Fig. 7: RiboSNitches are associated with RBP dynamic binding sites and human diseases.
From: Predicting dynamic cellular protein–RNA interactions by deep learning using in vivo RNA structures
a The bottom-left triangle presents the number of putative riboSNitches detected in pairwise comparisons between two cell lines; the top-right triangle presents the number of these putative riboSNitches in the dynamic RBP binding sites predicted by PrismNet. b Enrichment of riboSNitches in dynamic RBP binding sites compared to common binding sites predicted by PrismNet for each RBP. “All pairwise cell lines” here refers to a pairwise comparisons among all cell lines. c Enrichment of riboSNitches relative to VSSs within HARs in human disease (from ClinVar). “All pairwise cell lines” here refers to a pairwise comparisons among all cell lines, while “VSS” refers to “variations of stable structure”, i.e., those genetic variations without RNA structure changes. In b and c, each dot represents an RBP, with significant enrichment shown in color (Fisher’s exact test). d Structural profiles of the icSHAPE scores around a riboSNitch in the PNPO transcript in HEK293 and K562 cells. e Structural models of a riboSNitch and flanking sequences in the PNPO transcript in HEK293 and K562 cells, predicted by RNAshapes with the corresponding icSHAPE scores as constraints. Red stars indicate the mutation sites. f Binding probabilities and saliency maps of TARDBP on the PNPO transcript in HEK293 and K562 cells. g Splicing of the PNPO transcript in K562 and HEK293 cells (n = 3 replicates). h Splicing of the PNPO transcript in WT and TARDBP knockdown K562 cells. FUS knockdown K562 cells were included as a negative control.
