Fig. 4

The G-to-A SNP changes the secondary structure of an RNA segment from ZR3. A Predicted secondary structures for 105-nt ZR3 reference and alternative sequences (chr3:20310428–20310522, 20311150–20311157), including the added GG at the 5′-end added to improve T7 transcription, making the final length 105 nt. The SNP is identified by an arrow. Structures were folded using RNAstructure [38] and outputted using R2R (https://help.rc.ufl.edu/doc/R2R) [40]. B MutaRNA dot plot [39] displays the probability of base pairing of the reference (above the diagonal) and alternative (below the diagonal) sequences. The color scale shows the strength of base pairing probability. The position of the SNP is denoted with dashed red crosshairs. C–F DMS reactivity of a 77-nt portion of the ZR3 RNA segment (nucleotides corresponding to the primer binding site for the in vitro probing and compressed data at the top of the gel could not be mapped) is plotted in C from an in vivo dataset from plants grown at 21 °C [6], as well as for two in vitro DMS experiments conducted at D 20 °C and E 37 °C. In vitro DMS reactivity was derived from two sequencing gels provided in Additional file 4: Fig. S2. F The delta DMS reactivity of the alternative and reference sequences at both 20 °C and 37 °C