Treatment of methicillin-resistant Staphylococcus aureus (MRSA) infections is dependent on the efficacy of last-line antibiotics like vancomycin. Changes in expression of regulatory RNA transcripts have been correlated with antibiotic stress responses in vancomycin-intermediate resistance isolates. The 5’ and 3’ untranslated regions (UTRs) of mRNAs are often the site of regulatory RNA interactions but these UTRs regions are often poorly annotated and uncharacterized. This talk will explore the use of three RNA sequencing techniques (RNA-seq, dRNA-seq and Term-Seq) to identify transcripts and their start and termination sites and the use of the ANNOgesic pipeline to analyse these data and generate a detailed transcriptome architecture of the methicillin-resistant Staphylococcus aureus JKD6009. We also discuss the use a custom Snakemake pipeline to identify RNA-RNA interactions from sequencing data generated from the endoribonuclease RNase III capture and RNA proximity-dependent ligation technique termed CLASH. We identified over 900 RNA-RNA interactions, which suggested mRNA-mRNA regulation of co-expression are much more widespread than previously appreciated.