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Volume 31 Issue 2
April 2016
    Citation: Yingying Shi, Huilin Tu, Xiong Chen, Yingying Zhang, Liujun Chen, Zhongchun Liu, Jiqun Sheng, Song Han, Jun Yin, Biwen Peng, Xiaohua He, Wanhong Liu. The long non-coding RNA expression profile of Coxsackievirus A16 infected RD cells identified by RNA-seq .VIROLOGICA SINICA, 2016, 31(2) : 131-141.  http://dx.doi.org/10.1007/s12250-015-3693-1
    shu

    The long non-coding RNA expression profile of Coxsackievirus A16 infected RD cells identified by RNA-seq

    • 1.

      Pathogenic Organism and Infectious Diseases Research Institute, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China

    • 2.

      Hubei Province Key Laboratory of Allergy and Immunology, Wuhan 430071, China

    • 3.

      Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China

    • 4.

      Institute of Neuropsychiatry, Renmin Hospital, Wuhan University, Wuhan 430060, China

    • 5.

      College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China

    • Wanhong Liu, ORCID: 0000-0003-3271-4342
    • Received Date: 27 November 2015
      Accepted Date: 02 March 2016
      Published Date: 31 March 2016
      Available online: 01 April 2016
    • Coxsackievirus A16 (CVA16) is one of major pathogens of hand, foot and mouth disease (HFMD) in children. Long non-coding RNAs (IncRNAs) have been implicated in various biological processes, but they have not been associated with CVA16 infection. In this study, we comprehensively characterized the landscape of IncRNAs of normal and CVA16 infected rhabdomyosarcoma (RD) cells using RNA-Seq to investigate the functional relevance of IncRNAs. We showed that a total of 760 IncRNAs were upregulated and 1210 IncRNAs were downregulated. Out of these dysregulated IncRNAs, 43.64% were intergenic, 22.31% were sense, 15.89% were intronic, 8.67% were bidirectional, 5.59% were antisense, 3.85% were sRNA host IncRNAs and 0.05% were enhancer. Six dysregulated IncRNAs were validated by quantitative PCR assays and the secondary structures of these IncRNAs were projected. Moreover, we conducted a bioinformatics analysis of an IncRNAs (ENST00000602478) to elucidate the diversity of modification and functions of IncRNAs. In summary, the current study compared the dysregulated IncRNAs profile upon CVA16 challenge and illustrated the intricate relationship between coding and IncRNAs transcripts. These results may not only provide a complete picture of transcription in CVA16 infected cells but also provide novel molecular targets for treatments of HFMD.
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      The long non-coding RNA expression profile of Coxsackievirus A16 infected RD cells identified by RNA-seq

      • Wanhong Liu, ORCID: 0000-0003-3271-4342
      • 1. Pathogenic Organism and Infectious Diseases Research Institute, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
      • 2. Hubei Province Key Laboratory of Allergy and Immunology, Wuhan 430071, China
      • 3. Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
      • 4. Institute of Neuropsychiatry, Renmin Hospital, Wuhan University, Wuhan 430060, China
      • 5. College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
      • Received Date: 27 November 2015
      • Accepted Date: 02 March 2016
      • Published Date: 31 March 2016

      Abstract: Coxsackievirus A16 (CVA16) is one of major pathogens of hand, foot and mouth disease (HFMD) in children. Long non-coding RNAs (IncRNAs) have been implicated in various biological processes, but they have not been associated with CVA16 infection. In this study, we comprehensively characterized the landscape of IncRNAs of normal and CVA16 infected rhabdomyosarcoma (RD) cells using RNA-Seq to investigate the functional relevance of IncRNAs. We showed that a total of 760 IncRNAs were upregulated and 1210 IncRNAs were downregulated. Out of these dysregulated IncRNAs, 43.64% were intergenic, 22.31% were sense, 15.89% were intronic, 8.67% were bidirectional, 5.59% were antisense, 3.85% were sRNA host IncRNAs and 0.05% were enhancer. Six dysregulated IncRNAs were validated by quantitative PCR assays and the secondary structures of these IncRNAs were projected. Moreover, we conducted a bioinformatics analysis of an IncRNAs (ENST00000602478) to elucidate the diversity of modification and functions of IncRNAs. In summary, the current study compared the dysregulated IncRNAs profile upon CVA16 challenge and illustrated the intricate relationship between coding and IncRNAs transcripts. These results may not only provide a complete picture of transcription in CVA16 infected cells but also provide novel molecular targets for treatments of HFMD.

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