Figure 6.

SHAPE-MaP overview. RNA is treated with a SHAPE reagent that reacts at conformationally dynamic nucleotides. Specialized reverse transcription conditions allow the polymerase to read through chemical adducts in the RNA and to record the site as a nucleotide non-complementary to the original sequence (red) in the cDNA. The resulting cDNA is subjected to massively parallel sequencing to create a mutational profile. Sequencing reads are then converted to a SHAPE reactivity profile. SHAPE reactivities can be used to model secondary structures, visualize competing and alternative structures, discover functional RNA motifs, and quantify any process that modulates local nucleotide RNA dynamics. Figure reprinted from Ref. 26.