2018
Immunoprecipitation of Tri-methylated Capped RNA.
Hayes KE, Barr JA, Xie M, Steitz JA, Martinez I. Immunoprecipitation of Tri-methylated Capped RNA. Bio-protocol 2018, 8 PMID: 29527542, PMCID: PMC5842925, DOI: 10.21769/bioprotoc.2717.Peer-Reviewed Original ResearchPri-miRNAsCellular quiescenceAlternative miRNA biogenesis pathwaysMiRNA biogenesis pathwayNon-coding RNAsBiogenesis pathwayDNA replicationTotal RNA extractsRNA immunoprecipitationOrgan regenerationRNA extractsFibroblast cellsImmunoprecipitationRNASpecific isolationProteinQuiescenceWound healingImportant roleTrimethylguanosineMicroRNAsAutophagyCytoplasmP27Pathway
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
2013
Mammalian 5′-Capped MicroRNA Precursors that Generate a Single MicroRNA
Xie M, Li M, Vilborg A, Lee N, Shu MD, Yartseva V, Šestan N, Steitz JA. Mammalian 5′-Capped MicroRNA Precursors that Generate a Single MicroRNA. Cell 2013, 155: 1568-1580. PMID: 24360278, PMCID: PMC3899828, DOI: 10.1016/j.cell.2013.11.027.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsArgonaute ProteinsBase SequenceBiosynthetic PathwaysDEAD-box RNA HelicasesGenome-Wide Association StudyGuanosineHumansKaryopherinsMiceMicroRNAsMolecular Sequence DataReceptors, Cytoplasmic and NuclearRibonuclease IIIRNA CapsRNA Polymerase IIRNA, Small InterferingTranscription Termination, GeneticConceptsCap-binding protein eIF4EMiRNA biogenesis pathwayNuclear-cytoplasmic transportGuide strand selectionShRNA expression constructsTranscription start siteBiogenesis pathwayCytoplasmic DicerMicroprocessor complexTranscription terminationProtein eIF4EExportin-5MicroRNA precursorsMiRNA hairpinsPrimary transcriptStrand selectionGene regulatorsStart siteDicer cleavageExpression constructsSingle microRNAMiRNAsMicroRNAsPathwayMicroRNPs
2006
Identification of a Rapid Mammalian Deadenylation-Dependent Decay Pathway and Its Inhibition by a Viral RNA Element
Conrad NK, Mili S, Marshall EL, Shu MD, Steitz JA. Identification of a Rapid Mammalian Deadenylation-Dependent Decay Pathway and Its Inhibition by a Viral RNA Element. Molecular Cell 2006, 24: 943-953. PMID: 17189195, DOI: 10.1016/j.molcel.2006.10.029.Peer-Reviewed Original ResearchConceptsQuality control pathwaysViral RNA elementsPAN RNAPolyadenylated transcriptsMammalian cellsNuclear RNASuch transcriptsRNA elementsCellular RNAGene expressionNuclear accumulationNuclear extractsNaked RNARNADecay pathwaysTranscriptsDeadenylationDependent fashionPathwayDeadenylaseIntronsAccumulationMRNAHybridizationIntramolecular hybridization
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-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 cellsProteinCellsPathwayAn Intronic Enhancer Regulates Splicing of the Twintron of Drosophila melanogaster prospero Pre-mRNA by Two Different Spliceosomes
Scamborova P, Wong A, Steitz JA. An Intronic Enhancer Regulates Splicing of the Twintron of Drosophila melanogaster prospero Pre-mRNA by Two Different Spliceosomes. Molecular And Cellular Biology 2004, 24: 1855-1869. PMID: 14966268, PMCID: PMC350559, DOI: 10.1128/mcb.24.5.1855-1869.2004.Peer-Reviewed Original ResearchConceptsPurine-rich elementSplicing pathwaySplice siteU12-type spliceosomeU12-type splicingVitro splicing systemForms of mRNAAlternative splicingEarly embryogenesisKc cellsIntron sequencesPre-mRNASystematic deletionIntronic enhancerSplicingSequence requirementsIntron regionsEnhancer elementsNucleotides downstreamMolecular mechanismsTwintronSpliceosomeSplicing systemMutation analysisPathway
2002
Branchpoint selection in the splicing of U12-dependent introns in vitro.
McConnell TS, Cho SJ, Frilander MJ, Steitz JA. Branchpoint selection in the splicing of U12-dependent introns in vitro. RNA 2002, 8: 579-86. PMID: 12022225, PMCID: PMC1370279, DOI: 10.1017/s1355838202028029.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceHumansIn Vitro TechniquesIntronsModels, GeneticPol1 Transcription Initiation Complex ProteinsRibonucleoproteins, Small NuclearRibosomal ProteinsRNARNA SplicingRNA-Binding ProteinsSaccharomyces cerevisiae ProteinsSpliceosomesTranscription FactorsXenopusXenopus ProteinsConceptsU12-dependent intronsU12-type intronsSixth intronBranchpoint sequenceSplicing of intronsU12-type splicingU12-type spliceosomeU12-dependent splicingBase-pairing mechanismHeLa nuclear extractsAdditional intronConsecutive adenosinesSplicing substrateThird intronU12 snRNAHuman p120First intronIntronsNuclear extractsSplicingGenesBranch sitePathwayBranchpointP120