2019
Quantitative Fluorescence In Situ Hybridization (FISH) and Immunofluorescence (IF) of Specific Gene Products in KSHV-Infected Cells.
Vallery TK, Steitz JA. Quantitative Fluorescence In Situ Hybridization (FISH) and Immunofluorescence (IF) of Specific Gene Products in KSHV-Infected Cells. Journal Of Visualized Experiments 2019 PMID: 31524859, PMCID: PMC6750728, DOI: 10.3791/59697.Peer-Reviewed Original ResearchConceptsRNA FISHSarcoma-associated herpesvirusSpecific RNAViral replication compartmentsSpecific gene productsSitu hybridizationKaposi's sarcoma-associated herpesvirusMultiple cell typesReplication compartmentsGene productsViral genesHost cellsCell typesQuantitative fluorescenceNuclear factoriesFishCell morphologyHuman hostMechanistic insightsSpatiotemporal activityUninfected cellsBehavior of biomoleculesRNAProteinCellsIdiosyncrasies of Viral Noncoding RNAs Provide Insights into Host Cell Biology
Withers JB, Mondol V, Pawlica P, Rosa-Mercado NA, Tycowski KT, Ghasempur S, Torabi SF, Steitz JA. Idiosyncrasies of Viral Noncoding RNAs Provide Insights into Host Cell Biology. Annual Review Of Virology 2019, 6: 1-21. PMID: 31039329, PMCID: PMC6768742, DOI: 10.1146/annurev-virology-092818-015811.Peer-Reviewed Original ResearchConceptsHost cell biologyCell biologyMessenger RNA stabilityHost cell machineryHost gene expressionDiverse biological rolesHost immune evasionLong ncRNAsMicroRNA biogenesisCell machineryNoncoding RNAsRNA stabilityCircular RNAsCellular transformationCellular survivalNcRNAsViral noncoding RNAsBiological roleGene expressionAnimal virusesNoncanonical pathwayHost cellsViral ncRNAsNovel mechanismBiogenesis
2018
Two herpesviral noncoding PAN RNAs are functionally homologous but do not associate with common chromatin loci
Withers JB, Li ES, Vallery TK, Yario TA, Steitz JA. Two herpesviral noncoding PAN RNAs are functionally homologous but do not associate with common chromatin loci. PLOS Pathogens 2018, 14: e1007389. PMID: 30383841, PMCID: PMC6233925, DOI: 10.1371/journal.ppat.1007389.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell LineCell NucleusChromatinGene Expression Regulation, ViralGene Knockdown TechniquesHEK293 CellsHerpesviridaeHerpesviridae InfectionsHerpesvirus 8, HumanHost-Pathogen InteractionsHumansMacaca mulattaRhadinovirusRNA, Long NoncodingRNA, MessengerRNA, NuclearRNA, ViralTumor Virus InfectionsViral ProteinsVirus ReplicationConceptsKaposi's sarcoma-associated herpesvirusPAN RNAPAN RNA expressionGene expressionChromatin lociSarcoma-associated herpesvirusViral mRNAsSpecific chromatin lociNuclear mRNA exportNucleotide sequence conservationAbundant nuclear RNARNA expressionLytic viral gene expressionViral gene expressionMRNA exportRNA associationSequence conservationPolyadenylated transcriptsViral chromatinLoci differHost chromatinRNA functionCell fractionationNuclear RNAProgeny virion releaseKaposi's Sarcoma-Associated Herpesvirus mRNA Accumulation in Nuclear Foci Is Influenced by Viral DNA Replication and Viral Noncoding Polyadenylated Nuclear RNA
Vallery TK, Withers JB, Andoh JA, Steitz JA. Kaposi's Sarcoma-Associated Herpesvirus mRNA Accumulation in Nuclear Foci Is Influenced by Viral DNA Replication and Viral Noncoding Polyadenylated Nuclear RNA. Journal Of Virology 2018, 92: 10.1128/jvi.00220-18. PMID: 29643239, PMCID: PMC6002709, DOI: 10.1128/jvi.00220-18.Peer-Reviewed Original ResearchConceptsKaposi's sarcoma-associated herpesvirusViral replication compartmentsSarcoma-associated herpesvirusReplication compartmentsViral DNA replicationViral DNA synthesisPAN RNANuclear fociDNA replicationNuclear RNAViral mRNAsDNA synthesisViral transcriptsLytic phaseIntronless viral mRNAsHijack host machineryActive viral DNA replicationPolyadenylated Nuclear RNAHost cell nucleusViral noncoding RNAViral RNA accumulationShutoff effectHuman cell hostSpatiotemporal regulationViral life cycle
2015
EBV 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
2012
Tracking expression and subcellular localization of RNA and protein species using high-throughput single cell imaging flow cytometry
Borah S, Nichols LA, Hassman LM, Kedes DH, Steitz JA. Tracking expression and subcellular localization of RNA and protein species using high-throughput single cell imaging flow cytometry. RNA 2012, 18: 1573-1579. PMID: 22745225, PMCID: PMC3404377, DOI: 10.1261/rna.033126.112.Peer-Reviewed Original ResearchConceptsKaposi's sarcoma-associated herpesvirusSarcoma-associated herpesvirusSubcellular localizationProtein moleculesHigh-throughput approachPAN RNAProtein speciesNoncoding RNAsNuclear RNAProtein C1Imaging Flow CytometryFlow cytometryRNANuclear translocationHigh-throughput applicationsLytic phaseViral RNATranslocationExpressionLocalizationCellsHeterogeneous populationPABPC1CytometryMolecules
2011
A Viral Nuclear Noncoding RNA Binds Re-localized Poly(A) Binding Protein and Is Required for Late KSHV Gene Expression
Borah S, Darricarrère N, Darnell A, Myoung J, Steitz JA. A Viral Nuclear Noncoding RNA Binds Re-localized Poly(A) Binding Protein and Is Required for Late KSHV Gene Expression. PLOS Pathogens 2011, 7: e1002300. PMID: 22022268, PMCID: PMC3192849, DOI: 10.1371/journal.ppat.1002300.Peer-Reviewed Original ResearchConceptsPAN RNAKaposi's Sarcoma-Associated HerpesvirusNuclear noncoding RNANuclear noncoding RNAsShutoff effectLytic phaseKSHV gene expressionRepertoire of functionsTail of mRNATransient transfection experimentsConsequence of expressionLate viral proteinsNoncoding RNAsExonuclease proteinNuclear RNAProtein C1Translation efficiencyHost mRNAsMRNA stabilityGene expressionUnknown functionTransfection experimentsViral mRNAsPABPC1Binding protein
1975
F factor-mediated inhibition of bacteriophage T7 growth: Analysis of T7 RNA and protein synthesis In vivo and In vitro using male and female Escherichia coli
Condit RC, Steitz JA. F factor-mediated inhibition of bacteriophage T7 growth: Analysis of T7 RNA and protein synthesis In vivo and In vitro using male and female Escherichia coli. Journal Of Molecular Biology 1975, 98: 31-43. PMID: 1104867, DOI: 10.1016/s0022-2836(75)80099-4.Peer-Reviewed Original ResearchConceptsT7 growthProtein synthesisE. coliPolyacrylamide gel electrophoresisEscherichia coliPhage protein synthesisGel electrophoresisTranslation apparatusT7 proteinsPhage proteinsT7 infectionT7 DNAT7 RNAFaithful synthesisRNA synthesisProteinMale cellsRNAColiTranscriptionSimultaneous inhibitionSpecific modificationsT7InhibitionElectrophoresis
1974
T7 Early messenger RNAs are the direct products of ribonuclease III cleavage
Rosenberg M, Kramer R, Steitz J. T7 Early messenger RNAs are the direct products of ribonuclease III cleavage. Journal Of Molecular Biology 1974, 89: 777-782. PMID: 4615167, DOI: 10.1016/0022-2836(74)90052-7.Peer-Reviewed Original Research