title: RNA-Seq reveals differential gene expression in Staphylococcus aureus with single-nucleotide resolution.
abstract: Staphylococcus aureus is a gram-positive cocci and an important human commensal bacteria and pathogen. S. aureus infections are increasingly difficult to treat because of the emergence of highly resistant MRSA (methicillin-resistant S. aureus) strains. Here we present a method to study differential gene expression in S. aureus using high-throughput RNA-sequencing (RNA-seq). We used RNA-seq to examine gene expression in S. aureus RN4220 cells containing an exogenously expressed transcription factor and between two S. aureus strains (RN4220 and NCTC8325-4). We investigated the sequence and gene expression differences between RN4220 and NCTC8325-4 and used the RNA-seq data to identify S. aureus promoters suitable for in vitro analysis. We used RNA-seq to describe, on a genome wide scale, genes positively and negatively regulated by the phage encoded transcription factor gp67. RNA-seq offers the ability to study differential gene expression with single-nucleotide resolution, and is a considerable improvement over the predominant genome-wide transcriptome technologies used in S. aureus.
authors.affiliation: Laboratory of Molecular Biophysics, the Rockefeller University, New York, New York, United States of America.
authors.forename: Joseph
authors.initials: J
authors.lastname: Osmundson
authors.forename: Scott
authors.initials: S
authors.lastname: Dewell
authors.forename: Seth A
authors.initials: SA
authors.lastname: Darst
mesh_terms: D001483:Base Sequence; D020869:Gene Expression Profiling / Q000379:methods*; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial / Q000235:genetics; D006801:Humans; D055029:Inverted Repeat Sequences / Q000235:genetics; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA / Q000379:methods*; D013045:Species Specificity; D013203:Staphylococcal Infections / Q000382:microbiology; D013211:Staphylococcus aureus / Q000145:classification / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014157:Transcription Factors; D014764:Viral Proteins