2017
Settling the m6A debate: methylation of mature mRNA is not dynamic but accelerates turnover
Rosa-Mercado NA, Withers JB, Steitz JA. Settling the m6A debate: methylation of mature mRNA is not dynamic but accelerates turnover. Genes & Development 2017, 31: 957-958. PMID: 28637691, PMCID: PMC5495124, DOI: 10.1101/gad.302695.117.Peer-Reviewed Original ResearchConceptsPre-mRNA splicing eventsPost-transcriptional modificationsMRNA biogenesisDifferent subcellular fractionsMRNA biologySplicing eventsMature mRNABiochemical approachesRNA transcriptsPivotal regulatorMethylation levelsHeLa cellsSubcellular fractionsRNA nucleosidesMethylationTranscriptsBiogenesisChromatinSplicingMethyladenosineExonsGenesRNABiologyRegulator
2016
Calcium signaling and transcription: elongation, DoGs, and eRNAs.
Vilborg A, Passarelli MC, Steitz JA. Calcium signaling and transcription: elongation, DoGs, and eRNAs. Receptors & Clinical Investigation 2016, 3 PMID: 29147672, PMCID: PMC5685190, DOI: 10.14800/rci.1169.Peer-Reviewed Original ResearchGene-specific transcription factorsPhases of transcriptionCertain stress conditionsTranscription terminationReadthrough transcriptionTranscription initiationAlternative splicingCellular processesTranscription factorsRegulated processKey intracellularSignaling cascadesTranscriptionCalcium signalingStress conditionsDiverse classSuch CaERNAsSplicingGenesTranscriptsSignalingCalcium ionsIntracellularCascade
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 yieldsNMDMutationsMRNATri-snRNP-associated proteins interact with subunits of the TRAMP and nuclear exosome complexes, linking RNA decay and pre-mRNA splicing
Nag A, Steitz JA. Tri-snRNP-associated proteins interact with subunits of the TRAMP and nuclear exosome complexes, linking RNA decay and pre-mRNA splicing. RNA Biology 2012, 9: 334-342. PMID: 22336707, PMCID: PMC3384585, DOI: 10.4161/rna.19431.Peer-Reviewed Original ResearchConceptsDecay machineryMRNA splicingRNA decay machineryRNA decay factorsTri-snRNP complexNuclear exosome complexPM/SclYeast counterpartIntergenic transcriptsSnoRNA biogenesisExosome complexTri-snRNPRNA decayRRNA processingPhosphorylation sitesMRNA processingPutative componentsMtr4Prp31MachinerySplicingDifferent pathwaysProteinSpliceosomeBiogenesis
2009
Nuclear networking fashions pre-messenger RNA and primary microRNA transcripts for function
Pawlicki JM, Steitz JA. Nuclear networking fashions pre-messenger RNA and primary microRNA transcripts for function. Trends In Cell Biology 2009, 20: 52-61. PMID: 20004579, PMCID: PMC2821161, DOI: 10.1016/j.tcb.2009.10.004.Peer-Reviewed Original ResearchConceptsMature messenger RNAGene expressionRNA polymerase II transcriptsProtein-coding genesPolymerase II transcriptsRNA polymerase IIMessenger RNAPre-messenger RNARNA processing reactionsCotranscriptional eventsPolymerase IIProcessing eventsProcessing reactionsExtensive molecular interactionsEarly stepsTranscriptsRNAExquisite couplingMolecular interactionsMicroRNAsExpressionNuclear networkCrucial roleFinal fateSplicingDrosophila 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
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 downstreamSpliceosomeIntronsSplicingAn 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
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
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
1998
Modifications of U2 snRNA are required for snRNP assembly and pre‐mRNA splicing
Yu Y, Shu M, Steitz J. Modifications of U2 snRNA are required for snRNP assembly and pre‐mRNA splicing. The EMBO Journal 1998, 17: 5783-5795. PMID: 9755178, PMCID: PMC1170906, DOI: 10.1093/emboj/17.19.5783.Peer-Reviewed Original ResearchConceptsEnd of U2Native gel analysisPre-mRNA splicingU2 snRNP particleGlycerol gradient analysisPseudouridylation activityGuanosine capSnRNP assemblySpliceosomal snRNAsSplicing activityTMG capSpliceosome assemblyU2 RNAU2 snRNAU2 functionProtein profilesGel analysisSnRNP particlesXenopus oocytesInternal modificationSnRNASplicingPotent inhibitorU2Extensive modification
1997
Inhibition of mammalian spliceosome assembly and pre-mRNA splicing by peptide inhibitors of protein kinases.
Parker AR, Steitz JA. Inhibition of mammalian spliceosome assembly and pre-mRNA splicing by peptide inhibitors of protein kinases. RNA 1997, 3: 1301-12. PMID: 9409621, PMCID: PMC1369569.Peer-Reviewed Original ResearchConceptsCalmodulin binding domainMammalian spliceosome assemblySpliceosome assemblyMRNA splicingSplicing activityCaMK IIGS peptideProtein kinase CAutophosphorylation eventsCalmodulin kinase IIProlonged incubationProtein kinaseSplicing reactionSplicing assaysBinding domainsKinase IISplicingKinase CPeptide inhibitorDistinct mechanismsProteinKinaseCompetitive inhibitorAssemblyDistinct events
1996
More Sm snRNAs from Vertebrate Cells
Yu Y, Tarn W, Yario T, Steitz J. More Sm snRNAs from Vertebrate Cells. Experimental Cell Research 1996, 229: 276-281. PMID: 8986610, DOI: 10.1006/excr.1996.0372.Peer-Reviewed Original ResearchA 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 classU11
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
1993
The U5 and U6 Small Nuclear RNAs as Active Site Components of the Spliceosome
Sontheimer E, Steitz J. The U5 and U6 Small Nuclear RNAs as Active Site Components of the Spliceosome. Science 1993, 262: 1989-1996. PMID: 8266094, DOI: 10.1126/science.8266094.Peer-Reviewed Original ResearchConceptsSmall nuclear RNANuclear RNAPrecursor messenger RNA splicingLariat intermediateU6 small nuclear RNAMessenger RNA splicingExon 1Self-splicing intronsActive site componentsRNA splicingMammalian spliceosomeU6 RNARNA contactsMechanistic parallelsPre-mRNAVitro splicingSubsequent splicingSplicingSpliceosomeSplice siteLast residueFirst residueFunctional interactionIntron productsRNAA 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 extractsSplicing
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 photoactivationSnRNPMammalianInteractions 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