DDX3X-sensitive 5′ UTRs are highly structured. (A) SHAPE-MaP reactivity and mutation rate for the 5′ UTR of RAC1 in vitro. In vitro transcribed mRNA containing the 5′ UTR of RAC1 and the ORF of luciferase was probed with 200 mM NAI or DMSO control for SHAPE-MaP. The RNA was reverse transcribed, sequenced, and analyzed to obtain mutation profiles and SHAPE reactivity with the ShapeMapper tool. (B) Diagram of the structure of the RAC1 5′ UTR in vitro, based on data from A and computed with ShapeMapper 2.1.3 (Busan and Weeks 2018). (C) SHAPE-MaP reactivity and mutation rate for the 5′ UTR of RAC1 in vitro. In vitro transcribed mRNA containing the 5′ UTR of ODC1 and the ORF of luciferase was probed with 200 mM NAI or DMSO control for SHAPE-MaP. The RNA was reverse transcribed and sequenced. The mutation rate was calculated at each position for both treated and control samples. The SHAPE reactivity was calculated based on the difference in mutation rate. SHAPE reactivity is cropped for space, the full figure can be found in Supplemental Figure S2A. (D) Diagram of the structure of the ODC1 5′ UTR in vitro, based on data from C and computed with ShapeMapper 2.1.3 (Busan and Weeks 2018).
