Fig. 4: DHX36 binding-induced 3’UTR structural change is associated with post-transcriptional regulation of mRNA abundance.

A Schematic illustration showing the method for defining DHX36-induced post-transcriptional regulatory effect. The post-transcriptional fold change (pFC) of mRNA abundance was calculated by dividing the fold change in chromatin fraction by that in the whole cell. Created in BioRender. Zhang, Y. (2021) BioRender.com/a92l088. B Scatterplot showing the definition of pUGs and pDGs based on the pFC of mRNA abundance. C Venn diagram showing the overlapping between DHX36-bound mRNAs and pUGs or pDGs. Statistical significance was calculated by the Chi-square test. D Comparison of pFCs of DHX36-bound mRNAs and all protein-coding genes. E Comparison of ΔReactivity of pDG (n = 149) and pUG targets (n = 517). 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). A two-sided Wilcoxon rank-sum test was used to calculate the statistical significance in (D, E). F–I Scatterplots showing the correlations of mRNA abundance pFCs with reactivity changes of (F) entire mRNAs, G 5’UTRs, H CDSs, and I 3’UTRs of DHX36-bound mRNAs. r and P represent the correlation coefficient and statistical significance calculated by the Pearson correlation test. J Heatmaps showing the hierarchical clustering on the DHX36-bound mRNAs based on their abundance changes and the average reactivity changes of 5’UTR (left), CDS (mid), and 3’UTR (right). For each cluster, the Pearson correlation between the structure changes and the abundance changes was displayed in a scatterplot. The error bands in (F–J) represent the 95% CIs. K Average SHAPE reactivity across DHX36 binding sites within the designated regions of pUGs and pDGs. The colored horizontal lines represent the means of average reactivity across the binding sites. Position 0 represents the exact crosslink sites identified by PAR-CLIP data. L ΔReactivity of DHX36 binding sites within the designated regions of pUGs (n = 517) and pDGs (n = 149). Error bars represent 95% CI of the mean of ΔReactivity. P values were calculated by unpaired two-sided Student’s t-test.