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 factorsCellsCRISPRCodonHomology
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
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 TransductionT-LymphocytesTime FactorsTransfectionConceptsMitogen-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
2012
Association of Argonaute proteins and microRNAs can occur after cell lysis
Riley KJ, Yario TA, Steitz JA. Association of Argonaute proteins and microRNAs can occur after cell lysis. RNA 2012, 18: 1581-1585. PMID: 22836356, PMCID: PMC3425773, DOI: 10.1261/rna.034934.112.Peer-Reviewed Original ResearchConceptsHuman AgosMiRNA-protein complexesMicroRNA target identificationDirect mRNA targetsCore protein componentsArgonaute proteinsAGO proteinsMRNA targetsImmunoprecipitation experimentsProtein componentsMiRNA mimicsRNAEndogenous interactionCell lysisTarget identificationImmunopurification techniquesGlobal analysisProteinInteraction artifactsOrigin of interactionsExperimental approachArgonauteVivoAgoMiRNAs
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 mRNAMRNARegulationActivationArrestMicroRNPsTarget mRNAs are repressed as efficiently by microRNA-binding sites in the 5′ UTR as in the 3′ UTR
Lytle JR, Yario TA, Steitz JA. Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5′ UTR as in the 3′ UTR. Proceedings Of The National Academy Of Sciences Of The United States Of America 2007, 104: 9667-9672. PMID: 17535905, PMCID: PMC1887587, DOI: 10.1073/pnas.0703820104.Peer-Reviewed Original ResearchConceptsInternal ribosome entry siteTarget mRNAsMiRNA-mediated repressionRepression of translationLuciferase reporter mRNAMiRNA target sitesInitiation of translationMiRNA-binding sitesHuman HeLa cellsRibosome entry siteMicroRNA-binding sitesLet-7 complementary sitesHuman Ago2Reporter mRNAMicroRNAs (miRNAs) bindEndogenous mRNATranslational efficiencyLet-7a miRNAUTRProtein synthesisDNA transfectionComplementary sitesHeLa cellsEntry siteTarget site
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 Rays
2004
Splicing of U12-type introns deposits an exon junction complex competent to induce nonsense-mediated mRNA decay
Hirose T, Shu MD, Steitz JA. Splicing of U12-type introns deposits an exon junction complex competent to induce nonsense-mediated mRNA decay. Proceedings Of The National Academy Of Sciences Of The United States Of America 2004, 101: 17976-17981. PMID: 15608055, PMCID: PMC539812, DOI: 10.1073/pnas.0408435102.Peer-Reviewed Original ResearchMeSH KeywordsCell LineCell NucleusCodon, NonsenseDNA, ComplementaryEvolution, MolecularExonsGene Expression RegulationHeLa CellsHumansImmunoprecipitationIntronsMutagenesis, Site-DirectedOpen Reading FramesPlasmidsRibonuclease HRibonucleoproteins, Small NuclearRNARNA PrecursorsRNA SplicingRNA, MessengerRNA, Small NuclearSpliceosomesTime FactorsTransfectionConceptsExon junction complexU12-type intronsOpen reading frameNonsense-mediated mRNA decayU12-type spliceosomeNonsense-mediated decaySmall nuclear ribonucleoproteinU2-type spliceosomePremature termination codonEJC assemblyMetazoan cellsMRNA decayEvolutionary ageDownstream functionsIntron removalNuclear ribonucleoproteinReading frameExon junctionsTermination codonJunction complexGene expressionIntron downstreamSpliceosomeIntronsSplicingEvidence 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 Research
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
2001
Communication of the Position of Exon-Exon Junctions to the mRNA Surveillance Machinery by the Protein RNPS1
Lykke-Andersen J, Shu M, Steitz J. Communication of the Position of Exon-Exon Junctions to the mRNA Surveillance Machinery by the Protein RNPS1. Science 2001, 293: 1836-1839. PMID: 11546874, DOI: 10.1126/science.1062786.Peer-Reviewed Original ResearchMeSH Keywords3' Untranslated RegionsAnimalsCell LineDNA-Binding ProteinsExonsFungal ProteinsGlobinsHeLa CellsHumansMacromolecular SubstancesMiceModels, BiologicalPrecipitin TestsProtein BindingRecombinant Fusion ProteinsRibonucleoproteinsRNA HelicasesRNA SplicingRNA, MessengerRNA-Binding ProteinsSaccharomyces cerevisiae ProteinsTrans-ActivatorsTransfectionConceptsNonsense-mediated decayExon-exon junctionsMRNA surveillanceMRNA quality controlMRNA surveillance machinerySelective nuclear exportBeta-globin mRNAPremature termination codonUpf complexMature mRNASurveillance machineryNuclear exportAberrant mRNAsMammalian cellsTermination codonUntranslated regionSplice junctionsRNPS1MRNADual roleCentral componentComplexesCodonSubunitsMachinery
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
1998
HNS, a nuclear-cytoplasmic shuttling sequence in HuR
Fan X, Steitz J. HNS, a nuclear-cytoplasmic shuttling sequence in HuR. Proceedings Of The National Academy Of Sciences Of The United States Of America 1998, 95: 15293-15298. PMID: 9860962, PMCID: PMC28036, DOI: 10.1073/pnas.95.26.15293.Peer-Reviewed Original ResearchMeSH Keywords3T3 CellsAmino Acid SequenceAnimalsAntigens, SurfaceCell NucleusConserved SequenceCytoplasmELAV ProteinsELAV-Like Protein 1HeLa CellsHeterogeneous-Nuclear Ribonucleoprotein KHumansMiceMolecular Sequence DataRecombinant ProteinsRibonucleoproteinsRNA, MessengerRNA-Binding ProteinsSequence AlignmentSequence Homology, Amino AcidTransfectionXenopusConceptsHeterogeneous nuclear ribonucleoprotein KNuclear localization signal activityClassical nuclear localization signalAU-rich element-containing mRNAsExport of mRNAHeterogeneous nuclear ribonucleoprotein A1Nuclear export signalNuclear localization signalNuclear transport processRNA-binding proteinAU-rich elementsExport signalLocalization signalM9 sequenceNuclear poresDomain sequencesCytoplasmic compartmentUntranslated regionLabile mRNAsCell nucleiSpecific signalsHuRProteinBidirectional transportMRNA
1997
AU-rich elements target small nuclear RNAs as well as mRNAs for rapid degradation
Fan X, Myer V, Steitz J. AU-rich elements target small nuclear RNAs as well as mRNAs for rapid degradation. Genes & Development 1997, 11: 2557-2568. PMID: 9334320, PMCID: PMC316563, DOI: 10.1101/gad.11.19.2557.Peer-Reviewed Original ResearchMeSH KeywordsAntigens, SurfaceBase SequenceELAV ProteinsELAV-Like Protein 1Gene Expression RegulationGenes, ReporterGlobinsHerpesvirus 2, SaimiriineMolecular Sequence DataMutationRepetitive Sequences, Nucleic AcidRibonucleasesRNA, MessengerRNA, Small NuclearRNA, ViralRNA-Binding ProteinsTranscription, GeneticTransfectionConceptsAU-rich elementsMRNA degradation machinerySmall nuclear RNAHSUR 1Host RNA moleculesDegradation machineryMammalian mRNAsNuclear RNARNA moleculesMutational analysisSequence requirementsTarget RNAHuR proteinOngoing translationRNA 1MRNARapid degradationRNASimilar mechanismDegradation activityDeadenylationSnRNAMachineryProteinDegradation
1991
Multiple processing-defective mutations in a mammalian histone pre-mRNA are suppressed by compensatory changes in U7 RNA both in vivo and in vitro.
Bond UM, Yario TA, Steitz JA. Multiple processing-defective mutations in a mammalian histone pre-mRNA are suppressed by compensatory changes in U7 RNA both in vivo and in vitro. Genes & Development 1991, 5: 1709-1722. PMID: 1885007, DOI: 10.1101/gad.5.9.1709.Peer-Reviewed Original ResearchConceptsHistone downstream elementHistone pre-mRNAMammalian histone pre-mRNAsPre-mRNAHeLa cellsBase pair regionMammalian histonesU7 geneSm snRNPsU7 snRNPGenetic evidenceU7 snRNAUnexpected toleranceU7 RNANuclear extractsDownstream elementsSuppressor geneCompensatory changesGenesBlock substitutionsRNAVivoSnRNPsSnRNPCells
1990
Herpesvirus saimiri U RNAs are expressed and assembled into ribonucleoprotein particles in the absence of other viral genes
Lee SI, Steitz JA. Herpesvirus saimiri U RNAs are expressed and assembled into ribonucleoprotein particles in the absence of other viral genes. Journal Of Virology 1990, 64: 3905-3915. PMID: 2164602, PMCID: PMC249686, DOI: 10.1128/jvi.64.8.3905-3915.1990.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceCallitrichinaeCell NucleusCell Transformation, ViralGene ExpressionGenes, ViralHeLa CellsHerpesvirus 2, SaimiriineHumansMolecular Sequence DataNucleic Acid ConformationPlasmidsRestriction MappingRibonucleoproteinsRibonucleoproteins, Small NuclearRNA, Small NuclearT-LymphocytesTransfection
1988
Correct in vivo splicing of the mouse immunoglobulin kappa light-chain pre-mRNA is dependent on 5' splice-site position even in the absence of transcription.
Kedes DH, Steitz JA. Correct in vivo splicing of the mouse immunoglobulin kappa light-chain pre-mRNA is dependent on 5' splice-site position even in the absence of transcription. Genes & Development 1988, 2: 1448-1459. PMID: 2463211, DOI: 10.1101/gad.2.11.1448.Peer-Reviewed Original Research