Structure-seq2 data align well with known riboswitches and reveal functionally significant regions. (A) Change in DMS reactivity displayed on the secondary structure of the B. subtilis glyQS T-box element. Blue shows nucleotides that had decreased DMS reactivity without amino acids (darker shade shows more extensive change of DMS reactivity), green shows nucleotides that did not change in DMS reactivity, and yellow shows nucleotides that had increased DMS reactivity without amino acids. Secondary structure model adapted from Caserta et al. (2015). (B) Change in DMS reactivity displayed on the crystal structure of the G. kaustophilus glyQS T-box (Grigg and Ke 2013). Blue and yellow are nucleotides that had decreased or increased DMS reactivity without amino acids, respectively, and the tRNA ligand is displayed in forest green. PDBID: 4MGN. (C) Change in DMS reactivity displayed on the secondary structure of the B. subtilis yitJ SAM riboswitch. Color scheme is the same as in A, and nucleotides reported to have decreased DMS reactivity with bound SAM in a previous in vitro study are in red font (Winkler et al. 2003). (D) Change in DMS reactivity displayed on the crystal structure of the yitJ SAM riboswitch (Lu et al. 2010). Blue and yellow are nucleotides that had decreased or increased DMS reactivity without amino acids, respectively, and the SAM ligand is displayed in forest green. PDBID: 4KQY. (E,F) Highly overrepresented sequences that increased in DMS reactivity without amino acids from sliding windows of the 5′UTRs of the 30 resolved transcripts. (E) This region corresponds to the anti-antiterminator which would open up upon removal of SAM (dashed box in C). (F) This region corresponds to the 3′-end of the terminator, which would become exposed upon removal of SAM (black box in C).
