Transcript DMS reactivity and abundance changes in the stringent response and CodY regulons are controlled by RNA accessibility. (A) Transcripts previously reported to be positively (teal) and negatively (red) regulated by the stringent response were subset from the data and plotted, comparing the change (Δ) in reactivity against the change (Δ) in abundance as per Figure 2. Abundance changes from our work clearly parallel reported abundance changes; the majority of positively regulated transcripts increased in abundance in −AA media (quadrant II). Likewise, the majority of negatively regulated transcripts decreased in abundance (quadrant IV). (B) Transcript names of positively regulated transcripts from quadrant II and (C) negatively regulated transcripts from quadrant IV. (D–F) Same analysis but for the CodY regulon, where repressed transcripts are also found in quadrant II and activated transcripts in quadrant IV. A full table summarizing these data is included (Supplemental Tables L.1, L.2).
