title: The long non-coding RNA expression profile of Coxsackievirus A16 infected RD cells identified by RNA-seq.
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.
authors.affiliation: Pathogenic Organism and Infectious Diseases Research Institute, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China.|Hubei Province Key Laboratory of Allergy and Immunology, Wuhan, 430071, China.
authors.forename: Yingying
authors.initials: Y
authors.lastname: Shi
authors.affiliation: Pathogenic Organism and Infectious Diseases Research Institute, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China.
authors.forename: Huilin
authors.initials: H
authors.lastname: Tu
authors.affiliation: Pathogenic Organism and Infectious Diseases Research Institute, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China.
authors.forename: Xiong
authors.initials: X
authors.lastname: Chen
authors.affiliation: Pathogenic Organism and Infectious Diseases Research Institute, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China.
authors.forename: Yingying
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Pathogenic Organism and Infectious Diseases Research Institute, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China.
authors.forename: Liujun
authors.initials: L
authors.lastname: Chen
authors.affiliation: Institute of Neuropsychiatry, Renmin Hospital, Wuhan University, Wuhan, 430060, China.
authors.forename: Zhongchun
authors.initials: Z
authors.lastname: Liu
authors.affiliation: College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China.
authors.forename: Jiqun
authors.initials: J
authors.lastname: Sheng
authors.affiliation: Pathogenic Organism and Infectious Diseases Research Institute, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China.
authors.forename: Song
authors.initials: S
authors.lastname: Han
authors.affiliation: Pathogenic Organism and Infectious Diseases Research Institute, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Yin
authors.affiliation: Pathogenic Organism and Infectious Diseases Research Institute, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China.|Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China.
authors.forename: Biwen
authors.initials: B
authors.lastname: Peng
authors.affiliation: Pathogenic Organism and Infectious Diseases Research Institute, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China.|Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China.
authors.forename: Xiaohua
authors.initials: X
authors.lastname: He
authors.affiliation: Pathogenic Organism and Infectious Diseases Research Institute, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China. liuwanhong@whu.edu.cn.|Hubei Province Key Laboratory of Allergy and Immunology, Wuhan, 430071, China. liuwanhong@whu.edu.cn.
authors.forename: Wanhong
authors.initials: W
authors.lastname: Liu
mesh_terms: D001483:Base Sequence; D002460:Cell Line; D003384:Coxsackievirus Infections / Q000821:virology*; D004770:Enterovirus / Q000235:genetics* / Q000378:metabolism*; D015967:Gene Expression Regulation, Viral; D006232:Hand, Foot and Mouth Disease / Q000821:virology; D006801:Humans; D025202:Molecular Diagnostic Techniques / Q000379:methods; D062085:RNA, Long Noncoding / Q000096:biosynthesis* / Q000737:chemistry / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics / Q000302:isolation & purification; D060888:Real-Time Polymerase Chain Reaction; D012208:Rhabdomyosarcoma / Q000821:virology
chemical_list: D062085:RNA, Long Noncoding; D012367:RNA, Viral
keywords: Coxsackievirus A16 (CVA16); Long non-coding RNA(IncRNA); RNA-Seq; gene expression