2016
A 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 ResearchMeSH KeywordsCell CompartmentationHEK293 CellsHeLa CellsHumansRNA, Small NuclearRNA-Binding ProteinsConceptsRNA-protein interactionsSpecific RNA-protein interactionsProximity ligation assayTarget RNAProtein-protein interactionsSame cellular compartmentCellular compartmentsRNA targetsIntact cellsLigation assayRNADiscrete compartmentsProteinDNA oligonucleotideFluorescent signalOligonucleotide complementaryCellsCompartmentsAssaysColocalizationHigh specificityInteractionStaining methodOligonucleotideAdaptationEBV 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
A heterotrimer model of the complete Microprocessor complex revealed by single-molecule subunit counting
Herbert KM, Sarkar SK, Mills M, De la Herran H, Neuman KC, Steitz JA. A heterotrimer model of the complete Microprocessor complex revealed by single-molecule subunit counting. RNA 2015, 22: 175-183. PMID: 26683315, PMCID: PMC4712668, DOI: 10.1261/rna.054684.115.Peer-Reviewed Original ResearchConceptsPri-miRNA substratesMicroprocessor complexHeterotrimeric complexDeletion constructsSingle-molecule subunit countingRNA-binding proteinFull-length proteinAbsence of RNAStem-loop structureSingle-molecule photobleachingSize exclusion chromatographyPresence of RNARNaseIII enzymesPhotobleaching assaysMicroRNA biogenesisSubunit countingMammalian cellsDroshaDGCR8Fluorescent proteinHuman cellsMultiple copiesRNAProteinExact stoichiometry
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 ResearchMeSH KeywordsAnimalsArtifactsCell FractionationChromatin ImmunoprecipitationGenomeHumansProteomicsRNA-Binding Proteins
2012
Human spliceosomal protein CWC22 plays a role in coupling splicing to exon junction complex deposition and nonsense-mediated decay
Alexandrov A, Colognori D, Shu MD, Steitz JA. Human spliceosomal protein CWC22 plays a role in coupling splicing to exon junction complex deposition and nonsense-mediated decay. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 21313-21318. PMID: 23236153, PMCID: PMC3535618, DOI: 10.1073/pnas.1219725110.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceCarrier ProteinsEukaryotic Initiation Factor-4AEukaryotic Initiation Factor-4GExonsGene Knockdown TechniquesHEK293 CellsHeLa CellsHumansMolecular Sequence DataMutationNonsense Mediated mRNA DecayNuclear ProteinsPeptidylprolyl IsomeraseProtein BindingRNA SplicingRNA, MessengerRNA-Binding ProteinsSpliceosomesConceptsExon junction complexEJC depositionMultiprotein exon junction complexNonsense-mediated decay pathwayNonsense-mediated decaySpecific roleEJC assemblyEJC formationComplex eukaryotesDisrupts associationMetazoan mRNAsSpliceosomal proteinsCellular mRNAsHost genesSplicing defectsJunction complexDownstream eventsSplicingNatural substrateDecay pathwaysCWC22Depletion yieldsNMDMutationsMRNA
2011
Human eIF4AIII interacts with an eIF4G-like partner, NOM1, revealing an evolutionarily conserved function outside the exon junction complex
Alexandrov A, Colognori D, Steitz JA. Human eIF4AIII interacts with an eIF4G-like partner, NOM1, revealing an evolutionarily conserved function outside the exon junction complex. Genes & Development 2011, 25: 1078-1090. PMID: 21576267, PMCID: PMC3093123, DOI: 10.1101/gad.2045411.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsDEAD-box RNA HelicasesEukaryotic Initiation Factor-4AEukaryotic Initiation Factor-4GEvolution, MolecularExonsGene DeletionGenetic Complementation TestHumansModels, MolecularMolecular Sequence DataMutationNuclear ProteinsPhenotypeProtein Structure, TertiaryRNA, Ribosomal, 18SRNA-Binding ProteinsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSequence AlignmentConceptsExon junction complexEIF4GJunction complexDEAD-box helicasePre-rRNA processingDirect physical interactionEIF4G complexExtragenic suppressorsBiogenesis defectsLethal phenotypeGrowth defectTranslation initiationHuman orthologEIF4AIIISaccharomyces cerevisiaeHuman cellsNOM1Physical interactionComplex actsG complexX-ray structureMutationsResiduesComplexesOrthologsPosttranscriptional activation of gene expression in Xenopus laevis oocytes by microRNA–protein complexes (microRNPs)
Mortensen RD, Serra M, Steitz JA, Vasudevan S. Posttranscriptional activation of gene expression in Xenopus laevis oocytes by microRNA–protein complexes (microRNPs). Proceedings Of The National Academy Of Sciences Of The United States Of America 2011, 108: 8281-8286. PMID: 21536868, PMCID: PMC3100953, DOI: 10.1073/pnas.1105401108.Peer-Reviewed Original ResearchConceptsMicroRNA–protein complexesProtein kinase AIIXenopus laevis oocytesImmature Xenopus laevis oocytesGene expression activationMammalian cell linesLaevis oocytesHuman Ago2Target reporterMammalian cellsExpression activationMyt1 kinaseGene expressionPosttranscriptional activationRegulated expressionSpecific mRNAsPhysiological relevanceQuiescent cellsMicroRNAsOocyte stateCell linesOocytesReporterCAMP levelsExpression
2009
miRNPs: versatile regulators of gene expression in vertebrate cells1
Steitz JA, Vasudevan S. miRNPs: versatile regulators of gene expression in vertebrate cells1. Biochemical Society Transactions 2009, 37: 931-935. PMID: 19754429, DOI: 10.1042/bst0370931.Peer-Reviewed Original ResearchConceptsPost-transcriptional controlAssociation of Ago2Role of miRNAsImmature Xenopus oocytesTNFalpha AREProtein FXR1Contact-inhibited cellsTranslational regulationTranslation activationVersatile regulatorsTranslational efficiencyNegative regulatorGene expressionSpecific miRNACell cycleEffector moleculesCell growthXenopus oocytesAgo2FXR1A Conserved WD40 Protein Binds the Cajal Body Localization Signal of scaRNP Particles
Tycowski KT, Shu MD, Kukoyi A, Steitz JA. A Conserved WD40 Protein Binds the Cajal Body Localization Signal of scaRNP Particles. Molecular Cell 2009, 34: 47-57. PMID: 19285445, PMCID: PMC2700737, DOI: 10.1016/j.molcel.2009.02.020.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAnimalsBase SequenceCell LineChromatography, AffinityCoiled BodiesDrosophila melanogasterDrosophila ProteinsHeLa CellsHumansMolecular Sequence DataNucleic Acid ConformationRecombinant Fusion ProteinsRegulatory Sequences, Ribonucleic AcidRibonucleoproteinsRNA-Binding ProteinsSequence AlignmentConceptsCAB boxCB localizationSmall Cajal bodyWD40 proteinsRNP functionCajal bodiesLocalization signalACA motifDomain RNATelomerase RNAHuman homologPosttranscriptional modificationsSmall nuclearWDR79ScaRNAsRNA elementsCentral playerUV crosslinkNuclear RNPCore proteinRNAProteinAdditional interactionsBindingLocalization
2007
Switching from Repression to Activation: MicroRNAs Can Up-Regulate Translation
Vasudevan S, Tong Y, Steitz JA. Switching from Repression to Activation: MicroRNAs Can Up-Regulate Translation. Science 2007, 318: 1931-1934. PMID: 18048652, DOI: 10.1126/science.1149460.Peer-Reviewed Original ResearchMeSH Keywords3' Untranslated RegionsArgonaute ProteinsBase PairingCell CycleCell LineCell ProliferationComputational BiologyEukaryotic Initiation Factor-2Gene Expression RegulationHeLa CellsHMGA2 ProteinHumansInterphaseMicroRNAsProtein BiosynthesisRibonucleoproteinsRNA, MessengerRNA-Binding ProteinsTransfectionTumor Necrosis Factor-alphaUp-RegulationConceptsAU-rich elementsCell cycle arrestCycle arrestUntranslated regionMental retardation-related protein 1MicroRNA target sitesMicroRNA let-7Messenger RNA (mRNA) 3' untranslated regionsRegulates TranslationTranslation regulationTarget mRNAsGene expressionCell cycleCommon functionProtein 1ArgonauteTarget siteActivation signalsRepressionTumor necrosis factor-alpha mRNAMRNARegulationActivationArrestMicroRNPsU2 snRNP Binds Intronless Histone Pre-mRNAs to Facilitate U7-snRNP-Dependent 3′ End Formation
Friend K, Lovejoy AF, Steitz JA. U2 snRNP Binds Intronless Histone Pre-mRNAs to Facilitate U7-snRNP-Dependent 3′ End Formation. Molecular Cell 2007, 28: 240-252. PMID: 17964263, PMCID: PMC2149891, DOI: 10.1016/j.molcel.2007.09.026.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceCell NucleusDEAD-box RNA HelicasesHeLa CellsHistonesHumansIntronsMiceModels, MolecularOocytesProtein ConformationRibonucleoprotein, U2 Small NuclearRibonucleoprotein, U7 Small NuclearRibonucleoproteins, Small NuclearRNA 3' End ProcessingRNA PrecursorsRNA-Binding ProteinsRNA, MessengerTime FactorsXenopus laevisAU-Rich-Element-Mediated Upregulation of Translation by FXR1 and Argonaute 2
Vasudevan S, Steitz JA. AU-Rich-Element-Mediated Upregulation of Translation by FXR1 and Argonaute 2. Cell 2007, 128: 1105-1118. PMID: 17382880, PMCID: PMC3430382, DOI: 10.1016/j.cell.2007.01.038.Peer-Reviewed Original ResearchMeSH Keywords3' Untranslated RegionsArgonaute ProteinsCell CycleCell LineChromatography, AffinityCulture Media, Serum-FreeEukaryotic Initiation Factor-2Genes, ReporterHumansLuciferases, FireflyMonocytesPeptide Initiation FactorsPolyribosomesProtein BiosynthesisRegulatory Sequences, Ribonucleic AcidRibonucleoproteinsRNA-Binding ProteinsSerumTumor Necrosis Factor-alphaUp-RegulationConceptsAU-rich elementsArgonaute 2Posttranscriptional regulatory systemsAffinity purification methodShRNA knockdown experimentsCell cycle arrestHuman cell linesTranslation activationRegulatory signalsMRNA stabilityGene expressionSerum starvationAU-RichFXR1Activation roleRegulatory systemProtein 1Cell linesMRNA levelsNew insightsDevelopmental consequencesTranslation conditionsUpregulationDirect evidencePurification method
2006
Multiple 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 RaysMetazoan oocyte and early embryo development program: a progression through translation regulatory cascades
Vasudevan S, Seli E, Steitz JA. Metazoan oocyte and early embryo development program: a progression through translation regulatory cascades. Genes & Development 2006, 20: 138-146. PMID: 16418480, DOI: 10.1101/gad.1398906.Peer-Reviewed Original ResearchAnimalsCarrier ProteinsCell Cycle ProteinsCytoplasmFemaleGene Expression Regulation, DevelopmentalHumansMaleModels, GeneticMRNA Cleavage and Polyadenylation FactorsOocytesPoly(A)-Binding ProteinsPolyadenylationProtein BiosynthesisRNA, Messenger, StoredRNA-Binding ProteinsTranscription FactorsXenopus laevisXenopus Proteins
2004
Evidence for reassociation of RNA-binding proteins after cell lysis: Implications for the interpretation of immunoprecipitation analyses
Mili S, Steitz JA. Evidence for reassociation of RNA-binding proteins after cell lysis: Implications for the interpretation of immunoprecipitation analyses. RNA 2004, 10: 1692-1694. PMID: 15388877, PMCID: PMC1370654, DOI: 10.1261/rna.7151404.Peer-Reviewed Original ResearchA molecular link between SR protein dephosphorylation and mRNA export
Huang Y, Yario TA, Steitz JA. A molecular link between SR protein dephosphorylation and mRNA export. Proceedings Of The National Academy Of Sciences Of The United States Of America 2004, 101: 9666-9670. PMID: 15210956, PMCID: PMC470732, DOI: 10.1073/pnas.0403533101.Peer-Reviewed Original ResearchConceptsNuclear export factor 1Multiple RNA-binding proteinsMRNA-protein complexesSR protein dephosphorylationMRNA nuclear exportASF/SF2RNA-binding proteinMRNA exportProtein dephosphorylationProtein complexesProtein adaptersNuclear exportSpliced mRNAPhosphorylation stateMolecular linkFactor 1MRNAHigh affinityMetazoansDephosphorylationExportComplexesSerineAdapterProteinThe 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-Binding ProteinsRNA, MessengerRNA, Small NuclearRNA, ViralT-LymphocytesConceptsAU-rich elementsSmall nuclear RNAHSURs 1Herpesvirus saimiriNuclear RNAMRNA decay pathwayMarmoset T cellsHSUR 1HnRNP DPosttranscriptional regulationHost mRNAsHost proteinsMicroarray analysisUnknown functionProtein tristetraprolinVivo interactionDecay pathwaysHSURsMRNARNAMRNA levelsT cellsProteinCellsPathwayTransportins 1 and 2 are redundant nuclear import factors for hnRNP A1 and HuR
Rebane A, Aab A, Steitz JA. Transportins 1 and 2 are redundant nuclear import factors for hnRNP A1 and HuR. RNA 2004, 10: 590-599. PMID: 15037768, PMCID: PMC1370549, DOI: 10.1261/rna.5224304.Peer-Reviewed Original ResearchMeSH KeywordsActive Transport, Cell NucleusAmino Acid SequenceAntigens, SurfaceBeta KaryopherinsCell NucleusELAV ProteinsELAV-Like Protein 1HeLa CellsHeterogeneous Nuclear Ribonucleoprotein A1Heterogeneous-Nuclear Ribonucleoprotein Group A-BHumansMolecular Sequence DataMutationProtein Structure, TertiaryRan GTP-Binding ProteinReceptors, Cytoplasmic and NuclearRNA-Binding ProteinsSequence Analysis, ProteinConceptsHnRNP A1Transportin-1Import factorsDigitonin-permeabilized HeLa cellsNuclear import factorsMRNA-binding proteinRecombinant hnRNP A1Binding of HuRImp betaImport pathwayCargo specificityNuclear importExport receptorTransportin-2TransportinTransport signalHeLa cellsLikely actsHuRTrn1ProteinInteraction studiesImportTRN2RanGTP
2003
SR Splicing Factors Serve as Adapter Proteins for TAP-Dependent mRNA Export
Huang Y, Gattoni R, Stévenin J, Steitz JA. SR Splicing Factors Serve as Adapter Proteins for TAP-Dependent mRNA Export. Molecular Cell 2003, 11: 837-843. PMID: 12667464, DOI: 10.1016/s1097-2765(03)00089-3.Peer-Reviewed Original ResearchAmino Acid SequenceAnimalsArginineBinding, CompetitiveBiological TransportCell NucleusGenes, DominantGlutathione TransferaseModels, BiologicalMolecular Sequence DataNucleocytoplasmic Transport ProteinsOocytesPeptidesPlasmidsPrecipitin TestsProtein BindingProtein Structure, TertiaryRecombinant Fusion ProteinsRNA, MessengerRNA-Binding ProteinsSerineTransfectionXenopus