Extended Data Fig. 2: Deep mutagenesis analyses reveal key structural and sequence features.

a,c,e, Impact of mutagenesis represented by log₂ fold change (36 h/0 h) for single-substitution (top) and deletions (bottom) mutants of each element. Horizontal grey dotted lines indicate the fold change of each wild-type element. Circle size represents adjusted p-values. P-values were calculated by Wald test with multiple testing adjustments. b,d,f, Mean log₂ fold change (36 h/0 h, Log₂FC) of single substitutions or 1-nt deletion represented along the RNA secondary structure of each element. ΔLog₂ fold change (log₂ fold change of paired nucleotides - log₂ fold change of unpaired nucleotides, ΔLog₂FC) is indicated with the width of the blue lines between the pairing bases. g-j, Log₂ fold change distribution of sequences categorized by stem-loop features, including the presence or absence of the CNGG(N)_0-2 motif and stem-loop size. Each dot represents the mean Log₂ fold change of tiles across four sequencing replicates. Boxes represent the interquartile range with median (red line), and whiskers extend to 1.5 times the interquartile range.