RNA-Sequencing Analysis of 5 Capped RNAs Identifies Many New Differentially Expressed Genes in Acute Hepatitis C Virus Infection 英文参考文献.docVIP

Viruses 2012, 4, 581-612; doi:10.3390/v4040581 OPEN ACCESS viruses ISSN 1999-4915 /journal/viruses Article RNA-Sequencing Analysis of 5 Capped RNAs Identifies Many New Differentially Expressed Genes in Acute Hepatitis C Virus Infection Neven Papic 1,?, Christopher I. Maxwell 1,2,?, Don A. Delker 1, Shuanghu Liu 1, Bret S. E. Heale 1 and Curt H. Hagedorn 1,3,* 1 Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA; E-Mails: neven.papic@ (N.P.); christopher.maxwell@ (C.I.M.); don.delker@ (D.A.D.); shuanghu.liu@ (S.L.); bret.heale@ (B.S.E.H.) 2 Huntsman Cancer Institute, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA 3 Department of Experimental Pathology, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA ? These authors contributed equally to this work. * Author to whom correspondence should be addressed; E-Mail: curt.hagedorn@; Tel.: +1-801-587-4619; Fax: +1-801-585-0187. Received: 7 February 2012; in revised form: 31 March 2012 / Accepted: 3 April 2012 / Published: 16 April 2012 Abstract: We describe the first report of RNA sequencing of 5 capped (Pol II) RNAs isolated from acutely hepatitis C virus (HCV) infected Huh 7.5 cells that provides a general approach to identifying differentially expressed annotated and unannotated genes that participate in viral-host interactions. We identified 100, 684, and 1,844 significantly differentially expressed annotated genes in acutely infected proliferative Huh 7.5 cells at 6, 48, and 72 hours, respectively (fold change ≥ 1.5 and Bonferroni adjusted p-values 0.05). Most of the differentially expressed genes (80%) and biological pathways (such as adipocytokine, Notch, Hedgehog and NOD-like receptor signaling) were not identified by previous gene array studies. These genes are critical components of host immune, inflammatory and oncogenic pathway