Fig. 5: Characterization of the CKS2 uORF-regulating RNA structural switch.
a, Secondary structure models for the two conformations of the CKS2 5′ UTR as identified by ensemble deconvolution from targeted DMS-MaPseq analysis, with overlaid in vivo DMS reactivities, along with reactivity profiles and base-pairing probabilities for both conformations. Reactivities are averaged across the two replicate experiments. The scatter plots depict the correlation of base reactivities for the deconvolved conformations across the two replicate experiments. b, Structure models for the two conformations of the CKS2 5′ UTR, inferred by phylogenetic analysis. Base pairs showing significant covariation (as determined by R-scape) are boxed in dark green (E < 0.05) or purple (E < 0.1). Helices showing helix-level covariation support are boxed in light green (E < 0.05) or light purple (E < 0.1). c, Histogram depicting the median of cell’s mean fluorescence in HEK293 cells expressing a dual-frame vector, harboring the 5′ UTR of CKS2, either wild type or mutagenized to stabilize either of the two conformations. Error bars represent the s.d. of three independent biological replicates. d, Western blot analysis of EGFP and HA expression in HEK293 cells expressing a dual-frame vector, harboring the 5′ UTR of CKS2, either wild type or mutagenized to stabilize either of the two conformations. GAPDH was used as the loading control. Analysis is representative of two independent biological replicates.
