Co-transcriptomic Analysis by RNA Sequencing to Simultaneously Measure Regulated Gene Expression in Host and Bacterial Pathogen
Mavromatis, Charalampos Harris
Bokil, Nilesh J.
Schembri, Mark A.
Sweet, Matthew J.
KAUST DepartmentIntegrative Systems Biology Lab
Biological and Environmental Sciences and Engineering (BESE) Division
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
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AbstractIntramacrophage 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.
CitationRavasi, T., Mavromatis, C.H., Bokil, N.J., Schembri, M.A. and Sweet, M.J., Co-transcriptomic Analysis by RNA Sequencing to Simultaneously Measure Regulated Gene Expression in Host and Bacterial Pathogen.
PublisherSpringer Science + Business Media
JournalMethods in Molecular Biology
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