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 biomoleculesRNAProteinCells
2016
Fluorescence Amplification Method for Forward Genetic Discovery of Factors in Human mRNA Degradation
Alexandrov A, Shu MD, Steitz JA. Fluorescence Amplification Method for Forward Genetic Discovery of Factors in Human mRNA Degradation. Molecular Cell 2016, 65: 191-201. PMID: 28017590, PMCID: PMC5301997, DOI: 10.1016/j.molcel.2016.11.032.Peer-Reviewed Original ResearchConceptsNonsense-mediated decayPremature termination codonNMD factorsNMD pathwayMRNA degradationHuman cellsForward genetic screeningGenetic screen identifiesHuman genetic diseasesHuman candidate genesNonsense suppression therapyModel organismsGenetic screeningScreen identifiesTermination codonCandidate genesGenetic discoveriesReporter fluorescenceGenetic diseasesPathwayAdditional key factorsCellsCRISPRCodonHomologyA proximity-dependent assay for specific RNA–protein interactions in intact cells
Zhang W, Xie M, Shu MD, Steitz JA, DiMaio D. A proximity-dependent assay for specific RNA–protein interactions in intact cells. RNA 2016, 22: 1785-1792. PMID: 27659050, PMCID: PMC5066630, DOI: 10.1261/rna.058248.116.Peer-Reviewed Original ResearchConceptsRNA-protein interactionsSpecific RNA-protein interactionsProximity ligation assayTarget RNAProtein-protein interactionsSame cellular compartmentCellular compartmentsRNA targetsIntact cellsLigation assayRNADiscrete compartmentsProteinDNA oligonucleotideFluorescent signalOligonucleotide complementaryCellsCompartmentsAssaysColocalizationHigh specificityInteractionStaining methodOligonucleotideAdaptation
2014
3′-Biotin-tagged microRNA-27 does not associate with Argonaute proteins in cells
Guo YE, Steitz JA. 3′-Biotin-tagged microRNA-27 does not associate with Argonaute proteins in cells. RNA 2014, 20: 985-988. PMID: 24821854, PMCID: PMC4114695, DOI: 10.1261/rna.045054.114.Peer-Reviewed Original ResearchAlternative Capture of Noncoding RNAs or Protein-Coding Genes by Herpesviruses to Alter Host T Cell Function
Guo YE, Riley KJ, Iwasaki A, Steitz JA. Alternative Capture of Noncoding RNAs or Protein-Coding Genes by Herpesviruses to Alter Host T Cell Function. Molecular Cell 2014, 54: 67-79. PMID: 24725595, PMCID: PMC4039351, DOI: 10.1016/j.molcel.2014.03.025.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntigens, CDAntigens, Differentiation, T-LymphocyteBase SequenceCallithrixEnzyme ActivationGene Expression RegulationGPI-Linked ProteinsGRB2 Adaptor ProteinHEK293 CellsHerpesvirus 2, SaimiriineHigh-Throughput Nucleotide SequencingHost-Pathogen InteractionsHumansImmunoprecipitationInterferon-gammaJurkat CellsLectins, C-TypeLymphocyte ActivationMicroRNAsMitogen-Activated Protein KinasesMolecular Sequence DataReceptors, Antigen, T-CellRNA StabilityRNA, UntranslatedRNA, ViralSemaphorinsSequence Analysis, RNASignal TransductionTime FactorsT-LymphocytesTransfectionConceptsMitogen-activated protein kinaseMiR-27Protein coding genesHerpesvirus saimiriHigh-throughput sequencingTCR-induced activationCell functionHSUR 1Γ-herpesvirusesNoncoding RNAsProtein kinaseEctopic expressionOncogenic γ-herpesvirusesTarget genesInduction of CD69MicroRNA-27Key modulatorRNACommon targetAlHV-1GenesCell receptorDiverse strategiesHost T-cell functionCells
2013
Phosphorylation of DGCR8 Increases Its Intracellular Stability and Induces a Progrowth miRNA Profile
Herbert KM, Pimienta G, DeGregorio SJ, Alexandrov A, Steitz JA. Phosphorylation of DGCR8 Increases Its Intracellular Stability and Induces a Progrowth miRNA Profile. Cell Reports 2013, 5: 1070-1081. PMID: 24239349, PMCID: PMC3892995, DOI: 10.1016/j.celrep.2013.10.017.Peer-Reviewed Original ResearchConceptsMicroprocessor complexRNA-binding proteinRNase III enzymeInhibition of phosphatasesStem-loop structureERK/MAPKSpecific processing activityMiRNA expression profilesExtracellular cuesMiRNA biogenesisDrosha proteinPhosphorylation sitesPrimary miRNAMammalian cellsProtein stabilityExpression profilesDGCR8Intracellular stabilityHeLa cellsCellular levelMiRNA profilesPhosphorylationMRNA levelsProteinCellsThe “Observer Effect” in Genome-wide Surveys of Protein-RNA Interactions
Riley KJ, Steitz JA. The “Observer Effect” in Genome-wide Surveys of Protein-RNA Interactions. Molecular Cell 2013, 49: 601-604. PMID: 23438856, PMCID: PMC3719848, DOI: 10.1016/j.molcel.2013.01.030.Peer-Reviewed Original Research
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
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 ResearchDown-Regulation of a Host MicroRNA by a Herpesvirus saimiri Noncoding RNA
Cazalla D, Yario T, Steitz JA. Down-Regulation of a Host MicroRNA by a Herpesvirus saimiri Noncoding RNA. Science 2010, 328: 1563-1566. PMID: 20558719, PMCID: PMC3075239, DOI: 10.1126/science.1187197.Peer-Reviewed Original ResearchConceptsHSURs 1Noncoding RNAsHost cell gene expressionMiR-27Binding-dependent mannerPotential binding sitesMiRNA pathwayHost cell microRNAsCoimmunoprecipitation experimentsEctopic expressionTarget genesTransient knockdownGene expressionUnknown functionHost microRNAsViral strategiesDown regulationBinding sitesMiRNAsMicroRNAsRNAExpressionCellsT cellsNcRNAComprehensive Analysis of Rhesus Lymphocryptovirus MicroRNA Expression
Riley K, Rabinowitz GS, Steitz JA. Comprehensive Analysis of Rhesus Lymphocryptovirus MicroRNA Expression. Journal Of Virology 2010, 84: 5148-5157. PMID: 20219930, PMCID: PMC2863793, DOI: 10.1128/jvi.00110-10.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 Rays
2005
GAS5 Gene
Hirose T, Steitz J. GAS5 Gene. 2005 DOI: 10.1038/npg.els.0005019.Peer-Reviewed Original Research
2004
The Herpesvirus saimiri Small Nuclear RNAs Recruit AU-Rich Element-Binding Proteins but Do Not Alter Host AU-Rich Element-Containing mRNA Levels in Virally Transformed T Cells
Cook HL, Mischo HE, Steitz JA. The Herpesvirus saimiri Small Nuclear RNAs Recruit AU-Rich Element-Binding Proteins but Do Not Alter Host AU-Rich Element-Containing mRNA Levels in Virally Transformed T Cells. Molecular And Cellular Biology 2004, 24: 4522-4533. PMID: 15121869, PMCID: PMC400482, DOI: 10.1128/mcb.24.10.4522-4533.2004.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntigens, SurfaceBase CompositionBase SequenceCallithrixCell LineCell Transformation, ViralELAV ProteinsELAV-Like Protein 1Herpesvirus 2, SaimiriineHeterogeneous-Nuclear Ribonucleoprotein DIn Vitro TechniquesMolecular Sequence DataMutationNucleic Acid ConformationProtein BindingRNA, MessengerRNA, Small NuclearRNA, ViralRNA-Binding ProteinsT-LymphocytesConceptsAU-rich elementsSmall nuclear RNAHSURs 1Herpesvirus saimiriNuclear RNAMRNA decay pathwayMarmoset T cellsHSUR 1HnRNP DPosttranscriptional regulationHost mRNAsHost proteinsMicroarray analysisUnknown functionProtein tristetraprolinVivo interactionDecay pathwaysHSURsMRNARNAMRNA levelsT cellsProteinCellsPathway
2001
HuR and mRNA stability
Brennan CM, Steitz* J. HuR and mRNA stability. Cellular And Molecular Life Sciences 2001, 58: 266-277. PMID: 11289308, PMCID: PMC11146503, DOI: 10.1007/pl00000854.Peer-Reviewed Original ResearchConceptsAU-rich elementsMessenger RNAsGene regulationMRNA decayPosttranscriptional gene regulationMRNA degradation pathwayDrosophila ELAVMammalian cellsHu familyHuR functionMRNA stabilityUntranslated regionStressed cellsProtein ligandsRole of HuRCultured cellsEnvironmental changesHuRDegradation pathwayRapid degradationImportant mechanismRegulationCellsELAVRNAs
2000
Human Upf Proteins Target an mRNA for Nonsense-Mediated Decay When Bound Downstream of a Termination Codon
Lykke-Andersen J, Shu M, Steitz J. Human Upf Proteins Target an mRNA for Nonsense-Mediated Decay When Bound Downstream of a Termination Codon. Cell 2000, 103: 1121-1131. PMID: 11163187, DOI: 10.1016/s0092-8674(00)00214-2.Peer-Reviewed Original ResearchConceptsNonsense-mediated decayExon-exon junctionsTermination codonMRNA exon-exon junctionsNovel human proteinTranslation termination siteHeLa cell extractsBeta-globin mRNAPremature termination codonUpf proteinsEukaryotic cellsAberrant mRNAsHuman proteinsTermination sitesIntact cellsCell extractsCodonHUpf2ProteinMRNAHUpf1CellsCytoplasmCytoplasmicTethering
1996
More Sm snRNAs from Vertebrate Cells
Yu Y, Tarn W, Yario T, Steitz J. More Sm snRNAs from Vertebrate Cells. Experimental Cell Research 1996, 229: 276-281. PMID: 8986610, DOI: 10.1006/excr.1996.0372.Peer-Reviewed Original Research
1995
ENHANCED PERSPECTIVE: Small RNA Chaperones for Ribosome Biogenesis
Steitz J, Tycowski K. ENHANCED PERSPECTIVE: Small RNA Chaperones for Ribosome Biogenesis. Science 1995, 270: 1626-1626. PMID: 7502072, DOI: 10.1126/science.270.5242.1626.Peer-Reviewed Original Research
1994
Requirement for Intron-Encoded U22 Small Nucleolar RNA in 18S Ribosomal RNA Maturation
Tycowski K, Shu M, Steitz J. Requirement for Intron-Encoded U22 Small Nucleolar RNA in 18S Ribosomal RNA Maturation. Science 1994, 266: 1558-1561. PMID: 7985025, DOI: 10.1126/science.7985025.Peer-Reviewed Original ResearchConceptsRibosomal RNASmall RNAsProtein-coding gene transcriptsRibosomal RNA maturationSmall nucleolar RNAsRNA maturationVertebrate cellsCellular functionsNucleolar RNAsHost genesIntron fragmentGene transcriptsRNAXenopus oocytesU22IntronsGenesTranscriptsNucleoliOocytesMaturationTargetingCellsFragmentsDepletion