FIGURE 6.

TPT1 mRNA secondary structures are similar in the presence and absence of protein. (A) Median reactivity data from RNA in cellular lysate over a moving window of 40 nt indicating structured (low median SHAPE) and unstructured regions (high median SHAPE) within corresponds closely with the pattern of (B) median reactivity data from naked RNA. A 5′ to 3′ decrease in median SHAPE is observed, consistent with a highly structured 5′ UTR and less structured 3′ UTR. (C) Supportive of the overall similar median reactivities, pattern correlation of SHAPE reactivity is high (>0.85 overall). We performed correlations over multiple windows, from 10 to 50, bottom to top, with lighter blue indicating higher correlation. Regions of difference are noticeable as darker bands in the CDS and 3′ UTR. (D) TPT1 secondary structure model informed with SHAPE reactivies from unbound RNA modification. Regions of interest are labeled, including the start codon, stop codon, proposed PKR activating helices in the 5′ UTR, and putative AREs in the 3′ UTR.