2018
Caution needs to be taken when assigning transcription start sites to ends of protein-coding genes: a rebuttal
Sabath N, Vilborg A, Steitz JA, Shalgi R. Caution needs to be taken when assigning transcription start sites to ends of protein-coding genes: a rebuttal. Human Genomics 2018, 12: 32. PMID: 29945683, PMCID: PMC6020437, DOI: 10.1186/s40246-018-0164-4.Peer-Reviewed Original ResearchConceptsTranscription start siteTranscriptional readthroughStart siteOsmotic stressProtein-coding genesGenome-wide comparisonEnd of genesStress-mediated inductionMammalian stress responseNIH3T3 mouse cellsDe novo initiationTranscription initiationGene endMammalian cellsLong transcriptsNIH3T3 cellsMouse cellsSimilar transcriptsStress responseTSS-seqHuman cellsReadthroughNovo initiationDramatic inductionStress conditions
2017
Comparative analysis reveals genomic features of stress-induced transcriptional readthrough
Vilborg A, Sabath N, Wiesel Y, Nathans J, Levy-Adam F, Yario TA, Steitz JA, Shalgi R. Comparative analysis reveals genomic features of stress-induced transcriptional readthrough. Proceedings Of The National Academy Of Sciences Of The United States Of America 2017, 114: e8362-e8371. PMID: 28928151, PMCID: PMC5635911, DOI: 10.1073/pnas.1711120114.Peer-Reviewed Original ResearchConceptsTranscriptional readthroughReadthrough transcriptionGenomic featuresOsmotic stressProtein-coding gene lociHeat shockUnique chromatin signatureGenome-wide mappingOpen chromatin statePolymerase II occupancyNuclear RNA-seqGenome-wide studiesChromatin signaturesChromatin stateNIH 3T3 mouse fibroblast cellsNeighboring genesRNA classesReadthrough transcriptsReadthrough phenomenonRegulated processRNA-seqGene transcriptionGene locusStress responsePotential regulator
2016
Readthrough transcription: How are DoGs made and what do they do?
Vilborg A, Steitz JA. Readthrough transcription: How are DoGs made and what do they do? RNA Biology 2016, 14: 632-636. PMID: 26861889, PMCID: PMC5449079, DOI: 10.1080/15476286.2016.1149680.Peer-Reviewed Original ResearchConceptsDoG inductionDownstream of genesMammalian gene expressionLevel of transcriptionPervasive transcriptionIntergenic transcriptionTranscription terminationPossible molecular mechanismsTranscriptional readthroughOsmotic stressGene expressionMolecular mechanismsEndoplasmic reticulumTranscriptionIP3 receptorOutstanding questionsTranscriptsBiogenesisGenomeInductionReadthroughGenesCalcium releaseReticulumMechanism
2013
Mammalian 5′-Capped MicroRNA Precursors that Generate a Single MicroRNA
Xie M, Li M, Vilborg A, Lee N, Shu MD, Yartseva V, Šestan N, Steitz JA. Mammalian 5′-Capped MicroRNA Precursors that Generate a Single MicroRNA. Cell 2013, 155: 1568-1580. PMID: 24360278, PMCID: PMC3899828, DOI: 10.1016/j.cell.2013.11.027.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsArgonaute ProteinsBase SequenceBiosynthetic PathwaysDEAD-box RNA HelicasesGenome-Wide Association StudyGuanosineHumansKaryopherinsMiceMicroRNAsMolecular Sequence DataReceptors, Cytoplasmic and NuclearRibonuclease IIIRNA CapsRNA Polymerase IIRNA, Small InterferingTranscription Termination, GeneticConceptsCap-binding protein eIF4EMiRNA biogenesis pathwayNuclear-cytoplasmic transportGuide strand selectionShRNA expression constructsTranscription start siteBiogenesis pathwayCytoplasmic DicerMicroprocessor complexTranscription terminationProtein eIF4EExportin-5MicroRNA precursorsMiRNA hairpinsPrimary transcriptStrand selectionGene regulatorsStart siteDicer cleavageExpression constructsSingle microRNAMiRNAsMicroRNAsPathwayMicroRNPs
2008
Cell cycle control of microRNA-mediated translation regulation
Vasudevan S, Tong Y, Steitz JA. Cell cycle control of microRNA-mediated translation regulation. Cell Cycle 2008, 7: 1545-1549. PMID: 18469529, PMCID: PMC2556257, DOI: 10.4161/cc.7.11.6018.Peer-Reviewed Original Research
2007
U2 snRNP Binds Intronless Histone Pre-mRNAs to Facilitate U7-snRNP-Dependent 3′ End Formation
Friend K, Lovejoy AF, Steitz JA. U2 snRNP Binds Intronless Histone Pre-mRNAs to Facilitate U7-snRNP-Dependent 3′ End Formation. Molecular Cell 2007, 28: 240-252. PMID: 17964263, PMCID: PMC2149891, DOI: 10.1016/j.molcel.2007.09.026.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceCell NucleusDEAD-box RNA HelicasesHeLa CellsHistonesHumansIntronsMiceModels, MolecularOocytesProtein ConformationRibonucleoprotein, U2 Small NuclearRibonucleoprotein, U7 Small NuclearRibonucleoproteins, Small NuclearRNA 3' End ProcessingRNA PrecursorsRNA-Binding ProteinsRNA, MessengerTime FactorsXenopus laevis
2006
A Spliceosomal Intron Binding Protein, IBP160, Links Position-Dependent Assembly of Intron-Encoded Box C/D snoRNP to Pre-mRNA Splicing
Hirose T, Ideue T, Nagai M, Hagiwara M, Shu MD, Steitz JA. A Spliceosomal Intron Binding Protein, IBP160, Links Position-Dependent Assembly of Intron-Encoded Box C/D snoRNP to Pre-mRNA Splicing. Molecular Cell 2006, 23: 673-684. PMID: 16949364, DOI: 10.1016/j.molcel.2006.07.011.Peer-Reviewed Original ResearchEpstein-Barr virus noncoding RNAs are confined to the nucleus, whereas their partner, the human La protein, undergoes nucleocytoplasmic shuttling
Fok V, Friend K, Steitz JA. Epstein-Barr virus noncoding RNAs are confined to the nucleus, whereas their partner, the human La protein, undergoes nucleocytoplasmic shuttling. Journal Of Cell Biology 2006, 173: 319-325. PMID: 16682524, PMCID: PMC2063832, DOI: 10.1083/jcb.200601026.Peer-Reviewed Original ResearchMeSH KeywordsActive Transport, Cell NucleusAnimalsAntibiotics, AntineoplasticAutoantigensCell LineCell Line, TumorCell NucleusDactinomycinFatty Acids, UnsaturatedFemaleHeLa CellsHerpesvirus 4, HumanHumansKaryopherinsMiceNIH 3T3 CellsOocytesProtein BindingRibonucleoproteinsRNA TransportRNA, UntranslatedRNA, ViralXenopus laevisIn vivo assembly of functional U7 snRNP requires RNA backbone flexibility within the Sm-binding site
Kolev NG, Steitz JA. In vivo assembly of functional U7 snRNP requires RNA backbone flexibility within the Sm-binding site. Nature Structural & Molecular Biology 2006, 13: 347-353. PMID: 16547514, DOI: 10.1038/nsmb1075.Peer-Reviewed Original Research
2005
An embryonic poly(A)-binding protein (ePAB) is expressed in mouse oocytes and early preimplantation embryos
Seli E, Lalioti MD, Flaherty SM, Sakkas D, Terzi N, Steitz JA. An embryonic poly(A)-binding protein (ePAB) is expressed in mouse oocytes and early preimplantation embryos. Proceedings Of The National Academy Of Sciences Of The United States Of America 2005, 102: 367-372. PMID: 15630085, PMCID: PMC544294, DOI: 10.1073/pnas.0408378102.Peer-Reviewed Original ResearchConceptsZygotic gene activationGene activationEarly embryosSomatic cellsTranslational activationGene expressionEmbryo developmentEarly preimplantation embryo developmentEarly Xenopus developmentEarly preimplantation embryosEight-cell stageEarly embryo developmentPreimplantation embryo developmentTwo-cell embryosCytoplasmic PABPMouse orthologXenopus developmentMammalian oocytesProphase ISomatic tissuesChromosome 2Preimplantation embryosEPABMouse oocytesOne-cell
2004
Evidence for reassociation of RNA-binding proteins after cell lysis: Implications for the interpretation of immunoprecipitation analyses
Mili S, Steitz JA. Evidence for reassociation of RNA-binding proteins after cell lysis: Implications for the interpretation of immunoprecipitation analyses. RNA 2004, 10: 1692-1694. PMID: 15388877, PMCID: PMC1370654, DOI: 10.1261/rna.7151404.Peer-Reviewed Original Research
2001
Communication of the Position of Exon-Exon Junctions to the mRNA Surveillance Machinery by the Protein RNPS1
Lykke-Andersen J, Shu M, Steitz J. Communication of the Position of Exon-Exon Junctions to the mRNA Surveillance Machinery by the Protein RNPS1. Science 2001, 293: 1836-1839. PMID: 11546874, DOI: 10.1126/science.1062786.Peer-Reviewed Original ResearchMeSH Keywords3' Untranslated RegionsAnimalsCell LineDNA-Binding ProteinsExonsFungal ProteinsGlobinsHeLa CellsHumansMacromolecular SubstancesMiceModels, BiologicalPrecipitin TestsProtein BindingRecombinant Fusion ProteinsRibonucleoproteinsRNA HelicasesRNA SplicingRNA-Binding ProteinsRNA, MessengerSaccharomyces cerevisiae ProteinsTrans-ActivatorsTransfectionConceptsNonsense-mediated decayExon-exon junctionsMRNA surveillanceMRNA quality controlMRNA surveillance machinerySelective nuclear exportBeta-globin mRNAPremature termination codonUpf complexMature mRNASurveillance machineryNuclear exportAberrant mRNAsMammalian cellsTermination codonUntranslated regionSplice junctionsRNPS1MRNADual roleCentral componentComplexesCodonSubunitsMachinery
1998
HNS, a nuclear-cytoplasmic shuttling sequence in HuR
Fan X, Steitz J. HNS, a nuclear-cytoplasmic shuttling sequence in HuR. Proceedings Of The National Academy Of Sciences Of The United States Of America 1998, 95: 15293-15298. PMID: 9860962, PMCID: PMC28036, DOI: 10.1073/pnas.95.26.15293.Peer-Reviewed Original ResearchMeSH Keywords3T3 CellsAmino Acid SequenceAnimalsAntigens, SurfaceCell NucleusConserved SequenceCytoplasmELAV ProteinsELAV-Like Protein 1HeLa CellsHeterogeneous-Nuclear Ribonucleoprotein KHumansMiceMolecular Sequence DataRecombinant ProteinsRibonucleoproteinsRNA-Binding ProteinsRNA, MessengerSequence AlignmentSequence Homology, Amino AcidTransfectionXenopusConceptsHeterogeneous nuclear ribonucleoprotein KNuclear localization signal activityClassical nuclear localization signalAU-rich element-containing mRNAsExport of mRNAHeterogeneous nuclear ribonucleoprotein A1Nuclear export signalNuclear localization signalNuclear transport processRNA-binding proteinAU-rich elementsExport signalLocalization signalM9 sequenceNuclear poresDomain sequencesCytoplasmic compartmentUntranslated regionLabile mRNAsCell nucleiSpecific signalsHuRProteinBidirectional transportMRNAClassification 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 featureRibosomesRRNAFamilyModification 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 laevisOverexpression of HuR, a nuclear–cytoplasmic shuttling protein, increases the in vivo stability of ARE‐containing mRNAs
Fan X, Steitz J. Overexpression of HuR, a nuclear–cytoplasmic shuttling protein, increases the in vivo stability of ARE‐containing mRNAs. The EMBO Journal 1998, 17: 3448-3460. PMID: 9628880, PMCID: PMC1170681, DOI: 10.1093/emboj/17.12.3448.Peer-Reviewed Original ResearchConceptsAU-rich elementsOverexpression of HuRUntranslated regionRNA recognition motif 3Beta-globin reporter mRNAClass II AU-rich elementsAnti-HuR antibodyMouse L929 cellsMRNA decayELAV familyVivo decay ratesDeletion mutantsReporter mRNAL929 cellsMotif 3HuR functionMRNA stabilityCytoplasmic compartmentRNA sequencesRRMs 3HuR proteinVivo roleMessenger RNAHuRHuR antibody
1997
Identification 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-Binding ProteinsRNA, MessengerUltraviolet RaysConceptsAU-rich elementsMRNA decayUntranslated regionRNA-binding specificityARE-binding proteinsHeLa nuclear extractsGene familyMRNA degradationNuclear extractsEssential signalMessenger RNAProteinSequence's abilityHuRAUUUARapid degradationCritical roleHuR.RNAMachineryMRNADegradationRegulationSubsequent analysisExpression
1996
Length suppression in histone messenger RNA 3′-end maturation: Processing defects of insertion mutant premessenger RNAs can be compensated by insertions into the U7 small nuclear RNA
Scharl E, Steitz J. Length suppression in histone messenger RNA 3′-end maturation: Processing defects of insertion mutant premessenger RNAs can be compensated by insertions into the U7 small nuclear RNA. Proceedings Of The National Academy Of Sciences Of The United States Of America 1996, 93: 14659-14664. PMID: 8962110, PMCID: PMC26191, DOI: 10.1073/pnas.93.25.14659.Peer-Reviewed Original ResearchConceptsHistone downstream elementU7 RNAHistone messenger RNASmall nuclear RNARNA processing systemSmall ribonucleoproteinPremessenger RNANuclear RNAPre-mRNAU7 small nuclear RNADownstream elementsCleavage siteRNAMessenger RNAXenopus oocytesBase pairingProcessing defectsU7First demonstrationHistonesRNAsRibonucleoproteinInsertionMRNASitesA 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