title: Epstein-Barr virus induces global changes in cellular mRNA isoform usage that are important for the maintenance of latency.
abstract: Oncogenic viruses promote cell proliferation through the dramatic reorganization of host transcriptomes. In addition to regulating mRNA abundance, changes in mRNA isoform usage can have a profound impact on the protein output of the transcriptome. Using Epstein-Barr virus (EBV) transformation of primary B cells, we have studied the ability of an oncogenic virus to alter the mRNA isoform profile of its host. Using the algorithm called SplicerEX with two complementary Affymetrix microarray platforms, we uncovered 433 mRNA isoform changes regulated by EBV during B-cell transformation. These changes were largely orthogonal with the 2,163 mRNA abundance changes observed during transformation, such that less than one-third of mRNAs changing at the level of isoform also changed in overall abundance. While we observed no preference for a mechanistic class of mRNA isoform change, we detected a significant shortening of 3' untranslated regions and exclusion of cassette exons in EBV-transformed cells relative to uninfected B cells. Gene ontology analysis of the mRNA isoform changes revealed significant enrichment in nucleic acid binding proteins. We validated several of these isoform changes and were intrigued by those in two mRNAs encoding the proteins XBP1 and TCF4, which have both been shown to bind and activate the promoter of the major EBV lytic trans-activator BZLF1. Our studies indicate that EBV latent infection promotes the usage of mRNA isoforms of XBP1 and TCF4 that restrict BZLF1 activation. Therefore, characterization of global changes in mRNA isoform usage during EBV infection identifies a new mechanism for the maintenance of latent infection.
authors.affiliation: Department of Molecular Genetics and Microbiology, Center for Virology, Duke University Medical Center.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Homa
authors.forename: Raul
authors.initials: R
authors.lastname: Salinas
authors.forename: Eleonora
authors.initials: E
authors.lastname: Forte
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Robinson
authors.forename: Mariano A
authors.initials: MA
authors.lastname: Garcia-Blanco
authors.forename: Micah A
authors.initials: MA
authors.lastname: Luftig
mesh_terms: D001402:B-Lymphocytes / Q000378:metabolism / Q000821:virology; D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors / Q000235:genetics / Q000378:metabolism; D015415:Biomarkers / Q000378:metabolism; D015153:Blotting, Western; D002472:Cell Transformation, Viral / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D020031:Epstein-Barr Virus Infections / Q000235:genetics* / Q000821:virology; D020869:Gene Expression Profiling; D015967:Gene Expression Regulation, Viral; D004854:Herpesvirus 4, Human / Q000235:genetics / Q000472:pathogenicity; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic / Q000235:genetics; D059368:RNA Isoforms; D012333:RNA, Messenger / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction; D000071701:Regulatory Factor X Transcription Factors; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015534:Trans-Activators / Q000235:genetics / Q000378:metabolism; D000073940:Transcription Factor 4; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D017735:Virus Latency / Q000235:genetics*; D014779:Virus Replication; D000071717:X-Box Binding Protein 1
chemical_list: C063676:BZLF1 protein, Herpesvirus 4, Human; D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors; D015415:Biomarkers; D004268:DNA-Binding Proteins; D059368:RNA Isoforms; D012333:RNA, Messenger; D012367:RNA, Viral; D000071701:Regulatory Factor X Transcription Factors; C532096:TCF4 protein, human; D015534:Trans-Activators; D000073940:Transcription Factor 4; D014157:Transcription Factors; D000071717:X-Box Binding Protein 1; C000605543:XBP1 protein, human
references.citation: Virol J. 2009 Dec 29;6:231
references.pmid: 20040105
references.citation: Adv Cancer Res. 2007;97:81-109
references.pmid: 17419942
references.citation: EMBO J. 1994 Jul 15;13(14):3321-8
references.pmid: 8045261
references.citation: J Virol. 2000 Jan;74(2):710-20
references.pmid: 10623733
references.citation: Mol Cell Biol. 2011 Jan;31(1):138-50
references.pmid: 21041478
references.citation: J Virol. 2010 Jun;84(12):6139-52
references.pmid: 20375168
references.citation: J Virol. 1996 Sep;70(9):5909-15
references.pmid: 8709211
references.citation: Mol Cell. 2004 Jan 16;13(1):91-100
references.pmid: 14731397
references.citation: Cell. 2009 Aug 21;138(4):673-84
references.pmid: 19703394
references.citation: Biochim Biophys Acta. 2012 May;1819(5):375-81
references.pmid: 22207202
references.citation: J Virol. 1997 Nov;71(11):8552-62
references.pmid: 9343213
references.citation: Blood. 2011 Jun 9;117(23):6297-303
references.pmid: 21447826
references.citation: Science. 1991 Nov 8;254(5033):815-20
references.pmid: 1658933
references.citation: J Virol. 1990 Mar;64(3):1227-32
references.pmid: 2154606
references.citation: J Virol. 2009 May;83(10):5014-27
references.pmid: 19264782
references.citation: Proc Natl Acad Sci U S A. 2011 Feb 1;108(5):1919-24
references.pmid: 21245331
references.citation: RNA. 2012 Aug;18(8):1435-45
references.pmid: 22736799
references.citation: Proc Natl Acad Sci U S A. 1987 May;84(10):3452-6
references.pmid: 3033649
references.citation: Proc Natl Acad Sci U S A. 1994 Jan 18;91(2):772-6
references.pmid: 8290598
references.citation: Cell Mol Life Sci. 2001 Feb;58(2):266-77
references.pmid: 11289308
references.citation: J Virol. 2012 Oct;86(20):11096-106
references.pmid: 22855490
references.citation: J Gen Virol. 2003 Apr;84(Pt 4):959-964
references.pmid: 12655097
references.citation: Blood. 2000 Oct 1;96(7):2537-42
references.pmid: 11001908
references.citation: Int J Cancer. 1984 Jan 15;33(1):27-32
references.pmid: 6319296
references.citation: J Gen Virol. 2010 Mar;91(Pt 3):622-9
references.pmid: 19923262
references.citation: J Virol. 1990 Mar;64(3):1217-26
references.pmid: 2154605
references.citation: J Virol. 1995 May;69(5):3108-16
references.pmid: 7707539
references.citation: Cell. 2001 Dec 28;107(7):881-91
references.pmid: 11779464
references.citation: Nature. 2008 Nov 27;456(7221):470-6
references.pmid: 18978772
references.citation: J Virol. 2007 Sep;81(18):9748-58
references.pmid: 17609264
references.citation: Genome Res. 2013 Apr;23(4):604-15
references.pmid: 23335364
references.citation: Blood. 2011 Nov 17;118(20):5528-39
references.pmid: 21849482
references.citation: Virology. 1979 Apr 15;94(1):228-31
references.pmid: 220786
references.citation: J Biol Chem. 2001 Mar 16;276(11):7850-8
references.pmid: 11096110
references.citation: J Virol. 2012 Dec;86(24):13360-70
references.pmid: 23015717
references.citation: J Virol. 2011 May;85(10):5081-90
references.pmid: 21389123
references.citation: J Virol. 2004 Apr;78(8):4108-19
references.pmid: 15047827
references.citation: J Virol. 2012 Feb;86(3):1809-19
references.pmid: 22090141
references.citation: J Virol. 1998 Oct;72(10):8230-9
references.pmid: 9733866
references.citation: Proc Natl Acad Sci U S A. 2006 Sep 19;103(38):14188-93
references.pmid: 16966603
references.citation: Nat Rev Genet. 2007 Jul;8(7):533-43
references.pmid: 17572691
references.citation: PLoS Pathog. 2010 Jun 10;6(6):e1000951
references.pmid: 20548956
references.citation: J Biol Chem. 2005 Jun 3;280(22):21078-90
references.pmid: 15805103
references.citation: PLoS Genet. 2009 Aug;5(8):e1000595
references.pmid: 19680430
references.citation: PLoS Genet. 2011 Aug;7(8):e1002218
references.pmid: 21876675
references.citation: Biochim Biophys Acta. 2012 May;1819(5):446-53
references.pmid: 22387215
references.citation: J Gen Virol. 1994 Aug;75 ( Pt 8):1999-2006
references.pmid: 8046403
references.citation: Genes Dev. 2003 Feb 15;17(4):419-37
references.pmid: 12600935
references.citation: BMC Bioinformatics. 2010 Feb 25;11:108
references.pmid: 20184770
references.citation: J Biol Chem. 1995 Jul 28;270(30):17830-5
references.pmid: 7629084
references.citation: Nucleic Acids Res. 2011 Sep 1;39(16):6970-85
references.pmid: 21646333
references.citation: J Virol. 2012 May;86(9):4752-61
references.pmid: 22357272
references.citation: J Virol. 2007 Dec;81(24):13566-77
references.pmid: 17898050
references.citation: Bioessays. 2006 Apr;28(4):378-86
references.pmid: 16547952
references.citation: J Virol. 2007 Jul;81(14):7363-70
references.pmid: 17494074
references.citation: J Virol. 1995 Jun;69(6):3624-30
references.pmid: 7745710
references.citation: Genome Res. 2003 Sep;13(9):2129-41
references.pmid: 12952881
references.citation: BMC Genomics. 2008 Nov 07;9:529
references.pmid: 18990248
references.citation: Blood. 2011 Jan 27;117(4):1311-4
references.pmid: 21081713
references.citation: PLoS One. 2011;6(7):e22138
references.pmid: 21789225
references.citation: J Virol. 2011 Jun;85(11):5628-43
references.pmid: 21411522
references.citation: Science. 2008 Jun 20;320(5883):1643-7
references.pmid: 18566288