title: Co-transcriptomic Analysis by RNA Sequencing to Simultaneously Measure Regulated Gene Expression in Host and Bacterial Pathogen.
abstract: Intramacrophage pathogens subvert antimicrobial defence pathways using various mechanisms, including the targeting of host TLR-mediated transcriptional responses. Conversely, TLR-inducible host defence mechanisms subject intramacrophage pathogens to stress, thus altering pathogen gene expression programs. Important biological insights can thus be gained through the analysis of gene expression changes in both the host and the pathogen during an infection. Traditionally, research methods have involved the use of qPCR, microarrays and/or RNA sequencing to identify transcriptional changes in either the host or the pathogen. Here we describe the application of RNA sequencing using samples obtained from in vitro infection assays to simultaneously quantify both host and bacterial pathogen gene expression changes, as well as general approaches that can be undertaken to interpret the RNA sequencing data that is generated. These methods can be used to provide insights into host TLR-regulated transcriptional responses to microbial challenge, as well as pathogen subversion mechanisms against such responses.
authors.affiliation: Integrative Systems Biology Laboratory, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia. timothy.ravasi@kaust.edu.sa.|Division of Computer, Electricaland Mathematical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia. timothy.ravasi@kaust.edu.sa.|Division of Medical Genetics, Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. timothy.ravasi@kaust.edu.sa.
authors.forename: Timothy
authors.initials: T
authors.lastname: Ravasi
authors.affiliation: Integrative Systems Biology Laboratory, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.|Division of Computer, Electricaland Mathematical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.|Division of Medical Genetics, Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
authors.forename: Charalampos Harris
authors.initials: CH
authors.lastname: Mavromatis
authors.affiliation: Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.|Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
authors.forename: Nilesh J
authors.initials: NJ
authors.lastname: Bokil
authors.affiliation: Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.|School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Schembri
authors.affiliation: Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia. m.sweet@imb.uq.edu.au.|Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia. m.sweet@imb.uq.edu.au.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Sweet
mesh_terms: D000818:Animals; D001419:Bacteria / Q000235:genetics*; D001424:Bacterial Infections / Q000235:genetics* / Q000276:immunology / Q000382:microbiology; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D054884:Host-Pathogen Interactions / Q000235:genetics* / Q000276:immunology; D007113:Immunity, Innate; D008264:Macrophages / Q000276:immunology / Q000378:metabolism / Q000382:microbiology; D051379:Mice; D050296:Microbial Viability / Q000276:immunology; D017423:Sequence Analysis, RNA; D015398:Signal Transduction; D059467:Transcriptome
keywords: Host-pathogen; Innate immunity; Intracellular pathogens; Macrophages; RNA sequencing; Toll-like receptors; Transcriptomics; Urinary tract infections; Uropathogenic E. coli