{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T00:42:45Z","timestamp":1791852165862,"version":"4.3.4"},"reference-count":88,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2012,4,16]],"date-time":"2012-04-16T00:00:00Z","timestamp":1334534400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>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 \u2265 1.5 and Bonferroni adjusted p-values &lt; 0.05). Most of the differentially expressed genes (&gt;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 pathways and provide new information regarding changes that may benefit the virus or mediate HCV induced pathology. RNAi knockdown studies of newly identified highly upregulated FUT1 and KLHDC7B genes provide evidence that their gene products regulate and facilitate HCV replication in hepatocytes. Our approach also identified novel Pol II unannotated transcripts that were upregulated. Results further identify new pathways that regulate HCV replication in hepatocytes and suggest that our approach will have general applications in studying viral-host interactions in model systems and clinical biospecimens.<\/jats:p>","DOI":"10.3390\/v4040581","type":"journal-article","created":{"date-parts":[[2012,4,16]],"date-time":"2012-04-16T11:07:38Z","timestamp":1334574458000},"page":"581-612","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":45,"title":["RNA-Sequencing Analysis of 5' Capped RNAs Identifies Many New Differentially Expressed Genes in Acute Hepatitis C Virus Infection"],"prefix":"10.3390","volume":"4","author":[{"given":"Neven","family":"Papic","sequence":"first","affiliation":[{"name":"Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher I.","family":"Maxwell","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA"},{"name":"Huntsman Cancer Institute, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Don A.","family":"Delker","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuanghu","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bret S. E.","family":"Heale","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Curt H.","family":"Hagedorn","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA"},{"name":"Department of Experimental Pathology, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2012,4,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1055\/s-2000-9505","article-title":"Recovery, persistence, and sequelae in hepatitis C virus infection: A perspective on long-term outcome","volume":"20","author":"Alter","year":"2000","journal-title":"Semin. Liver Dis."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1016\/j.cld.2006.08.003","article-title":"The changing epidemiology and natural history of hepatitis C virus infection","volume":"10","author":"Bialek","year":"2006","journal-title":"Clin. Liver Dis."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1146\/annurev-micro-090110-102954","article-title":"Turning hepatitis C into a real virus","volume":"65","author":"Murray","year":"2011","journal-title":"Annu. Rev. Microbiol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1207","DOI":"10.1056\/NEJMoa1009482","article-title":"Boceprevir for previously treated chronic HCV genotype 1 infection","volume":"364","author":"Bacon","year":"2011","journal-title":"New Engl. J. Med."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"975","DOI":"10.1056\/NEJMoa020047","article-title":"Peginterferon alfa-2a plus ribavirin for chronic hepatitis C virus infection","volume":"347","author":"Fried","year":"2002","journal-title":"New Engl. J. Med."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1195","DOI":"10.1056\/NEJMoa1010494","article-title":"Boceprevir for untreated chronic HCV genotype 1 infection","volume":"364","author":"Poordad","year":"2011","journal-title":"New Engl. J. Med."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1395","DOI":"10.1002\/hep.21210","article-title":"Hepatitis C vaccines: Inducing and challenging memory T cells","volume":"43","author":"Shiina","year":"2006","journal-title":"Hepatology"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"5404","DOI":"10.1128\/JVI.02529-09","article-title":"Gene expression profiling indicates the roles of host oxidative stress, apoptosis, lipid metabolism, and intracellular transport genes in the replication of hepatitis C virus","volume":"84","author":"Blackham","year":"2010","journal-title":"J. Virol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"e1000269","DOI":"10.1371\/journal.ppat.1000269","article-title":"Genomic analysis reveals a potential role for cell cycle perturbation in HCV-mediated apoptosis of cultured hepatocytes","volume":"5","author":"Walters","year":"2009","journal-title":"PLoS Pathog."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1002\/hep.23733","article-title":"Transcriptome sequencing, microarray, and proteomic analyses reveal cellular and metabolic impact of hepatitis C virus infection in vitro","volume":"52","author":"Woodhouse","year":"2010","journal-title":"Hepatology"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"R16","DOI":"10.1186\/gb-2011-12-2-r16","article-title":"Genomewide characterization of non-polyadenylated RNAs","volume":"12","author":"Yang","year":"2011","journal-title":"Genome Biol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"7033","DOI":"10.1073\/pnas.1232347100","article-title":"Purifying mRNAs with a high-affinity eIF4E mutant identifies the short 3' poly(A) end phenotype","volume":"100","author":"Choi","year":"2003","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1957","DOI":"10.1261\/rna.7135204","article-title":"Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs","volume":"10","author":"Cai","year":"2004","journal-title":"RNA"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"e14697","DOI":"10.1371\/journal.pone.0014697","article-title":"ENCODE tiling array analysis identifies differentially expressed annotated and novel 5' capped RNAs in hepatitis C infected liver","volume":"6","author":"Folkers","year":"2011","journal-title":"PLoS One"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"7558","DOI":"10.1093\/nar\/gkq583","article-title":"Genome-wide characterization of methylguanosine-capped and polyadenylated small RNAs in the rice blast fungus Magnaporthe oryzae","volume":"38","author":"Gowda","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"620","DOI":"10.1038\/nsmb.1801","article-title":"Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors","volume":"17","author":"Oler","year":"2010","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/S0014-5793(02)02445-6","article-title":"Mutations in the S4-H2 loop of eIF4E which increase the affinity for m7GTP","volume":"516","author":"Friedland","year":"2002","journal-title":"FEBS Lett."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1577","DOI":"10.1126\/science.1113329","article-title":"Modulation of hepatitis C virus RNA abundance by a liver-specific MicroRNA","volume":"309","author":"Jopling","year":"2005","journal-title":"Science"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1186\/1471-2164-10-373","article-title":"Computational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human livers","volume":"10","author":"Peng","year":"2009","journal-title":"BMC Genom."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"941","DOI":"10.1073\/pnas.1112263109","article-title":"Stabilization of hepatitis C virus RNA by an Ago2-miR-122 complex","volume":"109","author":"Shimakami","year":"2012","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/S0962-8924(99)01673-6","article-title":"The kelch repeat superfamily of proteins: Propellers of cell function","volume":"10","author":"Adams","year":"2000","journal-title":"Trends Cell Biol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"16410","DOI":"10.1073\/pnas.0907439106","article-title":"A genome-wide genetic screen for host factors required for hepatitis C virus propagation","volume":"106","author":"Li","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1564","DOI":"10.1038\/cr.2011.84","article-title":"Coordinate activation of inflammatory gene networks, alveolar destruction and neonatal death in AKNA deficient mice","volume":"21","author":"Ma","year":"2011","journal-title":"Cell Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1528","DOI":"10.1038\/cr.2011.96","article-title":"AKNA: Another AT-hook transcription factor \"hooking-up\" with inflammation","volume":"21","author":"Moliterno","year":"2011","journal-title":"Cell Res."},{"key":"ref_25","unstructured":"Drummond, A.E., and Fuller, P.J. (2011). Activin and inhibin, estrogens and NFkappaB, play roles in ovarian tumourigenesis is there crosstalk?. Mol. Cell. Endocrinol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1007\/s10735-009-9246-x","article-title":"Inhibin\/activin-betaE subunit in normal and malignant human cervical tissue and cervical cancer cell lines","volume":"40","author":"Bergauer","year":"2009","journal-title":"J. Mol. Histol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"4401","DOI":"10.1128\/JVI.77.7.4401-4408.2003","article-title":"Cytoskeletal requirements for hepatitis C virus (HCV) RNA synthesis in the HCV replicon cell culture system","volume":"77","author":"Bost","year":"2003","journal-title":"J. Virol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"5487","DOI":"10.1128\/JVI.77.9.5487-5492.2003","article-title":"Identification of the hepatitis C virus RNA replication complex in Huh-7 cells harboring subgenomic replicons","volume":"77","author":"Gosert","year":"2003","journal-title":"J. Virol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"23852","DOI":"10.1074\/jbc.M001095200","article-title":"MIP-T3, a novel protein linking tumor necrosis factor receptor-associated factor 3 to the microtubule network","volume":"275","author":"Ling","year":"2000","journal-title":"J. Biol. Chem."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"949","DOI":"10.1021\/pr0499592","article-title":"Riboproteomics of the hepatitis C virus internal ribosomal entry site","volume":"3","author":"Lu","year":"2004","journal-title":"J. Proteome Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nbt.1621","article-title":"Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation","volume":"28","author":"Trapnell","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"ref_32","unstructured":"van Baren, M.J., Koebbe, B.C., and Brent, M.R. (2007). Current Protocols in Bioinformatics, John Wiley & Sons. Chapter 4, Units 4 and 8."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1102","DOI":"10.2144\/00286ir01","article-title":"The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences","volume":"28","author":"Stothard","year":"2000","journal-title":"BioTechniques"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1128\/jvi.37.2.549-558.1981","article-title":"Glycosylation sites of influenza viral glycoproteins: Characterization of tryptic glycopeptides from the A\/USSR(H1N1) hemagglutinin glycoprotein","volume":"37","author":"Basak","year":"1981","journal-title":"J. Virol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1143","DOI":"10.1016\/j.jmb.2005.11.002","article-title":"Glycan microarray analysis of the hemagglutinins from modern and pandemic influenza viruses reveals different receptor specificities","volume":"355","author":"Stevens","year":"2006","journal-title":"J. Mol. Biol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"10253","DOI":"10.1128\/JVI.01059-06","article-title":"Production of infectious hepatitis C virus by well-differentiated, growth-arrested human hepatoma-derived cells","volume":"80","author":"Sainz","year":"2006","journal-title":"J. Virol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1093\/nar\/28.5.1106","article-title":"Transactivation and growth suppression by the gut-enriched Kruppel-like factor (Kruppel-like factor 4) are dependent on acidic amino acid residues and protein-protein interaction","volume":"28","author":"Geiman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1186\/gb-2003-4-2-206","article-title":"Sp1- and Kruppel-like transcription factors","volume":"4","author":"Kaczynski","year":"2003","journal-title":"Genome Biol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"3134","DOI":"10.4049\/jimmunol.178.5.3134","article-title":"Differential recognition of TLR-dependent microbial ligands in human bronchial epithelial cells","volume":"178","author":"Mayer","year":"2007","journal-title":"J. Immunol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"8435","DOI":"10.4049\/jimmunol.179.12.8435","article-title":"Candida albicans triggers activation of distinct signaling pathways to establish a proinflammatory gene expression program in primary human endothelial cells","volume":"179","author":"Muller","year":"2007","journal-title":"J. Immunol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1180","DOI":"10.1038\/nm1303","article-title":"CCL5-CCR5 interaction provides antiapoptotic signals for macrophage survival during viral infection","volume":"11","author":"Tyner","year":"2005","journal-title":"Nat. Med."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1038\/35066602","article-title":"Regulation of CD40 and CD40 ligand by the AT-hook transcription factor AKNA","volume":"410","author":"Siddiqa","year":"2001","journal-title":"Nature"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1016\/j.tig.2011.04.003","article-title":"Strategies for viral RNA stability: Live long and prosper","volume":"27","author":"Dickson","year":"2011","journal-title":"Trends Genet."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1016\/j.chom.2010.07.003","article-title":"Sindbis virus usurps the cellular HuR protein to stabilize its transcripts and promote productive infections in mammalian and mosquito cells","volume":"8","author":"Sokoloski","year":"2010","journal-title":"Cell Host Microbe"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1126","DOI":"10.1017\/S1355838201010044","article-title":"Poly(rC) binding proteins mediate poliovirus mRNA stability","volume":"7","author":"Murray","year":"2001","journal-title":"RNA"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/j.virol.2009.03.012","article-title":"Altered interactions between stem-loop IV within the 5' noncoding region of coxsackievirus RNA and poly(rC) binding protein 2: Effects on IRES-mediated translation and viral infectivity","volume":"389","author":"Sean","year":"2009","journal-title":"Virology"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"12008","DOI":"10.1128\/JVI.76.23.12008-12022.2002","article-title":"Distinct poly(rC) binding protein KH domain determinants for poliovirus translation initiation and viral RNA replication","volume":"76","author":"Walter","year":"2002","journal-title":"J. Virol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1261\/rna.780708","article-title":"Identification of PCBP2, a facilitator of IRES-mediated translation, as a novel constituent of stress granules and processing bodies","volume":"14","author":"Fujimura","year":"2008","journal-title":"RNA"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"2622","DOI":"10.1038\/emboj.2011.171","article-title":"An RNA-protein complex links enhanced nuclear 3' processing with cytoplasmic mRNA stabilization","volume":"30","author":"Ji","year":"2011","journal-title":"EMBO J."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1038\/nsmb724","article-title":"The enzymes and control of eukaryotic mRNA turnover","volume":"11","author":"Parker","year":"2004","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"875","DOI":"10.1007\/s00018-009-0215-z","article-title":"The alpha-kinase family: An exceptional branch on the protein kinase tree","volume":"67","author":"Middelbeek","year":"2010","journal-title":"Cell. Mol. Life Sci."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"3363","DOI":"10.1073\/pnas.0511345103","article-title":"Gene expression patterns in dendritic cells infected with measles virus compared with other pathogens","volume":"103","author":"Zilliox","year":"2006","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref_53","unstructured":"Gene. Available online:http:\/\/www.ncbi.nlm.nih.gov\/gene."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"6473","DOI":"10.4049\/jimmunol.1100719","article-title":"MIP-T3 Is a Negative Regulator of Innate Type I IFN Response","volume":"187","author":"Ng","year":"2011","journal-title":"J. Immunol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"2689","DOI":"10.1128\/JVI.79.5.2689-2699.2005","article-title":"Regulating intracellular antiviral defense and permissiveness to hepatitis C virus RNA replication through a cellular RNA helicase, RIG-I","volume":"79","author":"Sumpter","year":"2005","journal-title":"J. Virol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1537","DOI":"10.3748\/wjg.15.1537","article-title":"Hepatitis C virus and type 2 diabetes","volume":"15","author":"Negro","year":"2009","journal-title":"World J. Gastroenterol."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1111\/j.1572-0241.2006.01038.x","article-title":"Clearance of HCV improves insulin resistance, beta-cell function, and hepatic expression of insulin receptor substrate 1 and 2","volume":"102","author":"Kawaguchi","year":"2007","journal-title":"Am. J. Gastroenterol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"2239","DOI":"10.2337\/diabetes.52.9.2239","article-title":"Molecular mechanisms of insulin resistance in IRS-2-deficient hepatocytes","volume":"52","author":"Valverde","year":"2003","journal-title":"Diabetes"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1016\/S0002-9440(10)62058-5","article-title":"Overexpression of insulin receptor substrate-2 in human and murine hepatocellular carcinoma","volume":"167","author":"Boissan","year":"2005","journal-title":"Am. J. Pathol."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1016\/j.jhep.2010.10.003","article-title":"Hedgehog signaling in the liver","volume":"54","author":"Omenetti","year":"2011","journal-title":"J. Hepatol."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"1690","DOI":"10.1038\/labinvest.2010.147","article-title":"Viral factors induce Hedgehog pathway activation in humans with viral hepatitis, cirrhosis, and hepatocellular carcinoma","volume":"90","author":"Witek","year":"2010","journal-title":"Lab. Investig."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"e23943","DOI":"10.1371\/journal.pone.0023943","article-title":"Hedgehog signaling antagonist promotes regression of both liver fibrosis and hepatocellular carcinoma in a murine model of primary liver cancer","volume":"6","author":"Philips","year":"2011","journal-title":"PLoS One"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"1580","DOI":"10.1002\/hep.24576","article-title":"Up-regulation of Hedgehog pathway is associated with cellular permissiveness for hepatitis C virus replication","volume":"54","author":"Choi","year":"2011","journal-title":"Hepatology"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1093\/glycob\/cwl083","article-title":"Virus-induced transcriptional activation of host FUT genes associated with neo-expression of Ley in cytomegalovirus-infected and sialyl-Lex in varicella-zoster virus-infected diploid human cells","volume":"17","author":"Nystrom","year":"2007","journal-title":"Glycobiology"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1559-0275-8-7","article-title":"Aberrant glycosylation associated with enzymes as cancer biomarkers","volume":"8","author":"Meany","year":"2011","journal-title":"Clin. Proteonomics"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1093\/jb\/mvn011","article-title":"Biological function of fucosylation in cancer biology","volume":"143","author":"Miyoshi","year":"2008","journal-title":"J. Biochem."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"41R","DOI":"10.1093\/glycob\/cwg054","article-title":"Fucose: Biosynthesis and biological function in mammals","volume":"13","author":"Becker","year":"2003","journal-title":"Glycobiology"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1093\/glycob\/cwp057","article-title":"Induction of sialyl-Lex expression by herpes simplex virus type 1 is dependent on viral immediate early RNA-activated transcription of host fucosyltransferase genes","volume":"19","author":"Nystrom","year":"2009","journal-title":"Glycobiology"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"015013","DOI":"10.1088\/1478-3975\/8\/1\/015013","article-title":"Biophysics of selectin-ligand interactions in inflammation and cancer","volume":"8","author":"Cheung","year":"2011","journal-title":"Phys. Biol."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.acthis.2007.07.003","article-title":"Cell surface glycosylation diversity of embryonic thymic tissues","volume":"110","author":"Balcan","year":"2008","journal-title":"Acta Histochem."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"2232","DOI":"10.1074\/jbc.M109.066191","article-title":"N- and O-glycans modulate galectin-1 binding, CD45 signaling, and T cell death","volume":"285","author":"Earl","year":"2010","journal-title":"J. Biol. Chem."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"2401","DOI":"10.1016\/j.molimm.2007.11.006","article-title":"Glycosylation changes in hFUT1 transgenic mice increase TCR signaling and apoptosis resulting in thymocyte maturation arrest","volume":"45","author":"Moore","year":"2008","journal-title":"Mol. Immunol."},{"key":"ref_73","unstructured":"GEO Profiles. Available online:http:\/\/www.ncbi.nlm.nih.gov\/geoprofiles."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1002\/ijc.22769","article-title":"HPV related VIN: Highly proliferative and diminished responsiveness to extracellular signals","volume":"121","author":"Santegoets","year":"2007","journal-title":"Int. J. Canc."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"1002","DOI":"10.1016\/j.micinf.2009.07.006","article-title":"Restriction of Chlamydia pneumoniae replication in human dendritic cell by activation of indoleamine 2,3-dioxygenase","volume":"11","author":"Njau","year":"2009","journal-title":"Microb. Infect."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"2644","DOI":"10.1128\/AAC.01618-07","article-title":"Impact of mycophenolic acid on the functionality of human polymorphonuclear neutrophils and dendritic cells during interaction with Aspergillus fumigatus","volume":"52","author":"Mezger","year":"2008","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1007\/s11568-009-9080-y","article-title":"Identification of gene biomarkers for respiratory syncytial virus infection in a bronchial epithelial cell line","volume":"2","author":"Huang","year":"2008","journal-title":"Genomic Med."},{"key":"ref_78","first-page":"256","article-title":"Microarray analysis of primary endothelial cells challenged with different inflammatory and immune cytokines","volume":"29","author":"Sana","year":"2005","journal-title":"Cytokine"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/S0378-1119(02)00887-9","article-title":"Characterization of a Drosophila melanogaster orthologue of muskelin","volume":"297","author":"Adams","year":"2002","journal-title":"Gene"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"13001","DOI":"10.1128\/JVI.76.24.13001-13014.2002","article-title":"Highly permissive cell lines for subgenomic and genomic hepatitis C virus RNA replication","volume":"76","author":"Blight","year":"2002","journal-title":"J. Virol."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1002\/jmv.1055","article-title":"Sequence analysis of hepatitis C virus isolated from a fulminant hepatitis patient","volume":"64","author":"Kato","year":"2001","journal-title":"J. Med. Virol."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1016\/j.antiviral.2010.11.004","article-title":"Measuring antiviral activity of benzimidazole molecules that alter IRES RNA structure with an infectious hepatitis C virus chimera expressing Renilla luciferase","volume":"89","author":"Liu","year":"2011","journal-title":"Antivir. Res."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"4546","DOI":"10.1021\/bi047645m","article-title":"A mutant of eukaryotic protein synthesis initiation factor eIF4E(K119A) has an increased binding affinity for both m7G cap analogues and eIF4G peptides","volume":"44","author":"Friedland","year":"2005","journal-title":"Biochemistry"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"2730","DOI":"10.1093\/bioinformatics\/btp472","article-title":"The Integrated Genome Browser: Free software for distribution and exploration of genome-scale datasets","volume":"25","author":"Nicol","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1186\/1471-2105-9-523","article-title":"Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks","volume":"9","author":"Nix","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nmeth.1226","article-title":"Mapping and quantifying mammalian transcriptomes by RNA-Seq","volume":"5","author":"Mortazavi","year":"2008","journal-title":"Nat. Methods"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"9294","DOI":"10.1073\/pnas.0503596102","article-title":"Robust hepatitis C virus infection in vitro","volume":"102","author":"Zhong","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U. S. 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