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

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 transcr...

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Bibliographic Details
Published in:BMC genomics Vol. 14; no. 1; p. 230
Main 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
Format: Journal Article
Language:English
Published: London BioMed Central 08.04.2013
BioMed Central Ltd
Springer Nature B.V
Subjects:
Academic libraries
Agriculture
Animal Genetics and Genomics
Animals
Antisense RNA
Biomedical and Life Sciences
Biomedical research
Bos taurus
Cattle
Female
Gene expression
Gene Expression Regulation
Gene Library
Genetic aspects
Genomes
Genomics
High-Throughput Nucleotide Sequencing
Host-Pathogen Interactions - genetics
Immune response
Infections
Library collections
Life Sciences
Macrophages
Macrophages - microbiology
Medical research
Microarrays
Microbial Genetics and Genomics
Molecular Sequence Annotation
Mycobacterium bovis
Non-human and non-rodent vertebrate genomics
Pathogens
Plant Genetics and Genomics
Proteomics
Research Article
RNA sequencing
Sequence Analysis, RNA
Transcriptome
Tuberculosis
Tuberculosis, Bovine - genetics
University colleges
Veterinary colleges
Veterinary medicine
United Kingdom
RNA-sequencing
Immune response
Microarray
Natural antisense transcript
Bovine tuberculosis
Transcriptome
ISSN:1471-2164, 1471-2164
Online Access:Get full text
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Summary: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.
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ISSN:1471-2164
1471-2164
DOI:10.1186/1471-2164-14-230