Staphylococcus aureus bona fide sRNAs in the model strain HG003

Accurate annotation of regulatory RNAs is a complex task but nevertheless essential as sRNA molecular and functional studies ensue from it. Several formerly considered small RNAs (sRNA) are now known to be parts of UTR transcripts. In light of experimental data, we review hundreds of Staphylococcus aureus putative regulatory RNAs. We pinpoint those that are likely acting in trans and are not expressed from the opposite strand of a coding gene. We conclude that HG003, a NCTC8325 derivative strain, has about 50 bona fide sRNAs, indicating that these RNAs are less numerous than commonly stated. Total RNA samples were extracted from HG003 grown in various biological conditions. All 16 RNA samples were pooled together for RNA sequencing. Pooled RNAs were processed using the MICROBExpress kit (Ambion, AM1905) as recommended by the suppliers, for rRNAs removal and before high-throughput sequencing using Illumina Genome Analyzer IIx generating single-end 40-nt reads.