2011
A Viral Nuclear Noncoding RNA Binds Re-localized Poly(A) Binding Protein and Is Required for Late KSHV Gene Expression
Borah S, Darricarrère N, Darnell A, Myoung J, Steitz JA. A Viral Nuclear Noncoding RNA Binds Re-localized Poly(A) Binding Protein and Is Required for Late KSHV Gene Expression. PLOS Pathogens 2011, 7: e1002300. PMID: 22022268, PMCID: PMC3192849, DOI: 10.1371/journal.ppat.1002300.Peer-Reviewed Original ResearchConceptsPAN RNAKaposi's Sarcoma-Associated HerpesvirusNuclear noncoding RNANuclear noncoding RNAsShutoff effectLytic phaseKSHV gene expressionRepertoire of functionsTail of mRNATransient transfection experimentsConsequence of expressionLate viral proteinsNoncoding RNAsExonuclease proteinNuclear RNAProtein C1Translation efficiencyHost mRNAsMRNA stabilityGene expressionUnknown functionTransfection experimentsViral mRNAsPABPC1Binding protein
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 downstreamSpliceosomeIntronsSplicing
2001
Proximity of the invariant loop of U5 snRNA to the second intron residue during pre‐mRNA splicing
McConnell T, Steitz J. Proximity of the invariant loop of U5 snRNA to the second intron residue during pre‐mRNA splicing. The EMBO Journal 2001, 20: 3577-3586. PMID: 11432844, PMCID: PMC125517, DOI: 10.1093/emboj/20.13.3577.Peer-Reviewed Original ResearchAnimalsAzidesBase SequenceCross-Linking ReagentsEnhancer Elements, GeneticGlobinsIntronsKineticsMammalsModels, MolecularMolecular Sequence DataNucleic Acid ConformationPlasmidsPolymerase Chain ReactionRibonuclease HRibonucleoproteins, Small NuclearRNA PrecursorsRNA SplicingRNA, Small NuclearThionucleotides
1999
Initial recognition of U12-dependent introns requires both U11/5′ splice-site and U12/branchpoint interactions
Frilander M, Steitz J. Initial recognition of U12-dependent introns requires both U11/5′ splice-site and U12/branchpoint interactions. Genes & Development 1999, 13: 851-863. PMID: 10197985, PMCID: PMC316595, DOI: 10.1101/gad.13.7.851.Peer-Reviewed Original ResearchAdenoviridaeBlotting, NorthernDose-Response Relationship, DrugEvolution, MolecularFicusinHeLa CellsHeterogeneous-Nuclear RibonucleoproteinsHumansIntronsModels, GeneticOligonucleotidesRibonuclease HRibonucleoprotein, U4-U6 Small NuclearRibonucleoproteinsRibonucleoproteins, Small NuclearRNA SplicingTime Factors
1998
Modification of U6 Spliceosomal RNA Is Guided by Other Small RNAs
Tycowski K, You Z, Graham P, Steitz J. Modification of U6 Spliceosomal RNA Is Guided by Other Small RNAs. Molecular Cell 1998, 2: 629-638. PMID: 9844635, DOI: 10.1016/s1097-2765(00)80161-6.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceCell FractionationCell LineCell NucleolusChromosomal Proteins, Non-HistoneDimerizationHeLa CellsHumansMethylationMiceMolecular Sequence DataNucleic Acid ConformationOligodeoxyribonucleotides, AntisenseOocytesPrecipitin TestsRibonuclease HRNA, Ribosomal, 28SRNA, Small NuclearSpliceosomesXenopus laevis
1997
The position of site-directed cleavage of RNA using RNase H and 2'-O-methyl oligonucleotides is dependent on the enzyme source.
Lapham J, Yu YT, Shu MD, Steitz JA, Crothers DM. The position of site-directed cleavage of RNA using RNase H and 2'-O-methyl oligonucleotides is dependent on the enzyme source. RNA 1997, 3: 950-1. PMID: 9292493, PMCID: PMC1369540.Peer-Reviewed Original ResearchA 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 cleavageA new method for detecting sites of 2'-O-methylation in RNA molecules.
Yu YT, Shu MD, Steitz JA. A new method for detecting sites of 2'-O-methylation in RNA molecules. RNA 1997, 3: 324-31. PMID: 9056769, PMCID: PMC1369484.Peer-Reviewed Original ResearchConceptsRNA moleculesEukaryotic ribosomal RNALong RNA moleculesSpecific rRNARibosomal RNAModification sitesRRNAMethylationCell nucleoliChimeric oligonucleotideSnoRNAsRNase H cleavagePrecursor moleculesRRNA transportSitesMoleculesRNANucleotidesCytoplasmNucleoliResiduesCleavageOligonucleotideH cleavageNucleus
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 classU11
1994
Organization of small nucleolar ribonucleoproteins (snoRNPs) by fluorescence in situ hybridization and immunocytochemistry.
Matera AG, Tycowski KT, Steitz JA, Ward DC. Organization of small nucleolar ribonucleoproteins (snoRNPs) by fluorescence in situ hybridization and immunocytochemistry. Molecular Biology Of The Cell 1994, 5: 1289-1299. PMID: 7535131, PMCID: PMC301158, DOI: 10.1091/mbc.5.12.1289.Peer-Reviewed Original ResearchThe site of 3′ end formation of histone messenger RNA is a fixed distance from the downstream element recognized by the U7 snRNP.
Scharl EC, Steitz JA. The site of 3′ end formation of histone messenger RNA is a fixed distance from the downstream element recognized by the U7 snRNP. The EMBO Journal 1994, 13: 2432-2440. PMID: 8194533, PMCID: PMC395109, DOI: 10.1002/j.1460-2075.1994.tb06528.x.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceCell NucleusCell-Free SystemCross-Linking ReagentsFurocoumarinsGuanosineHeLa CellsHistonesHumansMiceMolecular Sequence DataNucleic Acid ConformationProtein BindingRegulatory Sequences, Nucleic AcidRibonuclease HRibonucleoproteins, Small NuclearRNA Processing, Post-TranscriptionalRNA, MessengerStructure-Activity RelationshipSubstrate SpecificityConceptsHistone downstream elementU7 small nuclear ribonucleoproteinSmall nuclear ribonucleoproteinHistone messenger RNAInsertion mutantsEnd formationSite of cleavageEnd processingDownstream elementsA residuesMessenger RNAAnti-trimethylguanosine antibodyStem-loop structureWild-type substrateCross-linking studiesPremessenger RNANuclear ribonucleoproteinEnzymatic componentsNew cleavage siteNucleotides downstreamC residuesMolecular rulerCleavage siteRNAHistones
1992
Three novel functional variants of human U5 small nuclear RNA.
Sontheimer EJ, Steitz JA. Three novel functional variants of human U5 small nuclear RNA. Molecular And Cellular Biology 1992, 12: 734-746. PMID: 1310151, PMCID: PMC364287, DOI: 10.1128/mcb.12.2.734.Peer-Reviewed Original ResearchConceptsU5 small nuclear RNASmall nuclear RNANuclear RNAHeLa cellsSmall nuclear ribonucleoprotein particleTri-snRNP complexOligonucleotide-directed RNase H cleavageNuclear ribonucleoprotein particleNovel functional variantsFull-length speciesAffinity-purified spliceosomesTrimethylguanosine capAlternative splicingShorter speciesRibonucleoprotein particleMinimal domainHeLa extractsPrimer extensionFunctional variantsHigh abundanceBase changesNorthern blottingAbundant formRNASpecies
1991
Structural analyses of the 7SK ribonucleoprotein (RNP), the most abundant human small RNP of unknown function.
Wassarman DA, Steitz JA. Structural analyses of the 7SK ribonucleoprotein (RNP), the most abundant human small RNP of unknown function. Molecular And Cellular Biology 1991, 11: 3432-3445. PMID: 1646389, PMCID: PMC361072, DOI: 10.1128/mcb.11.7.3432.Peer-Reviewed Original Research
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 ResearchThe U3 small nucleolar ribonucleoprotein functions in the first step of preribosomal RNA processing
Kass S, Tyc K, Steitz J, Sollner-Webb B. The U3 small nucleolar ribonucleoprotein functions in the first step of preribosomal RNA processing. Cell 1990, 60: 897-908. PMID: 2156625, DOI: 10.1016/0092-8674(90)90338-f.Peer-Reviewed Original ResearchAnimalsBase SequenceBlotting, NorthernCarcinoma, Ehrlich TumorCell NucleolusDNA, RibosomalEndoribonucleasesMiceMolecular Sequence DataNucleic Acid ConformationOligonucleotide ProbesRibonuclease HRibonucleoproteinsRibonucleoproteins, Small NuclearRNA PrecursorsRNA Processing, Post-TranscriptionalRNA, Small NuclearTemplates, Genetic
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[31] Determination of RNA-protein and RNA-ribonucleoprotein interactions by nuclease probing
Parker K, Steitz J. [31] Determination of RNA-protein and RNA-ribonucleoprotein interactions by nuclease probing. Methods In Enzymology 1989, 180: 454-468. PMID: 2482428, DOI: 10.1016/0076-6879(89)80117-x.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntibodiesCarrier ProteinsElectrophoresis, Polyacrylamide GelEndoribonucleasesHumansIndicators and ReagentsKineticsMiceMicrococcal NucleaseNucleotide MappingRibonuclease HRibonuclease T1RibonucleasesRibonucleoproteinsRNARNA PrecursorsRNA SplicingRNA, Ribosomal, 28SRNA-Binding ProteinsTranscription, Genetic
1987
Identification of the Human U7 snRNP as One of Several Factors Involved in the 3′ End Maturation of Histone Premessenger RNA's
Mowry K, Steitz J. Identification of the Human U7 snRNP as One of Several Factors Involved in the 3′ End Maturation of Histone Premessenger RNA's. Science 1987, 238: 1682-1687. PMID: 2825355, DOI: 10.1126/science.2825355.Peer-Reviewed Original ResearchConceptsU7 snRNPPre-mRNAEnd processingDownstream elementsCleavage siteSmall nuclear ribonucleoprotein complexesMammalian pre-mRNAHeLa cell extractsNuclear ribonucleoprotein complexesHistone pre-mRNAEnd maturationEukaryotic cellsRibonucleoprotein complexesPremessenger RNARNA moietySplicing reactionGene transcriptsCell extractsSnRNPMessenger RNARNA
1985
U2 as well as U1 small nuclear ribonucleoproteins are involved in premessenger RNA splicing
Black D, Chabot B, Steitz J. U2 as well as U1 small nuclear ribonucleoproteins are involved in premessenger RNA splicing. Cell 1985, 42: 737-750. PMID: 2996775, DOI: 10.1016/0092-8674(85)90270-3.Peer-Reviewed Original Research