Fig. 1: RNase III interactions with the ANNOgesic annotated S. aureus JKD6009 transcriptome.

a Transcription start sites and putative promoter regions identified through the ANNOgesic workflow. b The consensus 10-nt stem-loop RNA structure identified within our RNA 3′ boundary ends. Nucleotides are represented as coloured dots specifying the nucleotide percentage identify. c Heatmap showing the two-sided Pearson’s correlation between replicate RNase III CRAC datasets. d Proportion of RNase III-bound reads mapping to genomic features for replicate datasets. e Cumulative count of RNase III-bound reads mapping across CDSs. Each CDS was divided into 100 bins and the read depth within each bin is indicated. f Cumulative count of RNase III-bound reads mRNA 5′UTR ends and 3′UTR ends. Read counts for each individual UTR were normalised to 1 to prevent biases from abundant sites. The read count represents the cumulative normalised read count at 5′ and 3′UTRs. g Distribution of RNase III-bound (n = 104) and not bound (n = 1052) UTR lengths (nts) (left) and structure (expressed as the free energy of the folded UTR, kcal/mol) (right). UTRs were classified as RNase III-bound if they contained >10 reads in two independent experiments. p-values were calculate using a two-sided t-test. For each boxplot, centre represents the median, box minima and maxima represent the 25th and 75th percentile respectively, and whiskers represent 1.5× the interquartile range.