Extended Data Fig. 3: Characterization of the TXNL4A uORF-regulating RNA structural switch.
(a) Secondary structure models for the two conformations of the TXNL4A 5′ UTR as identified via 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 TXNL4A 5′ UTR, inferred by phylogenetic analysis. Base-pairs showing significant covariation (as determined by R-scape) are boxed in dark green (E-value < 0.05) or purple (E-value < 0.1). Helices showing helix-level covariation support are boxed in light green (E-value < 0.05). (c) Histogram depicting the median of cell’s mean fluorescence in HEK293 cells expressing a dual-frame vector, harboring the 5′ UTR of TXNL4A, either wild type, with the uORF start codon mutagenized from CUG to CCG, or mutagenized to stabilize conformation B. Error bars represent the standard deviation of 3 independent biological replicates.
