing PAR-CLIP and Structure-seq data to identify DHX36 binding-induced structure remodeling. Created in BioRender. Zhang, Y. (2022) BioRender.com/p72o682. B The distribution of DHX36 binding sites in 5’UTRs, CDSs, and 3’UTRs. C The transcriptomic distribution of DHX36 binding sites. D rG4 formation was predicted in DHX36 binding sites, and the distribution of each subtype is shown. E The average SHAPE reactivity and Gini index of the reactivity scores of DHX36-bound mRNAs (n = 1787). The most abundant mRNA per gene was analyzed. The significance was calculated by a two-sided Wilcoxon signed-rank test. The fold change (FC) between the KO vs WT is shown. F Comparison of ΔReactivity and ΔGini (KO-WT) between DHX36-bound and unbound mRNAs. The significance was calculated by a two-sided Wilcoxon rank-sum test. G The binned average reactivity (top) and ΔReactivity (bottom) across the length of 5’UTRs (25 bins), CDSs (50 bins), and 3’UTRs (25 bins) of DHX36-bound mRNAs. The shaded area was plotted in the same way as Fig. 1G. H The average reactivity of 5’UTR, CDS, and 3’UTR of DHX36-bound mRNAs (n = 1787). The significance was calculated by a two-sided Wilcoxon signed-rank test. The boxes indicate median (center), Q25 and Q75 (bounds of box), the smallest value within 1.5 times interquatile range below Q25 and largest value within 1.5 times interquatile range above Q75 (whiskers). I Scatterplot showing regional ΔReactivity vs. GC content of the designated regions. r and P represent the correlation coefficient and statistical significance calculated by the Pearson correlation test. J The proportion of DHX36 depletion-induced DRRs located within (+DHX36) and outside (−DHX36) DHX36 binding sites. K The distribution of DHX36-induced DRRs across different regions of DHX36-bound mRNAs. L The distribution of DRRs across the mRNAs with DHX36 binding to 5’UTR (top), CDS (middle) or 3’UTR (bottom) only. The line plot shows the location of DHX36 binding sites, and the heatmap shows the DRR enrichment. M ΔReactivity (KO-WT) of PYCR1 and CCNA2 mRNA. DRRs and DHX36 binding sites are highlighted in the shaded areas and green arrows, respectively. ΔR and P represent the average difference in reactivity and the significance calculated by the two-sided Wilcoxon signed-rank test.