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. 2017 May 30;8:15622. doi: 10.1038/ncomms15622

Figure 7. SNP rs16260 influences folding of sense promoter-associated RNA.

Figure 7

(a) SHAPE reactivity gel analysis of the sense transcript (−688/−57) showing the region encompassing SNP rs16260 with C (left) and A (right) variants. G, A, and C, sequencing lanes. Samples were incubated with 0 (DMSO), 32 or 65 mM NMIA. Yellow boxes, position of the polymorphic site with either C or A variant. (b,c) Secondary structures of S-paRNA with the −160C (b) and −160A (c) allele built using RNAstructure based on SHAPE-derived constraints and visualized using VARNA. Colours mark nucleotides that are either unstructured (red, SHAPE ≥0.85), well-ordered (black, SHAPE <0.4), with intermediate reactivity (orange) or non-resolved/undetectable (gray). (d) Binding of HA-AGO1 to −160A and mutated −160A/G141U S-paRNA determined by RIP. B, bulges; dark gray box, isomiR-4534 binding site; L, loops; light gray boxes, base pair in −160C allele disrupted in −160A variant.