Fig. 1: In vivo RNA structurome profiling unveils DHX36 depletion-induced global increase of RNA structures.

A Left: schematic illustration of the CRISPR-Cas9 mediated generation of DHX36 knockout (KO) in HEK293T cells. 169 bp of exon 1 of the DHX36 gene was deleted by two single-guide RNAs and CRISPR-Cas9. Right: western blot confirmed the inactivation of DHX36 in KO cells with GAPDH as the loading control. Source data are provided as a Source Data file. B Schematic illustration of in vivo structure mapping in WT and DHX36-KO cells. Orange circle, SHAPE modification; NGS next-generation sequencing, RT reverse transcription. C Sequencing gel for 5.8S rRNA showing the RT stops induced by NAI modification. Source data are provided as a Source Data file. D The average SHAPE reactivity score and E Gini index of reactivity scores of all mRNAs (n = 7792) in WT and DHX36-KO. The most abundant mRNA per gene was analyzed. Wilcoxon signed-rank test was used to calculate the statistical significance. The average fold change (FC) between the KO vs WT is shown. The boxes indicate median (center), Q25, and Q75 (bounds of box), the smallest value within 1.5 times interquatile range below Q25 and the largest value within 1.5 times interquatile range above Q75 (whiskers). F Top: the binned average Gini index across the length of 5’UTRs (5 bins), CDSs (10 bins), and 3’UTRs (5 bins) of all mRNAs. Bottom: The binned ΔGini (KO-WT) across the above regions. G The binned average reactivity and ΔReactivity (KO-WT) across the 5’UTR (25 bins), CDS (50 bins) and 3’UTR (25 bins). The shaded area represents 95% confidence intervals (CIs) of the average ΔGini or ΔReactivity of each bin calculated by paired two-sided Student’s t-test.