Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection

Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington, USA.
mBio (Impact Factor: 6.79). 10/2011; 2(6). DOI: 10.1128/mBio.00198-11
Source: PubMed


We previously reported widespread differential expression of long non-protein-coding RNAs (ncRNAs) in response to virus infection. Here, we expanded the study through small RNA transcriptome sequencing analysis of the host response to both severe acute respiratory syndrome coronavirus (SARS-CoV) and influenza virus infections across four founder mouse strains of the Collaborative Cross, a recombinant inbred mouse resource for mapping complex traits. We observed differential expression of over 200 small RNAs of diverse classes during infection. A majority of identified microRNAs (miRNAs) showed divergent changes in expression across mouse strains with respect to SARS-CoV and influenza virus infections and responded differently to a highly pathogenic reconstructed 1918 virus compared to a minimally pathogenic seasonal influenza virus isolate. Novel insights into miRNA expression changes, including the association with pathogenic outcomes and large differences between in vivo and in vitro experimental systems, were further elucidated by a survey of selected miRNAs across diverse virus infections. The small RNAs identified also included many non-miRNA small RNAs, such as small nucleolar RNAs (snoRNAs), in addition to nonannotated small RNAs. An integrative sequencing analysis of both small RNAs and long transcripts from the same samples showed that the results revealing differential expression of miRNAs during infection were largely due to transcriptional regulation and that the predicted miRNA-mRNA network could modulate global host responses to virus infection in a combinatorial fashion. These findings represent the first integrated sequencing analysis of the response of host small RNAs to virus infection and show that small RNAs are an integrated component of complex networks involved in regulating the host response to infection.

Download full-text


Available from: Jennifer Tisoncik,
  • Source
    • "H3K3me3, Figure 4). Given virus infection and other inflammatory diseases have been shown to affect the expression of snoRNA’s and other non coding RNAs [33,34], these findings suggest that SNORA12 is a component of the antiviral or inflammatory processes within the airway epithelium. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Background Mechanisms underlying the development of virus-induced asthma exacerbations remain unclear. To investigate if epigenetic mechanisms could be involved in virus-induced asthma exacerbations, we undertook DNA methylation profiling in asthmatic and healthy nasal epithelial cells (NECs) during Human Rhinovirus (HRV) infection in vitro. Methods Global and loci-specific methylation profiles were determined via Alu element and Infinium Human Methylation 450 K microarray, respectively. Principal components analysis identified the genomic loci influenced the most by disease-status and infection. Real-time PCR and pyrosequencing were used to confirm gene expression and DNA methylation, respectively. Results HRV infection significantly increased global DNA methylation in cells from asthmatic subjects only (43.6% to 44.1%, p = 0.04). Microarray analysis revealed 389 differentially methylated loci either based on disease status, or caused by virus infection. There were disease-associated DNA methylation patterns that were not affected by HRV infection as well as HRV-induced DNA methylation changes that were unique to each group. A common methylation locus stood out in response to HRV infection in both groups, where the small nucleolar RNA, H/ACA box 12 (SNORA12) is located. Further analysis indicated that a relationship existed between SNORA12 DNA methylation and gene expression in response to HRV infection. Conclusions We describe for the first time that Human rhinovirus infection causes DNA methylation changes in airway epithelial cells that differ between asthmatic and healthy subjects. These epigenetic differences may possibly explain the mechanism by which respiratory viruses cause asthma exacerbations.
    BMC Medical Genomics 06/2014; 7(1):37. DOI:10.1186/1755-8794-7-37 · 2.87 Impact Factor
  • Source
    • "Predicted target genes of these miRNAs encoded cell death and inflammatory factors involved in influenza pathogenesis, which suggest that their regulation could play crucial roles in influenza virulence (Li et al., 2011). In mice, 45 miRNAs were differentially expressed in lung samples from different mouse strains during severe acute respiratory syndrome coronavirus (SARS-CoV) (MA15) or influenza virus (PR8) infection and expression of 6 miRNAs was confirmed to change after VN1203 infection (Peng et al., 2011). These miRNAs, such as miR155 that was previously implicated in lymphocyte function (Vigorito et al., 2007), represent potential important regulators of the host response and provide an interesting target to validate in studies focused on understanding their mechanisms. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The dynamics of H5N1 influenza virus pathogenesis are multifaceted and can be seen as an emergent property that cannot be comprehended without looking at the system as a whole. In past years, most of the high-throughput studies on H5N1-host interactions have focused on the host transcriptomic response, at the cellular or the lung tissue level. These studies pointed out that the dynamics and magnitude of the innate immune response and immune cell infiltration is critical to H5N1 pathogenesis. However, viral-host interactions are multidimensional and advances in technologies are creating new possibilities to systematically measure additional levels of 'omic data (e.g. proteomic, metabolomic, and RNA profiling) at each temporal and spatial scale (from the single cell to the organism) of the host response. Natural host genetic variation represents another dimension of the host response that determines pathogenesis. Systems biology models of H5N1 disease aim at understanding and predicting pathogenesis through integration of these different dimensions by using intensive computational modeling. In this review, we describe the importance of 'omic studies for providing a more comprehensive view of infection and mathematical models that are being developed to integrate these data. This review provides a roadmap for what needs to be done in the future and what computational strategies should be used to build a global model of H5N1 pathogenesis. It is time for systems biology of H5N1 pathogenesis to take center stage as the field moves towards a more comprehensive view of virus-host interactions.
    Virus Research 03/2013; 178(1). DOI:10.1016/j.virusres.2013.02.011 · 2.32 Impact Factor
  • Source
    • "ular interest since it is known to be directly regulated by p53 and involved in the regulation of p53 - mediated cell death ( Hermeking , 2010 ) . Interestingly , we have previously shown , by a transcriptional profiling approach , that members of the p53 pathway , including p53 transcriptional targets , are strongly downregulated upon infection ( Terrier et al . , 2011 ) . The absence or presence of miR - 34c in influenza - infected cells , at levels below the detection threshold , could play a role in p53 - mediated cell death upon infection and requires further investigation . This hypothesis is reinforced by the downregulation of miR - 34a , another member of the miR - 34 family , observed in infec"
    [Show abstract] [Hide abstract]
    ABSTRACT: While post-transcriptional regulation of gene expression by miRNAs have been shown to be involved in influenza virus replication cycle, only a few studies have further investigated this aspect in a human cellular model infected with human influenza viruses. In this study, we performed miRNA global profiling in human lung epithelial cells (A549) infected by two different subtypes of human influenza A viruses (H1N1 and H3N2). We identified a common miRNA signature in response to infection by the two different strains, highlighting a pool of five miRNAs commonly deregulated, which are known to be involved in the innate immune response or apoptosis. Among the five miRNA hits, the only up-regulated miRNA in response to influenza infection corresponded to miR-146a. Based on a previously published gene expression dataset, we extracted inversely correlated miR-146a target genes and determined their first-level interactants. This functional analysis revealed 8 distinct biological processes strongly associated with these interactants: TLR pathway, innate immune response, cytokine production and apoptosis. To better understand the biological significance of miR-146a up-regulation, using a reporter assay and a specific anti-miR-146a inhibitor, we confirmed that infection increases the endogenous miR-146a promoter activity and that inhibition of miR-146a significantly increased viral propagation. Altogether, our results suggest a functional role of miR-146a in the outcome of influenza infection, at the crossroads of several biological processes.
    Journal of General Virology 01/2013; 94(Pt 5). DOI:10.1099/vir.0.049528-0 · 3.18 Impact Factor
Show more