Statistical Bioinformatics Webinar: Pang -- Mapping the Transcriptome Architecture and RNA-RNA Interactions of the Multi-drug Resistant Staphylococcus aureus Uncovers a Mechanism of Antibiotic Resistance

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.