Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro

Hdl Handle:
http://hdl.handle.net/10147/287386
Title:
Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro
Authors:
Nalpas, Nicolas C; Park, Stephen DE; Magee, David A; Taraktsoglou, Maria; Browne, John A; Conlon, Kevin M; Rue-Albrecht, Kévin; Killick, Kate E; Hokamp, Karsten; Lohan, Amanda J; Loftus, Brendan J; Gormley, Eamonn; Gordon, Stephen V; MacHugh, David E
Citation:
BMC Genomics. 2013 Apr 08;14(1):230
Issue Date:
8-Apr-2013
URI:
http://dx.doi.org/10.1186/1471-2164-14-230; http://hdl.handle.net/10147/287386
Abstract:
Abstract Background Mycobacterium bovis, the causative agent of bovine tuberculosis, is an intracellular pathogen that can persist inside host macrophages during infection via a diverse range of mechanisms that subvert the host immune response. In the current study, we have analysed and compared the transcriptomes of M. bovis-infected monocyte-derived macrophages (MDM) purified from six Holstein-Friesian females with the transcriptomes of non-infected control MDM from the same animals over a 24 h period using strand-specific RNA sequencing (RNA-seq). In addition, we compare gene expression profiles generated using RNA-seq with those previously generated by us using the high-density Affymetrix® GeneChip® Bovine Genome Array platform from the same MDM-extracted RNA. Results A mean of 7.2 million reads from each MDM sample mapped uniquely and unambiguously to single Bos taurus reference genome locations. Analysis of these mapped reads showed 2,584 genes (1,392 upregulated; 1,192 downregulated) and 757 putative natural antisense transcripts (558 upregulated; 119 downregulated) that were differentially expressed based on sense and antisense strand data, respectively (adjusted P-value ≤ 0.05). Of the differentially expressed genes, 694 were common to both the sense and antisense data sets, with the direction of expression (i.e. up- or downregulation) positively correlated for 693 genes and negatively correlated for the remaining gene. Gene ontology analysis of the differentially expressed genes revealed an enrichment of immune, apoptotic and cell signalling genes. Notably, the number of differentially expressed genes identified from RNA-seq sense strand analysis was greater than the number of differentially expressed genes detected from microarray analysis (2,584 genes versus 2,015 genes). Furthermore, our data reveal a greater dynamic range in the detection and quantification of gene transcripts for RNA-seq compared to microarray technology. Conclusions This study highlights the value of RNA-seq in identifying novel immunomodulatory mechanisms that underlie host-mycobacterial pathogen interactions during infection, including possible complex post-transcriptional regulation of host gene expression involving antisense RNA.
Language:
en
Keywords:
GENETICS; TUBERCULOSIS

Full metadata record

DC FieldValue Language
dc.contributor.authorNalpas, Nicolas Cen_GB
dc.contributor.authorPark, Stephen DEen_GB
dc.contributor.authorMagee, David Aen_GB
dc.contributor.authorTaraktsoglou, Mariaen_GB
dc.contributor.authorBrowne, John Aen_GB
dc.contributor.authorConlon, Kevin Men_GB
dc.contributor.authorRue-Albrecht, Kévinen_GB
dc.contributor.authorKillick, Kate Een_GB
dc.contributor.authorHokamp, Karstenen_GB
dc.contributor.authorLohan, Amanda Jen_GB
dc.contributor.authorLoftus, Brendan Jen_GB
dc.contributor.authorGormley, Eamonnen_GB
dc.contributor.authorGordon, Stephen Ven_GB
dc.contributor.authorMacHugh, David Een_GB
dc.date.accessioned2013-05-02T11:27:34Z-
dc.date.available2013-05-02T11:27:34Z-
dc.date.issued2013-04-08-
dc.identifier.citationBMC Genomics. 2013 Apr 08;14(1):230en_GB
dc.identifier.urihttp://dx.doi.org/10.1186/1471-2164-14-230-
dc.identifier.urihttp://hdl.handle.net/10147/287386-
dc.description.abstractAbstract Background Mycobacterium bovis, the causative agent of bovine tuberculosis, is an intracellular pathogen that can persist inside host macrophages during infection via a diverse range of mechanisms that subvert the host immune response. In the current study, we have analysed and compared the transcriptomes of M. bovis-infected monocyte-derived macrophages (MDM) purified from six Holstein-Friesian females with the transcriptomes of non-infected control MDM from the same animals over a 24 h period using strand-specific RNA sequencing (RNA-seq). In addition, we compare gene expression profiles generated using RNA-seq with those previously generated by us using the high-density Affymetrix® GeneChip® Bovine Genome Array platform from the same MDM-extracted RNA. Results A mean of 7.2 million reads from each MDM sample mapped uniquely and unambiguously to single Bos taurus reference genome locations. Analysis of these mapped reads showed 2,584 genes (1,392 upregulated; 1,192 downregulated) and 757 putative natural antisense transcripts (558 upregulated; 119 downregulated) that were differentially expressed based on sense and antisense strand data, respectively (adjusted P-value ≤ 0.05). Of the differentially expressed genes, 694 were common to both the sense and antisense data sets, with the direction of expression (i.e. up- or downregulation) positively correlated for 693 genes and negatively correlated for the remaining gene. Gene ontology analysis of the differentially expressed genes revealed an enrichment of immune, apoptotic and cell signalling genes. Notably, the number of differentially expressed genes identified from RNA-seq sense strand analysis was greater than the number of differentially expressed genes detected from microarray analysis (2,584 genes versus 2,015 genes). Furthermore, our data reveal a greater dynamic range in the detection and quantification of gene transcripts for RNA-seq compared to microarray technology. Conclusions This study highlights the value of RNA-seq in identifying novel immunomodulatory mechanisms that underlie host-mycobacterial pathogen interactions during infection, including possible complex post-transcriptional regulation of host gene expression involving antisense RNA.-
dc.language.isoenen
dc.subjectGENETICSen_GB
dc.subjectTUBERCULOSISen_GB
dc.titleWhole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitroen_GB
dc.language.rfc3066en-
dc.rights.holderNicolas C Nalpas et al.; licensee BioMed Central Ltd.-
dc.description.statusPeer Reviewed-
dc.date.updated2013-05-01T15:04:34Z-
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