2021
Structural analyses of an RNA stability element interacting with poly(A)
Torabi SF, Chen YL, Zhang K, Wang J, DeGregorio SJ, Vaidya AT, Su Z, Pabit SA, Chiu W, Pollack L, Steitz JA. Structural analyses of an RNA stability element interacting with poly(A). Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2026656118. PMID: 33785601, PMCID: PMC8040590, DOI: 10.1073/pnas.2026656118.Peer-Reviewed Original ResearchConceptsRNA stability elementCis-acting RNA elementsGlobal conformational changesRich internal loopCryo-electron microscopyRice transposable elementsDiverse genomesDouble-helical regionsSmall-angle X-ray scatteringEne motifTransposable elementsGlobal structural changesRNA interactionsRNA stabilityBioinformatics studiesRNA elementsStability elementShort helixConformational changesDecay pathwaysInternal loopBiochemical structureTriplex structureBindingMotifHyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression
Rosa-Mercado NA, Zimmer JT, Apostolidi M, Rinehart J, Simon MD, Steitz JA. Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression. Molecular Cell 2021, 81: 502-513.e4. PMID: 33400923, PMCID: PMC7867636, DOI: 10.1016/j.molcel.2020.12.002.Peer-Reviewed Original ResearchConceptsWidespread transcriptional repressionTranscriptional repressionPol IIIntegrator complex subunitsRNA polymerase IIGenome-wide lossStress-induced redistributionParental genesTranscriptional outputDoG inductionPolymerase IIChIP sequencingHuman cell linesUpstream geneComplex subunitsPolyadenylation factorsTranscription profilesReadthrough transcriptsCatalytic subunitIntegrator activityCellular stressHyperosmotic stressTranscriptional levelTranscription resultsGenes
2015
Widespread Inducible Transcription Downstream of Human Genes
Vilborg A, Passarelli MC, Yario TA, Tycowski KT, Steitz JA. Widespread Inducible Transcription Downstream of Human Genes. Molecular Cell 2015, 59: 449-461. PMID: 26190259, PMCID: PMC4530028, DOI: 10.1016/j.molcel.2015.06.016.Peer-Reviewed Original ResearchConceptsOsmotic stressLong non-coding regionsDownstream of genesProtein-coding genesNon-coding regionsPervasive transcriptionHuman cell linesTranscription downstreamHuman genomeHuman genesTranscript inductionRNA-seqPolyA signalUpstream transcriptsUndescribed mechanismGenesCell linesTranscriptionTranscript typeActive regulationTranscriptsDetailed mechanistic studiesRNADownstreamMechanistic studiesRNA–RNA base-pairing: theme and variations
Steitz J. RNA–RNA base-pairing: theme and variations. RNA 2015, 21: 476-477. PMID: 25780100, PMCID: PMC4371242, DOI: 10.1261/rna.050427.115.Peer-Reviewed Original ResearchBase PairingRNA
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
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 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 cleavage
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 Research
1993
Uncoupling two functions of the U1 small nuclear ribonucleoprotein particle during in vitro splicing.
Seiwert SD, Steitz JA. Uncoupling two functions of the U1 small nuclear ribonucleoprotein particle during in vitro splicing. Molecular And Cellular Biology 1993, 13: 3135-3145. PMID: 7684489, PMCID: PMC359749, DOI: 10.1128/mcb.13.6.3135.Peer-Reviewed Original ResearchMeSH KeywordsAdenoviridaeAnimalsBase SequenceCaenorhabditis elegansCell NucleusExonsHeLa CellsHumansMolecular Sequence DataNucleic Acid ConformationOligodeoxyribonucleotidesPlasmidsRibonucleoprotein, U1 Small NuclearRNARNA SplicingRNA, Small NuclearSequence Homology, Nucleic AcidTranscription, GeneticTrypanosomatinaConceptsSmall nuclear ribonucleoprotein particleU1 small nuclear ribonucleoprotein particleNuclear ribonucleoprotein particleSplice site recognitionU1 snRNASL RNASplice site regionSplicing substrateRibonucleoprotein particleSpliced leader RNA sequencesVitro splicingSplice siteU1 snRNP functionsEssential splicing factorLeader RNA sequencesNative gel analysisSnRNP functionCaenorhabditis elegansSplicing complexesSplicing factorsLeptomonas collosomaSpliceosome assemblyDifferent intronsU1 RNAMethyl oligoribonucleotide
1992
The low-abundance U11 and U12 small nuclear ribonucleoproteins (snRNPs) interact to form a two-snRNP complex.
Wassarman KM, Steitz JA. The low-abundance U11 and U12 small nuclear ribonucleoproteins (snRNPs) interact to form a two-snRNP complex. Molecular And Cellular Biology 1992, 12: 1276-1285. PMID: 1372090, PMCID: PMC369560, DOI: 10.1128/mcb.12.3.1276.Peer-Reviewed Original Research
1991
An intact Box C sequence in the U3 snRNA is required for binding of fibrillarin, the protein common to the major family of nucleolar snRNPs.
Baserga SJ, Yang XD, Steitz JA. An intact Box C sequence in the U3 snRNA is required for binding of fibrillarin, the protein common to the major family of nucleolar snRNPs. The EMBO Journal 1991, 10: 2645-2651. PMID: 1714385, PMCID: PMC452965, DOI: 10.1002/j.1460-2075.1991.tb07807.x.Peer-Reviewed Original ResearchConceptsBox CU3 snRNANucleolar small RNAsSite-specific mutationsShort nucleotide sequencesFibrillarin proteinSmall RNAsDeletion analysisCommon binding siteBox DNucleotide sequenceSnRNPsMajor familiesSnRNAU3 snRNPRNAInput RNAFibrillarinBinding sitesC sequencesBindingProteinSequenceAnti-fibrillarin autoantibodiesBiogenesis
1990
Molecular analyses of the functions of SL and U3 snRNPs
Steitz JA, Bruzik JP, Tyc K, Kass S, Sollner-Webb B. Molecular analyses of the functions of SL and U3 snRNPs. Molecular Biology Reports 1990, 14: 123-123. PMID: 1694557, DOI: 10.1007/bf00360442.Peer-Reviewed Original Research
1989
Function of the mammalian La protein: evidence for its action in transcription termination by RNA polymerase III.
Gottlieb E, Steitz JA. Function of the mammalian La protein: evidence for its action in transcription termination by RNA polymerase III. The EMBO Journal 1989, 8: 851-861. PMID: 2470590, PMCID: PMC400884, DOI: 10.1002/j.1460-2075.1989.tb03446.x.Peer-Reviewed Original ResearchConceptsRNA polymerase III transcriptionPolymerase III transcriptionRNA polymerase IIITranscription complexPolymerase IIILa proteinTranscription termination factorFull-length transcriptsTranscription terminationTermination factorRNA productsTranscription intermediatesTranscriptsTranscriptionProteinComplexesPolymeraseRegulatorAbsence[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-Binding ProteinsRNA, Ribosomal, 28STranscription, Genetic
1988
Correct in vivo splicing of the mouse immunoglobulin kappa light-chain pre-mRNA is dependent on 5' splice-site position even in the absence of transcription.
Kedes DH, Steitz JA. Correct in vivo splicing of the mouse immunoglobulin kappa light-chain pre-mRNA is dependent on 5' splice-site position even in the absence of transcription. Genes & Development 1988, 2: 1448-1459. PMID: 2463211, DOI: 10.1101/gad.2.11.1448.Peer-Reviewed Original Research
1986
Pre-mRNA splicing in vitro requires intact U4/U6 small nuclear ribonucleoprotein
Black D, Steitz J. Pre-mRNA splicing in vitro requires intact U4/U6 small nuclear ribonucleoprotein. Cell 1986, 46: 697-704. PMID: 2427202, DOI: 10.1016/0092-8674(86)90345-4.Peer-Reviewed Original Research
1985
Association of the lupus antigen La with a subset of U6 snRNA molecules
Rinke J, Steitz J. Association of the lupus antigen La with a subset of U6 snRNA molecules. Nucleic Acids Research 1985, 13: 2617-2629. PMID: 2582364, PMCID: PMC341179, DOI: 10.1093/nar/13.7.2617.Peer-Reviewed Original Research
1984
U4 and U6 RNAs coexist in a single small nuclear ribonucleoprotein particle
Hashimoto C, Steitz J. U4 and U6 RNAs coexist in a single small nuclear ribonucleoprotein particle. Nucleic Acids Research 1984, 12: 3283-3293. PMID: 6201826, PMCID: PMC318745, DOI: 10.1093/nar/12.7.3283.Peer-Reviewed Original ResearchConceptsSmall nuclear ribonucleoproteinU6 RNARNA complexIntact small nuclear ribonucleoproteinRNA/RNA complexesHuman small nuclear ribonucleoproteinsSmall nuclear ribonucleoprotein particleRNA-RNA interactionsNuclear ribonucleoprotein particleSequence complementarityMammalian cellsNuclear ribonucleoproteinRibonucleoprotein particleSnRNP particlesRNABiological implicationsPolyacrylamide gelsProteinase KU4ComplexesSodium dodecyl sulfateRibonucleoproteinDodecyl sulfateU5U1The Ro small cytoplasmic ribonucleoproteins: identification of the antigenic protein and its binding site on the Ro RNAs.
Wolin SL, Steitz JA. The Ro small cytoplasmic ribonucleoproteins: identification of the antigenic protein and its binding site on the Ro RNAs. Proceedings Of The National Academy Of Sciences Of The United States Of America 1984, 81: 1996-2000. PMID: 6201849, PMCID: PMC345423, DOI: 10.1073/pnas.81.7.1996.Peer-Reviewed Original ResearchConceptsRibonucleoprotein particleHeLa cellsSmall cytoplasmic RNARibonuclease protection experimentsSmall ribonucleoprotein particlesSmall cytoplasmic ribonucleoproteinsHuman HeLa cellsCytoplasmic ribonucleoproteinMammalian speciesCytoplasmic RNARNA sequencesMajor proteinsRo RNAsProtection experimentsRo proteinPossible functionsBase pairsIdentical base pairsRNAProteinSystemic lupus erythematosusAntigenic proteinsAntigenic polypeptidesRo antibodiesLupus erythematosus