2009
Drosophila hnRNP A1 homologs Hrp36/Hrp38 enhance U2-type versus U12-type splicing to regulate alternative splicing of the prospero twintron
Borah S, Wong AC, Steitz JA. Drosophila hnRNP A1 homologs Hrp36/Hrp38 enhance U2-type versus U12-type splicing to regulate alternative splicing of the prospero twintron. Proceedings Of The National Academy Of Sciences Of The United States Of America 2009, 106: 2577-2582. PMID: 19196985, PMCID: PMC2636732, DOI: 10.1073/pnas.0812826106.Peer-Reviewed Original ResearchConceptsU12-type splicingPurine-rich elementAlternative splicingMRNA undergoes alternative splicingTranscription factor ProsperoU12-type spliceosomeHeterogeneous nuclear ribonucleoprotein A1Undergoes alternative splicingU2-type spliceosomeDrosophila homologDrosophila embryogenesisS2 cellsHnRNP A1TwintronSplicingNeuronal differentiationHrp38SpliceosomeIntronsEmbryogenesisProteinAxonal outgrowthHrp36HnRNPsHomolog
2008
Minor-class splicing occurs in the nucleus of the Xenopus oocyte
Friend K, Kolev NG, Shu MD, Steitz JA. Minor-class splicing occurs in the nucleus of the Xenopus oocyte. RNA 2008, 14: 1459-1462. PMID: 18567814, PMCID: PMC2491479, DOI: 10.1261/rna.1119708.Peer-Reviewed Original ResearchConceptsSmall nuclear ribonucleoproteinMinor class intronsU12-type splicingXenopus oocytesU12-dependent intronsNuclear envelope breakdownCertain eukaryotesMinor spliceosomeVertebrate cellsSplicing substrateNuclear compartmentNuclear ribonucleoproteinRNA intronsAccurate splicingEnvelope breakdownSplicingIntronsCytoplasmOocytesEukaryotesSpliceosomeMeiosisRibonucleoproteinNucleusSmall fraction
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
GAS5 Gene
Hirose T, Steitz J. GAS5 Gene. 2005 DOI: 10.1038/npg.els.0005019.Peer-Reviewed Original Research
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 downstreamSpliceosomeIntronsSplicingGuide RNAs with 5′ Caps and Novel Box C/D snoRNA-like Domains for Modification of snRNAs in Metazoa
Tycowski KT, Aab A, Steitz JA. Guide RNAs with 5′ Caps and Novel Box C/D snoRNA-like Domains for Modification of snRNAs in Metazoa. Current Biology 2004, 14: 1985-1995. PMID: 15556860, DOI: 10.1016/j.cub.2004.11.003.Peer-Reviewed Original ResearchConceptsModification guide RNAsGuide RNABox C/D snoRNAsInvariant G residueKink-turn structureGuide RNA genesShort guide RNASmall ribonucleoprotein particlesMetazoan organismsAncestral metazoanGuanosine capMetazoan cellsSingle intronD snoRNAsRNA genesSpliceosomal snRNAsTelomerase RNARibosomal RNASuch RNAsRibonucleoprotein particleMetazoansUpstream promoterIntronsG residuesCommon modification
2003
Splicing-Dependent and -Independent Modes of Assembly for Intron-Encoded Box C/D snoRNPs in Mammalian Cells
Hirose T, Shu MD, Steitz JA. Splicing-Dependent and -Independent Modes of Assembly for Intron-Encoded Box C/D snoRNPs in Mammalian Cells. Molecular Cell 2003, 12: 113-123. PMID: 12887897, DOI: 10.1016/s1097-2765(03)00267-3.Peer-Reviewed Original ResearchConceptsBox C/D snoRNAsSplice siteSnoRNP proteinsD snoRNAsSnoRNP assemblyMammalian cellsHost intronBox C/D snoRNPsSmall nucleolar RNAsD snoRNPsRRNA modificationNucleolar RNAsHost genesActive splicingNts upstreamIntronsEfficient expressionSnoRNAsStable stemSplicingVivo analysisProteinAssemblyBlockage experimentsStem
2002
The splicing of U12‐type introns can be a rate‐limiting step in gene expression
Patel AA, McCarthy M, Steitz JA. The splicing of U12‐type introns can be a rate‐limiting step in gene expression. The EMBO Journal 2002, 21: 3804-3815. PMID: 12110592, PMCID: PMC126102, DOI: 10.1093/emboj/cdf297.Peer-Reviewed Original ResearchConceptsU12-type intronsGene expressionDrosophila melanogaster S2 cellsProtein-coding genesU12-type spliceosomePost-transcriptional regulationHuman tissue culture cellsU2-type intronsMetazoan genomesTissue culture cellsS2 cellsU12-typeIntron removalIdentical mRNAIntronsFluorescent proteinQuantitative RT-PCR assayMinigene constructsCulture cellsRate-limiting stepSpliceosomeMRNAMinor classExpressionRT-PCR assaysBranchpoint 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 sitePathwayBranchpointP120The Divergent U12-Type Spliceosome Is Required for Pre-mRNA Splicing and Is Essential for Development in Drosophila
Otake LR, Scamborova P, Hashimoto C, Steitz JA. The Divergent U12-Type Spliceosome Is Required for Pre-mRNA Splicing and Is Essential for Development in Drosophila. Molecular Cell 2002, 9: 439-446. PMID: 11864616, DOI: 10.1016/s1097-2765(02)00441-0.Peer-Reviewed Original ResearchMeSH KeywordsAlternative SplicingAnimalsAnimals, Genetically ModifiedBase SequenceDrosophila melanogasterDrosophila ProteinsGenes, LethalIntronsLarvaMolecular Sequence DataMutagenesis, InsertionalNerve Tissue ProteinsNuclear ProteinsNucleic Acid ConformationProtein IsoformsRibonucleoprotein, U4-U6 Small NuclearRibonucleoproteins, Small NuclearRNA PrecursorsRNA SplicingRNA, Small NuclearSequence AlignmentSequence Homology, Nucleic AcidSpliceosomesTranscription FactorsTransgenesConceptsU12-type spliceosomeThird instar larvalU12-type intronsPre-mRNA splicingU4atac/U6atacMetazoan organismsHomeodomain proteinsU5 snRNPsDrosophila melanogasterU12 spliceosomeMRNA intronsU12 snRNASingle locusU6atacInstar larvalSpliceosomeEmbryonic stagesCNS developmentIntronsMinor classU12DrosophilaMelanogasterVertebratesSnRNPs
2001
Non-coding snoRNA host genes in Drosophila: expression strategies for modification guide snoRNAs
Tycowski K, Steitz J. Non-coding snoRNA host genes in Drosophila: expression strategies for modification guide snoRNAs. European Journal Of Cell Biology 2001, 80: 119-125. PMID: 11302516, DOI: 10.1078/0171-9335-00150.Peer-Reviewed Original ResearchConceptsSnoRNA host genesModification-guide snoRNAsHost genesGuide snoRNAsSplice siteDifferent eukaryotic kingdomsEukaryotic kingdomsPolycistronic unitsD. melanogasterProtein codingTranslational apparatusConserved distanceSnoRNA sequencesTrailer sequencesIntron lariatPrimary transcriptFunctional proteinsNucleotides upstreamExpression strategyExonucleolytic activitySnoRNAsIntronsGenesDebranching activityProtein
1998
Classification of gas5 as a Multi-Small-Nucleolar-RNA (snoRNA) Host Gene and a Member of the 5′-Terminal Oligopyrimidine Gene Family Reveals Common Features of snoRNA Host Genes
Smith C, Steitz J. Classification of gas5 as a Multi-Small-Nucleolar-RNA (snoRNA) Host Gene and a Member of the 5′-Terminal Oligopyrimidine Gene Family Reveals Common Features of snoRNA Host Genes. Molecular And Cellular Biology 1998, 18: 6897-6909. PMID: 9819378, PMCID: PMC109273, DOI: 10.1128/mcb.18.12.6897.Peer-Reviewed Original ResearchMeSH Keywords3T3 CellsAnimalsBase SequenceCell DivisionCell NucleolusCloning, MolecularHumansMembrane ProteinsMiceMolecular Sequence DataMultigene FamilyProtein BiosynthesisRibonucleoproteinsRibosomesRNA SplicingRNA, AntisenseRNA, MessengerRNA, Small NuclearRNA, Small NucleolarTranscription, GeneticConceptsHost genesGene familyGAS5 geneBox C/D snoRNAsSnoRNA host genesHost gene transcriptsCell growthInhibition of translationSmall nucleolar RNA host geneSmall nucleolarD snoRNAsGAS5 transcriptsMRNP particlesSpecific transcriptsGene transcriptsGenesTranscriptsSnoRNAsRNASequenceIntronsCommon featureRibosomesRRNAFamily
1997
A new strategy for introducing photoactivatable 4-thiouridine ((4S)U) into specific positions in a long RNA molecule.
Yu YT, Steitz JA. A new strategy for introducing photoactivatable 4-thiouridine ((4S)U) into specific positions in a long RNA molecule. RNA 1997, 3: 807-10. PMID: 9214662, PMCID: PMC1369526.Peer-Reviewed Original ResearchConceptsPre-mRNAPre-mRNA substrateAT-AC intronsPhage RNA polymeraseRNA-DNA chimerasFull-length RNALong RNA moleculesRNA polymeraseRNA moleculesT4 RNA ligaseT4 DNA ligaseRNA ligaseDNA ligaseRNARNase H cleavageLigaseSpecific sitesSpecific positionsIntronsPolymeraseChimerasNew strategyCleavageOligonucleotideH cleavage
1996
A Novel Spliceosome Containing U11, U12, and U5 snRNPs Excises a Minor Class (AT–AC) Intron In Vitro
Tarn W, Steitz J. A Novel Spliceosome Containing U11, U12, and U5 snRNPs Excises a Minor Class (AT–AC) Intron In Vitro. Cell 1996, 84: 801-811. PMID: 8625417, DOI: 10.1016/s0092-8674(00)81057-0.Peer-Reviewed Original ResearchMeSH KeywordsBase CompositionBase SequenceBlotting, NorthernCell NucleusHeLa CellsHumansMolecular Sequence DataNucleic Acid ConformationOligodeoxyribonucleotidesPlasmidsPolymerase Chain ReactionRibonuclease HRibonucleoprotein, U5 Small NuclearRibonucleoproteins, Small NuclearRNA PrecursorsRNA SplicingConceptsU5 small nuclear ribonucleoproteinSmall nuclear ribonucleoproteinU12 small nuclear ribonucleoproteinsMinor class intronsProtein coding genesPre-mRNA substrateNative gel electrophoresisCoding genesBranch site sequenceSplicing complexesNuclear ribonucleoproteinPre-mRNAP120 geneLariat intermediateSite sequenceIntronsHeLa cellsEssential roleSplicingGel electrophoresisBranch siteGenesU12Minor classU11A mammalian gene with introns instead of exons generating stable RNA products
Tycowski K, Shu M, Steitz J. A mammalian gene with introns instead of exons generating stable RNA products. Nature 1996, 379: 464-466. PMID: 8559254, DOI: 10.1038/379464a0.Peer-Reviewed Original ResearchConceptsProtein-coding genesRibosomal subunit assemblyRibosomal RNA transcriptionSmall nucleolar RNAsMammalian genesSnoRNA genesEukaryotic cellsProtein codingMature rRNANucleolar RNAsHost genesSubunit assemblyDifferent intronsRNA transcriptionRNA productsExtensive complementarityIntronsGenesSnoRNAsExonsRNARRNATranscriptionPolysomesMaturation1
1995
U12 snRNA in vertebrates: evolutionary conservation of 5' sequences implicated in splicing of pre-mRNAs containing a minor class of introns.
Tarn WY, Yario TA, Steitz JA. U12 snRNA in vertebrates: evolutionary conservation of 5' sequences implicated in splicing of pre-mRNAs containing a minor class of introns. RNA 1995, 1: 644-56. PMID: 7489523, PMCID: PMC1369308.Peer-Reviewed Original ResearchConceptsU12 snRNASnRNA genesMinor class intronsRNA polymerase IIU6 snRNA sequencesMinor classPutative branch siteNoncanonical splice sitesMajor classesEvolutionary conservationBranch site sequencePolymerase IIU2 genesFunctional genesSnRNA sequencesIntronsConsensus sequenceSnRNASite sequenceUpstream elementSplice siteSplicingGenesTranscriptionBranch site
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 oocytesU22IntronsGenesTranscriptsNucleoliOocytesMaturationTargetingCellsFragmentsDepletionSR proteins can compensate for the loss of U1 snRNP functions in vitro.
Tarn WY, Steitz JA. SR proteins can compensate for the loss of U1 snRNP functions in vitro. Genes & Development 1994, 8: 2704-2717. PMID: 7958927, DOI: 10.1101/gad.8.22.2704.Peer-Reviewed Original ResearchConceptsSR proteinsSplice site recognitionSplice siteU1 snRNPsU1 snRNP functionsEssential splicing factorPre-mRNA substrateSplice site choiceNative gel analysisSplice site selectionMethyl oligoribonucleotideCross-linking studiesSnRNP functionSplicing factorsU1 snRNPU1 snRNASite recognitionSite choiceGel analysisRescue splicingProteinSplicing systemIntronsSnRNPs
1990
Spliced 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 Research