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

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Toll-Like Receptors

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1390))

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.

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Acknowledgments

This work was supported by grants from the National Health and Medical Research Council (NHMRC) of Australia (APP1005315 and APP1068593). M.J.S. is supported by an Australian Research Council Future Fellowship (FT100100657), as well as an honorary NHMRC Senior Research Fellowship (APP1003470). M.A.S. is supported by an ARC Future Fellowship (FT100100662). T.R. and C.H.M. are supported by The King Abdullah University of Science and Technology.

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Correspondence to Timothy Ravasi or Matthew J. Sweet .

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Ravasi, T., Mavromatis, C.(., Bokil, N.J., Schembri, M.A., Sweet, M.J. (2016). Co-transcriptomic Analysis by RNA Sequencing to Simultaneously Measure Regulated Gene Expression in Host and Bacterial Pathogen. In: McCoy, C. (eds) Toll-Like Receptors. Methods in Molecular Biology, vol 1390. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3335-8_10

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  • DOI: https://doi.org/10.1007/978-1-4939-3335-8_10

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3333-4

  • Online ISBN: 978-1-4939-3335-8

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