Co-transcriptomic Analysis by RNA Sequencing to Simultaneously Measure Regulated Gene Expression in Host and Bacterial Pathogen

Handle URI:
http://hdl.handle.net/10754/596609
Title:
Co-transcriptomic Analysis by RNA Sequencing to Simultaneously Measure Regulated Gene Expression in Host and Bacterial Pathogen
Authors:
Ravasi, Timothy ( 0000-0002-9950-465X ) ; Mavromatis, Charalampos Harris ( 0000-0002-7327-231X ) ; Bokil, Nilesh J.; Schembri, Mark A.; Sweet, Matthew J.
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.
KAUST Department:
Integrative Systems Biology Lab; Biological and Environmental Sciences and Engineering (BESE) Division; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Citation:
Ravasi, 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.
Publisher:
Springer Science + Business Media
Journal:
Methods in Molecular Biology
Issue Date:
24-Jan-2016
DOI:
10.1007/978-1-4939-3335-8_10
Type:
Book Chapter
ISSN:
1064-3745
ISBN:
978-1-4939-3333-4
Additional Links:
http://link.springer.com/protocol/10.1007%2F978-1-4939-3335-8_10
Appears in Collections:
Book Chapters; Biological and Environmental Sciences and Engineering (BESE) Division; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorRavasi, Timothyen
dc.contributor.authorMavromatis, Charalampos Harrisen
dc.contributor.authorBokil, Nilesh J.en
dc.contributor.authorSchembri, Mark A.en
dc.contributor.authorSweet, Matthew J.en
dc.date.accessioned2016-02-18T13:59:41Zen
dc.date.available2016-02-18T13:59:41Zen
dc.date.issued2016-01-24en
dc.identifier.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.en
dc.identifier.isbn978-1-4939-3333-4en
dc.identifier.issn1064-3745en
dc.identifier.doi10.1007/978-1-4939-3335-8_10en
dc.identifier.urihttp://hdl.handle.net/10754/596609en
dc.description.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.en
dc.language.isoenen
dc.publisherSpringer Science + Business Mediaen
dc.relation.urlhttp://link.springer.com/protocol/10.1007%2F978-1-4939-3335-8_10en
dc.rightsThe final publication is available at Springer via http://dx.doi.org/10.1007/978-1-4939-3335-8_10en
dc.subjectHost-pathogenen
dc.subjectInnate immunityen
dc.subjectIntracellular pathogensen
dc.subjectMacrophagesen
dc.subjectRNA sequencingen
dc.subjectToll-like receptorsen
dc.subjectTranscriptomicsen
dc.subjectUrinary tract infectionsen
dc.subjectUropathogenic E. colien
dc.titleCo-transcriptomic Analysis by RNA Sequencing to Simultaneously Measure Regulated Gene Expression in Host and Bacterial Pathogenen
dc.typeBook Chapteren
dc.contributor.departmentIntegrative Systems Biology Laben
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.identifier.journalMethods in Molecular Biologyen
dc.eprint.versionPost-printen
dc.contributor.institutionDivision of Medical Genetics, Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USAen
dc.contributor.institutionInstitute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australiaen
dc.contributor.institutionAustralian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australiaen
dc.contributor.institutionSchool of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australiaen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorRavasi, Timothyen
kaust.authorMavromatis, Charalampos Harrisen
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