Supplementary Figure 4: Folding of the P1 and P3 stems.
From: Cotranscriptional folding of a riboswitch at nucleotide resolution
(a) Cotranscriptional SHAPE-seq reactivities for transcript length 40 of the B. cereus fluoride riboswitch are shown in the presence (top) and absence (bottom) of fluoride. S and L indicate P1 stem and loop nts, respectively. (b) The secondary structure of transcript length 40 is inferred from cotranscriptional SHAPE-seq reactivities, covariation analysis (Baker, J.L. et al., Science. 335, 233-5, 2012), and crystallographic data (Ren, A. et al., Nature. 486, 85-89, 2012). Nucleotide colors indicate cotranscriptional SHAPE-Seq reactivities with 10 mM NaF from (a). Gray nucleotides exist within the RNAP footprint at this length (Komissarova, N. and Kashlev, M., Proc Natl Acad Sci U S A. 95, 14699-14704, 1998). (c) Cartoon representation of P1 stem folding. Nucleotide colors correspond to key sequence elements as described in the main text and Figure 4. (d) Cotranscriptional SHAPE-Seq reactivities for transcript length 54 of the B. cereus fluoride riboswitch are shown in the presence (top) and absence (bottom) of fluoride. S and L indicate P3 stem and loop nts, respectively. (e) The secondary structure of transcript length 54 is inferred from cotranscriptional SHAPE-Seq reactivities, covariation analysis (Baker, J.L. et al., Science. 335, 233-5, 2012) and crystallographic data (Ren, A. et al., Nature. 486, 85-89, 2012). Nucleotide colors indicate cotranscriptional SHAPE-seq reactivities with 10 mM NaF from (d). Gray nucleotides exist within the RNAP footprint at this length (Komissarova, N. and Kashlev, M., Proc Natl Acad Sci U S A. 95, 14699-14704, 1998). (f) Cartoon representation of P3 stem folding is shown. Nucleotide colors correspond to key sequence elements as described in the main text and Fig. 4. Results shown are extracted from Fig. 3b.
