Fig. 5: The HTH-type DNA-binding protein CcpA binds hundreds of RNAs in vivo.

a, b Distribution of highly enriched CcpA binding sites (FDR ≤ 0.01) in USA300 sRNA (a) and mRNA (b) transcripts. The darker the blue signal in the heat map, the higher the number of reads found in a peak (maximum value was set at 10% of total peaks found in a transcript). The first heat map in a, b shows the peak distribution in all the identified sRNA (a) and mRNA (b) transcripts sorted by length (shortest top, longest bottom). The second heat map shows the distribution of the peaks around transcript 3’ ends. The total number of peaks in this region is indicated by the cumulative plot above the heat map. c The top 200 enriched CcpA CRAC peaks were analysed using the MEME suite³¹. The motif consensus sequence and the E-value of the motif are also provided. The motifs identified by MEME for tRNAs can be found in Supplementary Fig. 5a. d Enriched RNA structural motifs identified by BEAM (BEAr Motifs finder)³⁰ in the top 200 enriched CcpA CRAC peaks. The two most highly enriched structural motifs are shown. qBEAR: quick Brand nEw Alphabet for RNAs. Encoding: q: stem structures that are longer than 10 nucleotides; a: stem structures between 6 and 9 nucleotides; x: 3–9 nucleotide loops; *: any nucleotide. e Cumulative plot showing the location of MEME (orange) and BEAM (blue) motifs in 100 nucleotide peak intervals. f CcpA UV cross-linking sites are mostly found in the first half of the BEAM structural motifs. Plotted are the cumulative deletion frequencies around the centre of the loop in each hairpin structure (blow the plots). Predicted CcpA cross-linking sites are indicated. g Venn diagram showing the number of peak sequences that have BEAM and MEME motifs.