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 DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Integrative Systems Biology Lab
Online Publication Date2016-01-24
Print Publication Date2016
Permanent link to this recordhttp://hdl.handle.net/10754/596609
MetadataShow full item record
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.
JournalMethods in Molecular Biology
- The co-transcriptome of uropathogenic Escherichia coli-infected mouse macrophages reveals new insights into host-pathogen interactions.
- Authors: Mavromatis CH, Bokil NJ, Totsika M, Kakkanat A, Schaale K, Cannistraci CV, Ryu T, Beatson SA, Ulett GC, Schembri MA, Sweet MJ, Ravasi T
- Issue date: 2015 May
- For when bacterial infections persist: Toll-like receptor-inducible direct antimicrobial pathways in macrophages.
- Authors: Stocks CJ, Schembri MA, Sweet MJ, Kapetanovic R
- Issue date: 2018 Jan
- Comprehensive insights into transcriptional adaptation of intracellular mycobacteria by microbe-enriched dual RNA sequencing.
- Authors: Rienksma RA, Suarez-Diez M, Mollenkopf HJ, Dolganov GM, Dorhoi A, Schoolnik GK, Martins Dos Santos VA, Kaufmann SH, Schaap PJ, Gengenbacher M
- Issue date: 2015 Feb 5
- Mammalian microRNAs and long noncoding RNAs in the host-bacterial pathogen crosstalk.
- Authors: Duval M, Cossart P, Lebreton A
- Issue date: 2017 May
- Single-Cell RNA Sequencing to Understand Host-Pathogen Interactions.
- Authors: Penaranda C, Hung DT
- Issue date: 2019 Mar 8