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    Integrative deep sequencing of the mouse lung transcriptome reveals differential expression of diverse classes of small RNAs in response to respiratory virus infection

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    Author
    Peng, X.
    Gralinski, L.
    Frieman, M.B.
    Date
    2011
    Journal
    mBio
    Type
    Article
    
    Metadata
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    See at
    https://doi.org/10.1128/mBio.00198-11
    Abstract
    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. Copyright 2011 Peng et al.
    Keyword
    severe acute respiratory syndrome coronavirus
    SARS-CoV
    influenza virus
    small RNA transcriptome sequencing analysis
    SARS Virus
    microRNAs
    Collaborative Cross Mice
    RNA, Small Nucleolar
    Virus Diseases
    Identifier to cite or link to this item
    https://www.scopus.com/inward/record.uri?eid=2-s2.0-84855231262&doi=10.1128%2fmBio.00198-11&partnerID=40&md5=b967ef6c095868ce3da90bdd9e8d22a1; http://hdl.handle.net/10713/12426
    ae974a485f413a2113503eed53cd6c53
    10.1128/mBio.00198-11
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    UMB Coronavirus Publications

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