Structure-seq2 probing of RNA structure upon amino acid starvation reveals both known and novel RNA switches in Bacillus subtilis

Average DMS reactivity positively correlates with transcript abundance. (A) The mean transcript reactivity is positively correlated to transcript abundance in +AA conditions, such that more reactive, accessible transcripts tend to be more abundant (r = 0.51, P < 2.26 × 10⁻¹⁶). (B) All transcripts resolved in both ±AA conditions are plotted as an arrow originating at the reactivity and abundance (log₂ TPM) of each respective transcript's +AA values, and ending at that transcripts −AA reactivity and abundance values. (C) A subset of B, limiting the data to the top 5% largest increases and decreases of transcript abundance for better visualization. Arrow lines show where DMS reactivity decreased (blue) or increased (red) from +AA to −AA, while arrow origins show where abundance decreased (red) or increased (blue) from +AA to −AA.