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
2005
Anaplasma phagocytophilum Modulates gp91phox Gene Expression through Altered Interferon Regulatory Factor 1 and PU.1 Levels and Binding of CCAAT Displacement Protein
Thomas V, Samanta S, Wu C, Berliner N, Fikrig E. Anaplasma phagocytophilum Modulates gp91phox Gene Expression through Altered Interferon Regulatory Factor 1 and PU.1 Levels and Binding of CCAAT Displacement Protein. Infection And Immunity 2005, 73: 208-218. PMID: 15618156, PMCID: PMC538944, DOI: 10.1128/iai.73.1.208-218.2005.Peer-Reviewed Original ResearchMeSH KeywordsAnaplasma phagocytophilumDNA-Binding ProteinsGene Expression RegulationHL-60 CellsHomeodomain ProteinsHumansInterferon Regulatory Factor-1Membrane GlycoproteinsNADPH Oxidase 2NADPH OxidasesNuclear ProteinsPhosphoproteinsPhosphorylationPromoter Regions, GeneticProto-Oncogene ProteinsRepressor ProteinsSTAT1 Transcription FactorTrans-ActivatorsTranscription FactorsTranscription, GeneticConceptsCCAAT displacement proteinRegulatory factor 1IRF-1IRF-1 promoterRegulation of genesA. phagocytophilum-infected cellsFirst molecular mechanismFactor 1Interferon regulatory factor 1IFN-gamma signalingActivator proteinGene transcriptionAnaplasma phagocytophilumTranscriptional inhibitionGene expressionMolecular mechanismsNuclear extractsGamma interferon stimulationPhosphorylated STAT1Interferon stimulationGenesA. phagocytophilum infectionProteinProtein expressionReduced expression
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
1997
The transcriptional activator Sp1, a novel autoantigen
Spain T, Sun R, Gradzka M, Lin S, Craft J, Miller G. The transcriptional activator Sp1, a novel autoantigen. Arthritis & Rheumatism 1997, 40: 1085-1095. PMID: 9182919, DOI: 10.1002/art.1780400613.Peer-Reviewed Original ResearchConceptsTranscriptional activator Sp1Novel autoantigenComplex of DNAGC-rich sequencesActivator Sp1Undifferentiated connective tissue diseaseSp1 proteinTranscription activatorConnective tissue diseaseExtractable nuclear antigensEpstein-Barr virusSp1Nuclear extractsCellular DNAMalar rashAntinuclear antibodiesClinical characteristicsProteinDNARaynaud's phenomenonTissue diseaseAutoantigenic proteinsAutoimmune seraElectrophoretic mobilityAutoantigensIdentification of HuR as a protein implicated in AUUUA‐mediated mRNA decay
Myer V, Fan X, Steitz J. Identification of HuR as a protein implicated in AUUUA‐mediated mRNA decay. The EMBO Journal 1997, 16: 2130-2139. PMID: 9155038, PMCID: PMC1169815, DOI: 10.1093/emboj/16.8.2130.Peer-Reviewed Original ResearchMeSH Keywords3T3 CellsAmino Acid SequenceAnimalsAntigens, SurfaceBase CompositionCell ExtractsCross-Linking ReagentsELAV ProteinsELAV-Like Protein 1Gene Expression RegulationHeLa CellsHumansMiceMolecular Sequence DataMolecular WeightRegulatory Sequences, Nucleic AcidRNA, MessengerRNA-Binding ProteinsUltraviolet RaysConceptsAU-rich elementsMRNA decayUntranslated regionRNA-binding specificityARE-binding proteinsHeLa nuclear extractsGene familyMRNA degradationNuclear extractsEssential signalMessenger RNAProteinSequence's abilityHuRAUUUARapid degradationCritical roleHuR.RNAMachineryMRNADegradationRegulationSubsequent analysisExpression
1996
"Cytosolic" phospholipase A2 is in the nucleus of subconfluent endothelial cells but confined to the cytoplasm of confluent endothelial cells and redistributes to the nuclear envelope and cell junctions upon histamine stimulation.
Sierra-Honigmann MR, Bradley JR, Pober JS. "Cytosolic" phospholipase A2 is in the nucleus of subconfluent endothelial cells but confined to the cytoplasm of confluent endothelial cells and redistributes to the nuclear envelope and cell junctions upon histamine stimulation. Laboratory Investigation 1996, 74: 684-95. PMID: 8600319.Peer-Reviewed Original ResearchConceptsSubconfluent endothelial cellsConfluent endothelial cellsNuclear envelopeNuclear localizationConfocal immunofluorescence microscopyEndothelial cellsDose-dependent redistributionGrowth-arrested cellsSubcellular localizationCell density dependencePlasma membraneCell cycleCytoplasmic enzymeNuclear extractsCell junctionsPhospholipase A2 enzymeBovine endothelial cellsHeLa cellsImmunofluorescence microscopyCell lysatesCell nucleiIntercellular junctionsSubconfluent cellsPredominant MrAcid metabolism
1995
Functional Analysis of the Human Endothelial Nitric Oxide Synthase Promoter SP1 AND GATA FACTORS ARE NECESSARY FOR BASAL TRANSCRIPTION IN ENDOTHELIAL CELLS (∗)
Zhang R, Min W, Sessa W. Functional Analysis of the Human Endothelial Nitric Oxide Synthase Promoter SP1 AND GATA FACTORS ARE NECESSARY FOR BASAL TRANSCRIPTION IN ENDOTHELIAL CELLS (∗). Journal Of Biological Chemistry 1995, 270: 15320-15326. PMID: 7541039, DOI: 10.1074/jbc.270.25.15320.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid OxidoreductasesAnimalsAortaBase SequenceBinding SitesCattleDNA PrimersDNA-Binding ProteinsEndothelium, VascularGATA2 Transcription FactorGene ExpressionHumansLuciferasesMolecular Sequence DataMutagenesis, Site-DirectedNitric Oxide SynthasePolymerase Chain ReactionPromoter Regions, GeneticRecombinant ProteinsRestriction MappingSp1 Transcription FactorTranscription FactorsTranscription, GeneticTransfectionConceptsBovine aortic endothelial cellsPromoter activitySp1 sitesBasal transcriptionGATA siteFurther deletionNuclear extractsENOS promoter activityAntibody supershift analysisDNA-protein complexesLuciferase activityENOS promoterLuc constructGel shift analysisSp-1 sitesBasal promoter activityLuciferase reporter geneSynthase gene expressionSp1 mutantGATA factorsNuclear proteinsGATA-2Mutant constructsReporter geneGel shiftModulation of 5' splice site choice in pre-messenger RNA by two distinct steps.
Tarn WY, Steitz JA. Modulation of 5' splice site choice in pre-messenger RNA by two distinct steps. Proceedings Of The National Academy Of Sciences Of The United States Of America 1995, 92: 2504-2508. PMID: 7708674, PMCID: PMC42246, DOI: 10.1073/pnas.92.7.2504.Peer-Reviewed Original ResearchConceptsSmall nuclear ribonucleoproteinU1 small nuclear ribonucleoproteinSplice site choicePre-messenger RNASR proteinsSplice site selectionSplice siteSite choiceSer/Arg-rich (SR) proteinsU2 small nuclear ribonucleoproteinU1 snRNP functionsHeLa cell nuclear extractsEssential splicing factorArg-rich proteinsCell nuclear extractsDistinct stepsSnRNP functionSite selectionSplicing factorsU1 bindingNuclear ribonucleoproteinU1 RNANuclear extractsProteinRNA
1994
Purification and nucleic acid binding properties of a fragment of type C1/C2 heterogeneous nuclear ribonucleoprotein from thymic nuclear extracts.
Amrute S, Abdul-Manan Z, Pandey V, Williams K, Modak M. Purification and nucleic acid binding properties of a fragment of type C1/C2 heterogeneous nuclear ribonucleoprotein from thymic nuclear extracts. Biochemistry 1994, 33: 8282-91. PMID: 7518245, DOI: 10.1021/bi00193a015.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsCattleCell NucleusChromatographyChromatography, High Pressure LiquidCross-Linking ReagentsCyanogen BromideDNA, Single-StrandedHeterogeneous Nuclear Ribonucleoprotein A1Heterogeneous-Nuclear Ribonucleoprotein Group A-BHeterogeneous-Nuclear Ribonucleoprotein Group CHeterogeneous-Nuclear RibonucleoproteinsMolecular Sequence DataOligodeoxyribonucleotidesPeptide FragmentsRibonucleoproteinsRNASpectrometry, FluorescenceThymus GlandUltraviolet RaysConceptsHnRNP proteinsOccluded site sizeHeterogeneous nuclear ribonucleoproteinsNucleic acidsSingle-strand nucleic acidNH2-terminal sequencingEukaryotic RNATight tetramerSDS-polyacrylamide gel electrophoresisApparent molecular weightNuclear ribonucleoproteinNuclear extractsLimited proteolysisMass spectrometric analysisRNAProteinPhenylalanine 19Calf thymusGel electrophoresisAdditional ionic interactionsTerminal deoxynucleotidyl transferaseSite sizeAB formMajor siteCell disruption
1993
A base-pairing interaction between U2 and U6 small nuclear RNAs occurs in > 150S complexes in HeLa cell extracts: implications for the spliceosome assembly pathway.
Wassarman DA, Steitz JA. A base-pairing interaction between U2 and U6 small nuclear RNAs occurs in > 150S complexes in HeLa cell extracts: implications for the spliceosome assembly pathway. Proceedings Of The National Academy Of Sciences Of The United States Of America 1993, 90: 7139-7143. PMID: 8346227, PMCID: PMC47091, DOI: 10.1073/pnas.90.15.7139.Peer-Reviewed Original ResearchConceptsU6 small nuclear RNASmall nuclear RNAS100 extractsNuclear RNASer/Arg-rich (SR) proteinsBase pairingNuclear extractsLarge complexesArg-rich proteinsPre-RNA splicingSpliceosome assembly pathwayHeLa cell extractsHeLa nuclear extractsBase-pairing interactionsBase pair formsPossible functional relationshipRibonucleoprotein complexesSpliceosome complexMammalian cellsAssembly pathwaySplicing substratePsoralen crosslinkingGlycerol gradientsCell extractsSplicingRare scleroderma autoantibodies to the U11 small nuclear ribonucleoprotein and to the trimethylguanosine cap of U small nuclear RNAs.
Gilliam AC, Steitz JA. Rare scleroderma autoantibodies to the U11 small nuclear ribonucleoprotein and to the trimethylguanosine cap of U small nuclear RNAs. Proceedings Of The National Academy Of Sciences Of The United States Of America 1993, 90: 6781-6785. PMID: 8341699, PMCID: PMC47016, DOI: 10.1073/pnas.90.14.6781.Peer-Reviewed Original ResearchConceptsSmall nuclear ribonucleoprotein particleTrimethylguanosine capLow-abundance membersSmall nuclear RNASmall nuclear ribonucleoproteinNuclear ribonucleoprotein particleGlycerol gradient fractionsU RNAU11 small nuclear ribonucleoproteinsSnRNP complexTargeted degradationNuclear RNANuclear ribonucleoproteinRibonucleoprotein particleNuclear extractsSm classProtein componentsHeLa cellsRNPGradient fractionsRNAProteinScleroderma seraRibonucleoproteinCosediments
1992
Site-specific cross-linking of mammalian U5 snRNP to the 5' splice site before the first step of pre-mRNA splicing.
Wyatt JR, Sontheimer EJ, Steitz JA. Site-specific cross-linking of mammalian U5 snRNP to the 5' splice site before the first step of pre-mRNA splicing. Genes & Development 1992, 6: 2542-2553. PMID: 1340469, DOI: 10.1101/gad.6.12b.2542.Peer-Reviewed Original ResearchConceptsSplice siteMRNA splicingATP-dependent interactionHeLa nuclear extractsU5 snRNPMRNA substratesSplice site regionProtein factorsU5 snRNANucleotides upstreamU6 snRNAPre-mRNANuclear extractsSplicingSite regionLoop sequenceCross-link formationSnRNASplicing conditionsWatson-Crick complementarityCross-linking strategyU1Selective photoactivationSnRNPMammalianExpression of functional parvoviral NS1 from recombinant vaccinia virus: Effects of mutations in the nucleotide-binding motif
Noesch J, Cotmore S, Tattersall P. Expression of functional parvoviral NS1 from recombinant vaccinia virus: Effects of mutations in the nucleotide-binding motif. Virology 1992, 191: 406-416. PMID: 1413512, DOI: 10.1016/0042-6822(92)90202-z.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBase SequenceBiological TransportBlotting, WesternCell LineCell NucleusCloning, MolecularDNA ReplicationDNA, ViralGenes, ViralHumansMiceMinute virus of miceMolecular Sequence DataPlasmidsPolymerase Chain ReactionRecombinant ProteinsTranscriptional ActivationVaccinia virusViral Nonstructural ProteinsConceptsWild-type NS1Mutant formsEfficient cap-independent translationVaccinia thymidine kinase geneNucleotide-binding motifCap-independent translationBacteriophage T7 promoterT7 RNA polymeraseEffects of mutationsThymidine kinase geneExpression of NS1Recombinant vaccinia virusP38 promoterRNA polymeraseReplicative proteinsChromosomal sitesLysine codonPurine triphosphatesKinase geneT7 promoterUntranslated regionMouse cellsNuclear extractsVaccinia virusVTF7-3Interactions of Small Nuclear RNA's with Precursor Messenger RNA During in Vitro Splicing
Wassarman D, Steitz J. Interactions of Small Nuclear RNA's with Precursor Messenger RNA During in Vitro Splicing. Science 1992, 257: 1918-1925. PMID: 1411506, DOI: 10.1126/science.1411506.Peer-Reviewed Original ResearchConceptsPrecursor messenger RNASmall nuclear RNANuclear RNASplice siteMessenger RNAPrecursor messenger RNA splicingU6 small nuclear RNAMessenger RNA splicingHeLa nuclear extractsExcised lariat intronSmall RNAsRNA splicingLariat intronIntron sequencesVitro splicingNuclear extractsCleavage eventsSplicingRNAU5Branch siteFirst cleavage eventU6U2U1
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
Characterization Of Promoter Elements Of An Interferon-Inducible Ly-6E/A Differentiation Antigen, Which Is Expressed On Activated T Cells And Hematopoietic Stem Cells
Khan K, Lindwall G, Maher S, Bothwell A. Characterization Of Promoter Elements Of An Interferon-Inducible Ly-6E/A Differentiation Antigen, Which Is Expressed On Activated T Cells And Hematopoietic Stem Cells. Molecular And Cellular Biology 1990, 10: 5150-5159. DOI: 10.1128/mcb.10.10.5150-5159.1990.Peer-Reviewed Original ResearchLy-6CCAAT box-binding proteinGenomic DNA clonesInterferon-stimulated response elementElectrophoretic mobility shift assayCis-acting elementsCrude nuclear extractsInterferon-inducible promoterLy-6 genesChloramphenicol acetyltransferase geneMobility shift assayChloramphenicol acetyltransferase assayGenomic clonesBALB/3T3 cellsCharacterized cDNAsDNA clonesPromoter elementsDNA sequencesAcetyltransferase geneEnhancer elementsNuclear extractsPromoter regionActivated murine T cellsShift assaysAcetyltransferase assaySpliced leader RNA sequences can substitute for the essential 5′ end of U1 RNA during splicing in a mammalian in vitro system
Bruzik J, Steitz J. Spliced leader RNA sequences can substitute for the essential 5′ end of U1 RNA during splicing in a mammalian in vitro system. Cell 1990, 62: 889-899. PMID: 2168293, DOI: 10.1016/0092-8674(90)90264-f.Peer-Reviewed Original ResearchConserved sequences in the U2 snRNA-encoding genes of Kinetoplastida do not include the putative branchpoint recognition region
Tschudi C, Williams S, Ullu E. Conserved sequences in the U2 snRNA-encoding genes of Kinetoplastida do not include the putative branchpoint recognition region. Gene 1990, 91: 71-77. PMID: 2401409, DOI: 10.1016/0378-1119(90)90164-m.Peer-Reviewed Original ResearchConceptsU2 small nuclear RNASmall nuclear RNAU2 genesEvolutionary conservationOrder KinetoplastidaConserved sequencesNuclear RNASequence variationFlanking regionsNuclear extractsRecognition sequenceKinetoplastidaUpstream elementRecognition regionGenesRNACorresponding sequenceLeishmania mexicana amazonensisSequenceT. congolenseTrypanosoma congolenseBiosynthesisNucleotidesProteinCongolense
1989
The mammalian analogue of the yeast PRP8 splicing protein is present in the U4/5/6 small nuclear ribonucleoprotein particle and the spliceosome.
Pinto AL, Steitz JA. The mammalian analogue of the yeast PRP8 splicing protein is present in the U4/5/6 small nuclear ribonucleoprotein particle and the spliceosome. Proceedings Of The National Academy Of Sciences Of The United States Of America 1989, 86: 8742-8746. PMID: 2479028, PMCID: PMC298364, DOI: 10.1073/pnas.86.22.8742.Peer-Reviewed Original ResearchConceptsSmall nuclear ribonucleoproteinU5 small nuclear ribonucleoproteinHeLa cell nuclear extractsSmall nuclear ribonucleoprotein particleCell nuclear extractsAnti-trimethylguanosine antibodyNuclear ribonucleoprotein particleAffinity-purified spliceosomesSplicing proteinsMammalian proteinsYeast proteinsSnRNP complexMRNA splicingSplicing extractsRibonucleoprotein particleNuclear ribonucleoproteinMammalian analogueNuclear extractsSm classGradient fractionationSm epitopesProteinSpliceosomeProtein reactivePrp8
1988
Trans splicing involves a novel form of small nuclear ribonucleoprotein particles
Bruzik J, Doren K, Hirsh D, Steitz J. Trans splicing involves a novel form of small nuclear ribonucleoprotein particles. Nature 1988, 335: 559-562. PMID: 2971142, DOI: 10.1038/335559a0.Peer-Reviewed Original ResearchConceptsSmall nuclear ribonucleoproteinSL RNACis splicingSplice siteNuclear ribonucleoproteinPrecursor-messenger RNA (pre-mRNA) transcriptsHeLa cell nuclear extractsSame nuclear compartmentTrans-splicing reactionCell nuclear extractsPossible secondary structuresMessenger RNA transcriptsSm snRNPSplice acceptor siteTrans splicingCellular machineryLeader transcriptNuclear compartmentNucleotide sequenceSplicing processRNA transcriptsNuclear extractsSnRNPSplicingSecondary structure
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