2016
EBV noncoding RNA EBER2 interacts with host RNA-binding proteins to regulate viral gene expression
Lee N, Yario TA, Gao JS, Steitz JA. EBV noncoding RNA EBER2 interacts with host RNA-binding proteins to regulate viral gene expression. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 3221-3226. PMID: 26951683, PMCID: PMC4812724, DOI: 10.1073/pnas.1601773113.Peer-Reviewed Original ResearchMeSH KeywordsGene Expression Regulation, ViralGenes, ViralHEK293 CellsHerpesvirus 4, HumanHumansProtein BindingRNA, ViralRNA-Binding ProteinsConceptsNon-POU domain-containing octamer-binding proteinGene expressionNoncoding RNAsHost RNAAbundant noncoding RNAsCellular noncoding RNAsRNA-protein crosslinkingOctamer-binding proteinHost gene expressionBox protein 5Viral gene expressionHost transcription factorsGlutamine richFactor prolineIntermediary proteinsNuclear bodiesTranscription factorsRNA 2Host proteinsRecombinant proteinsProtein resultsProtein componentsProtein 5Protein 14RNA
2015
Noncoding RNA‐guided recruitment of transcription factors: A prevalent but undocumented mechanism?
Lee N, Steitz JA. Noncoding RNA‐guided recruitment of transcription factors: A prevalent but undocumented mechanism? BioEssays 2015, 37: 936-941. PMID: 26200477, PMCID: PMC4721591, DOI: 10.1002/bies.201500060.Peer-Reviewed Original ResearchConceptsTranscription factorsDomains of TFsCognate binding motifsDNA target sitesAssociated transcription factorsRNA-RNA interactionsTarget siteNascent transcriptsCell identityTarget lociCellular processesNoncoding RNAsBinding motifProper regulationViral genomeUndocumented mechanismGenomeDNAViral DNARNARecruitmentNcRNAsNcRNARNAsLociProteomics and Transcriptomics of BJAB Cells Expressing the Epstein-Barr Virus Noncoding RNAs EBER1 and EBER2
Pimienta G, Fok V, Haslip M, Nagy M, Takyar S, Steitz JA. Proteomics and Transcriptomics of BJAB Cells Expressing the Epstein-Barr Virus Noncoding RNAs EBER1 and EBER2. PLOS ONE 2015, 10: e0124638. PMID: 26121143, PMCID: PMC4487896, DOI: 10.1371/journal.pone.0124638.Peer-Reviewed Original ResearchConceptsMRNA-seq dataHost cell nucleusBJAB cellsCell proliferationGene expression featuresPro-survival effectsProtein adaptersAlternative splicingMRNA transcriptomeUpregulated proteinsSILAC dataRich elementsAkt activationPI3K-AktBiochemical assaysCell nucleiEBV latencySwitch eventsProteinMaintenance of latencyCell linesVEGFA proteinMechanistic explanationUpregulated oncogenesPIK3AP1In silico discovery and modeling of non-coding RNA structure in viruses
Moss WN, Steitz JA. In silico discovery and modeling of non-coding RNA structure in viruses. Methods 2015, 91: 48-56. PMID: 26116541, PMCID: PMC4684774, DOI: 10.1016/j.ymeth.2015.06.015.Peer-Reviewed Original ResearchMeSH KeywordsComputer SimulationHerpesvirus 4, HumanInfluenza A virusNucleic Acid ConformationRNA, UntranslatedRNA, ViralEBV Noncoding RNA Binds Nascent RNA to Drive Host PAX5 to Viral DNA
Lee N, Moss WN, Yario TA, Steitz JA. EBV Noncoding RNA Binds Nascent RNA to Drive Host PAX5 to Viral DNA. Cell 2015, 160: 607-618. PMID: 25662012, PMCID: PMC4329084, DOI: 10.1016/j.cell.2015.01.015.Peer-Reviewed Original ResearchConceptsTerminal repeatNascent RNANoncoding RNAsNuclear noncoding RNAB-cell transcription factor PAX5Greater sequence divergenceDNA target sitesTranscription factor Pax5Chromatin localizationTR lociSequence divergenceNascent transcriptsUndescribed functionTranscription factorsLatent EBV genomeRNATarget siteEssential rolePrimate herpesvirusesEBV lytic replicationPAX5Lytic replicationViral DNAEBER2Viral replication
2014
Nuclear Translocation and Regulation of Intranuclear Distribution of Cytoplasmic Poly(A)-Binding Protein Are Distinct Processes Mediated by Two Epstein Barr Virus Proteins
Park R, El-Guindy A, Heston L, Lin SF, Yu KP, Nagy M, Borah S, Delecluse HJ, Steitz J, Miller G. Nuclear Translocation and Regulation of Intranuclear Distribution of Cytoplasmic Poly(A)-Binding Protein Are Distinct Processes Mediated by Two Epstein Barr Virus Proteins. PLOS ONE 2014, 9: e92593. PMID: 24705134, PMCID: PMC3976295, DOI: 10.1371/journal.pone.0092593.Peer-Reviewed Original ResearchConceptsHost gene expressionIntranuclear distributionZEBRA mutantsReplication proteinsNuclear translocationGene expressionEssential replication proteinViral replication proteinsDownstream viral genesViral replication compartmentsLytic replicationNew protein synthesisBZIP proteinsGlobal shutoffViral alkaline nucleaseReplication compartmentsPABPCEssential functionsEpstein-Barr virus proteinsHost shutoffViral genesLytic programProtein synthesisBinding proteinProtein
2013
RNA families in Epstein–Barr virus
Moss WN, Lee N, Pimienta G, Steitz JA. RNA families in Epstein–Barr virus. RNA Biology 2013, 11: 10-17. PMID: 24441309, PMCID: PMC3929418, DOI: 10.4161/rna.27488.Peer-Reviewed Original ResearchConceptsEpstein-Barr virusFunctional importanceSmall regulatory RNAsNovel Epstein-Barr virusSmall nucleolar RNAsLikely functional importanceInternal ribosomal entry siteRNA-seq studiesHuman γ-herpesvirusEvolutionary conservationNovel ncRNARegulatory RNAsShort intronsRecent bioinformaticsNucleolar RNAsOncogenic typesRNA familiesTumorigenic phenotypeStructured RNAsEBV genomeEBNA1 mRNARepetitive regionsViral latencyHigh abundanceLatency maintenanceGenome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA
Moss WN, Steitz JA. Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA. BMC Genomics 2013, 14: 543. PMID: 23937650, PMCID: PMC3751371, DOI: 10.1186/1471-2164-14-543.Peer-Reviewed Original ResearchConceptsStable intronic sequence RNARNA structureSequence RNAComprehensive genome-wide surveyGenome-wide surveyGenome-wide analysisRNA-seq analysisComparative sequence analysisNon-coding RNAsSecondary structure modelRNA-seq dataRNAz programFunctional RNAsGenomic sequencesImportant human pathogenSequence analysisRNAEBV transcriptomeHuman pathogensHerpesvirus 4Future experimental analysisPotential functionTranscriptomeGenomeEBV genome
2012
AUF1/hnRNP D is a novel protein partner of the EBER1 noncoding RNA of Epstein-Barr virus
Lee N, Pimienta G, Steitz JA. AUF1/hnRNP D is a novel protein partner of the EBER1 noncoding RNA of Epstein-Barr virus. RNA 2012, 18: 2073-2082. PMID: 23012480, PMCID: PMC3479396, DOI: 10.1261/rna.034900.112.Peer-Reviewed Original ResearchMeSH Keywords3' Untranslated RegionsAptamers, NucleotideAU Rich ElementsBinding, CompetitiveCell Line, TumorHerpesvirus 4, HumanHeterogeneous Nuclear Ribonucleoprotein D0Heterogeneous-Nuclear Ribonucleoprotein DHost-Pathogen InteractionsHumansImmunoprecipitationMutagenesis, InsertionalProtein BindingProtein IsoformsRNA StabilityRNA, ViralConceptsAU-rich elementsProtein partnersAUF1/hnRNP DUntranslated regionBacteriophage MS2 coat proteinNovel protein partnersHigh abundanceElectrophoretic mobility shift assaysEpstein-Barr virusMS2 coat proteinStable isotope labelingMobility shift assaysInteracting proteinMolecular functionsHnRNP DAlternative splicingNoncoding RNAsShift assaysCoat proteinIsotope labelingP40 isoformRNA aptamersRNA 1AUF1UV crosslinkingEBV and human microRNAs co‐target oncogenic and apoptotic viral and human genes during latency
Riley KJ, Rabinowitz GS, Yario TA, Luna JM, Darnell RB, Steitz JA. EBV and human microRNAs co‐target oncogenic and apoptotic viral and human genes during latency. The EMBO Journal 2012, 31: 2207-2221. PMID: 22473208, PMCID: PMC3343464, DOI: 10.1038/emboj.2012.63.Peer-Reviewed Original ResearchConceptsHuman microRNAsLatent membrane protein 1Viral miRNA functionHigh-throughput sequencingHuman miRNA targetsMiRNA-binding sitesMiRNA functionEBV BHRF1Human genesMiRNA targetsMRNA targetsCellular miRNAsMembrane protein 1MiRNA clusterHuman miRNAsGene expressionCell cycleReporter assaysDistinct binding sitesViral mRNAsMiRNAsLytic genesLytic switchProtein 1EBV latent membrane protein 1
2010
Noncoding RNPs of Viral Origin
Steitz J, Borah S, Cazalla D, Fok V, Lytle R, Mitton-Fry R, Riley K, Samji T. Noncoding RNPs of Viral Origin. Cold Spring Harbor Perspectives In Biology 2010, 3: a005165. PMID: 20719877, PMCID: PMC3039937, DOI: 10.1101/cshperspect.a005165.Peer-Reviewed Original Research
2006
Epstein-Barr virus noncoding RNAs are confined to the nucleus, whereas their partner, the human La protein, undergoes nucleocytoplasmic shuttling
Fok V, Friend K, Steitz JA. Epstein-Barr virus noncoding RNAs are confined to the nucleus, whereas their partner, the human La protein, undergoes nucleocytoplasmic shuttling. Journal Of Cell Biology 2006, 173: 319-325. PMID: 16682524, PMCID: PMC2063832, DOI: 10.1083/jcb.200601026.Peer-Reviewed Original ResearchMeSH KeywordsActive Transport, Cell NucleusAnimalsAntibiotics, AntineoplasticAutoantigensCell LineCell Line, TumorCell NucleusDactinomycinFatty Acids, UnsaturatedFemaleHeLa CellsHerpesvirus 4, HumanHumansKaryopherinsMiceNIH 3T3 CellsOocytesProtein BindingRibonucleoproteinsRNA TransportRNA, UntranslatedRNA, ViralXenopus laevisMultiple domains of EBER 1, an Epstein-Barr virus noncoding RNA, recruit human ribosomal protein L22
Fok V, Mitton-Fry RM, Grech A, Steitz JA. Multiple domains of EBER 1, an Epstein-Barr virus noncoding RNA, recruit human ribosomal protein L22. RNA 2006, 12: 872-882. PMID: 16556938, PMCID: PMC1440895, DOI: 10.1261/rna.2339606.Peer-Reviewed Original ResearchMeSH KeywordsBinding SitesCarrier ProteinsCell LineCross-Linking ReagentsElectrophoretic Mobility Shift AssayHerpesvirus 4, HumanHumansIn Vitro TechniquesMaltose-Binding ProteinsNucleic Acid ConformationPlasmidsProtein BindingProtein Structure, TertiaryRecombinant Fusion ProteinsRibosomal ProteinsRNA, UntranslatedRNA, ViralRNA-Binding ProteinsSequence DeletionTranscription, GeneticTransfectionUltraviolet RaysThe Challenge of Viral snRNPs
CONRAD NK, FOK V, CAZALLA D, BORAH S, STEITZ JA. The Challenge of Viral snRNPs. Cold Spring Harbor Symposia On Quantitative Biology 2006, 71: 377-384. PMID: 17381320, DOI: 10.1101/sqb.2006.71.057.Peer-Reviewed Original ResearchConceptsNuclear noncoding RNAsHSURs 1Sarcoma-associated herpesvirusRibosomal protein L22Aggressive T-cell leukemiaT cell signalingViral gene expressionKaposi's sarcoma-associated herpesvirusHeterokaryon assayU RNADependent RNA degradationMammalian cellsNoncoding RNAsProtein L22Nuclear surveillanceRNA degradationHost mRNAsHost proteinsGene expressionMRNA transcriptsMutant virusHerpesvirus saimiriRNAImportant functionsRNAs
1994
The Epstein-Barr virus (EBV) small RNA EBER1 binds and relocalizes ribosomal protein L22 in EBV-infected human B lymphocytes.
Toczyski DP, Matera AG, Ward DC, Steitz JA. The Epstein-Barr virus (EBV) small RNA EBER1 binds and relocalizes ribosomal protein L22 in EBV-infected human B lymphocytes. Proceedings Of The National Academy Of Sciences Of The United States Of America 1994, 91: 3463-3467. PMID: 8159770, PMCID: PMC43597, DOI: 10.1073/pnas.91.8.3463.Peer-Reviewed Original ResearchConceptsEpstein-Barr virusHuman B lymphocytesB lymphocytesEBV-positive lymphocytesEBV-positive cellsEBER1 RNAUninfected human cellsCertain patientsEBER1Ribosomal protein L22LymphocytesChromosomal translocationsOncogenic herpesvirusProtein L22Situ hybridizationUninfected cell extractsNucleoplasmic stainingVivoCell transformationHigh levelsHuman cellsCellsPatientsLeukemiaCellular proteins
1993
The cellular RNA-binding protein EAP recognizes a conserved stem-loop in the Epstein-Barr virus small RNA EBER 1.
Toczyski DP, Steitz JA. The cellular RNA-binding protein EAP recognizes a conserved stem-loop in the Epstein-Barr virus small RNA EBER 1. Molecular And Cellular Biology 1993, 13: 703-710. PMID: 8380232, PMCID: PMC358948, DOI: 10.1128/mcb.13.1.703.Peer-Reviewed Original ResearchConceptsCellular RNA-binding proteinsRNA-binding proteinDetailed mutational analysisStem-loop structureSequence-specific mannerRNase protection experimentsEpstein‐Barr virus small RNA EBER‐1Double-stranded regionsSmall RNAsDeletion mutantsEBER-1Mutational analysisFusion proteinProtection experimentsViral proteinsProteinRNAEpstein-Barr virusBindingMutantsHerpesvirus papioNucleotidesHairpinAntibodiesCells
1991
EAP, a highly conserved cellular protein associated with Epstein‐Barr virus small RNAs (EBERs).
Toczyski DP, Steitz JA. EAP, a highly conserved cellular protein associated with Epstein‐Barr virus small RNAs (EBERs). The EMBO Journal 1991, 10: 459-466. PMID: 1846807, PMCID: PMC452667, DOI: 10.1002/j.1460-2075.1991.tb07968.x.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceB-LymphocytesBase SequenceCell LineCell Transformation, ViralCloning, MolecularDNAHerpesvirus 4, HumanHumansMolecular Sequence DataPolymerase Chain ReactionProteinsRibonucleoproteinsRibonucleoproteins, Small NuclearRibosomal ProteinsRNA-Binding ProteinsRNA, Small NuclearRNA, ViralSequence Homology, Nucleic Acid
1988
Structural analyses of EBER1 and EBER2 ribonucleoprotein particles present in Epstein-Barr virus-infected cells
Glickman JN, Howe JG, Steitz JA. Structural analyses of EBER1 and EBER2 ribonucleoprotein particles present in Epstein-Barr virus-infected cells. Journal Of Virology 1988, 62: 902-911. PMID: 2828685, PMCID: PMC253649, DOI: 10.1128/jvi.62.3.902-911.1988.Peer-Reviewed Original Research
1986
Localization of Epstein-Barr virus-encoded small RNAs by in situ hybridization.
Howe JG, Steitz JA. Localization of Epstein-Barr virus-encoded small RNAs by in situ hybridization. Proceedings Of The National Academy Of Sciences Of The United States Of America 1986, 83: 9006-9010. PMID: 3024161, PMCID: PMC387063, DOI: 10.1073/pnas.83.23.9006.Peer-Reviewed Original ResearchMeSH KeywordsCell NucleusCell Transformation, ViralCells, CulturedHerpesvirus 4, HumanNucleic Acid HybridizationRNA, Small NuclearRNA, Viral
1981
Striking similarities are exhibited by two small Epstein-Barr virus-encoded ribonucleic acids and the adenovirus-associated ribonucleic acids VAI and VAII.
Rosa MD, Gottlieb E, Lerner MR, Steitz JA. Striking similarities are exhibited by two small Epstein-Barr virus-encoded ribonucleic acids and the adenovirus-associated ribonucleic acids VAI and VAII. Molecular And Cellular Biology 1981, 1: 785-796. PMID: 9279391, PMCID: PMC369362, DOI: 10.1128/mcb.1.9.785.Peer-Reviewed Original ResearchConceptsEBER-1EBER-2Epstein-Barr virus-encoded ribonucleic acidEBER genesEpstein-Barr virus genomeEBV deoxyribonucleic acidSystemic lupus erythematosusAnti-La antibodiesEcoRI J fragmentRibonucleic acidSmall ribonucleic acidsLupus erythematosusUninfected cellsEBERVirus genomeViral genomeErythematosusVaII