2021
tRNA-like leader-trailer interaction promotes 3′-end maturation of MALAT1
Torabi SF, DeGregorio SJ, Steitz JA. tRNA-like leader-trailer interaction promotes 3′-end maturation of MALAT1. RNA 2021, 27: 1140-1147. PMID: 34253686, PMCID: PMC8457004, DOI: 10.1261/rna.078810.121.Peer-Reviewed Original Research
2016
Myriad Triple-Helix-Forming Structures in the Transposable Element RNAs of Plants and Fungi
Tycowski KT, Shu MD, Steitz JA. Myriad Triple-Helix-Forming Structures in the Transposable Element RNAs of Plants and Fungi. Cell Reports 2016, 15: 1266-1276. PMID: 27134163, PMCID: PMC4864102, DOI: 10.1016/j.celrep.2016.04.010.Peer-Reviewed Original ResearchConceptsTransposable elementsCellular noncoding RNAsPotential evolutionary consequencesCis-acting RNA structuresIntron lossEvolutionary consequencesBioinformatic identificationTE transcriptsReporter transcriptFish speciesNoncoding RNAsElement RNAHorizontal transferRNA structureTransposase geneRich tractHuman cellsTriple helix formationBase triplesRNAEne coreTranscriptsTriple helixIntronlessGenome
2015
EBV Noncoding RNA Binds Nascent RNA to Drive Host PAX5 to Viral DNA
Lee N, Moss WN, Yario TA, Steitz JA. EBV Noncoding RNA Binds Nascent RNA to Drive Host PAX5 to Viral DNA. Cell 2015, 160: 607-618. PMID: 25662012, PMCID: PMC4329084, DOI: 10.1016/j.cell.2015.01.015.Peer-Reviewed Original ResearchConceptsTerminal repeatNascent RNANoncoding RNAsNuclear noncoding RNAB-cell transcription factor PAX5Greater sequence divergenceDNA target sitesTranscription factor Pax5Chromatin localizationTR lociSequence divergenceNascent transcriptsUndescribed functionTranscription factorsLatent EBV genomeRNATarget siteEssential rolePrimate herpesvirusesEBV lytic replicationPAX5Lytic replicationViral DNAEBER2Viral replication
2014
Virus Meets Host MicroRNA: the Destroyer, the Booster, the Hijacker
Guo YE, Steitz JA. Virus Meets Host MicroRNA: the Destroyer, the Booster, the Hijacker. Molecular And Cellular Biology 2014, 34: 3780-3787. PMID: 25047834, PMCID: PMC4187717, DOI: 10.1128/mcb.00871-14.Peer-Reviewed Original ResearchConceptsKey regulatory stepSmall noncoding RNAsVirus-host interactionsViral life cycleNoncoding RNAsCellular miRNAsMiRNA interactionsRegulatory stepGene expressionProtein productionHost microRNAsRNA virusesRecent discoveryLife cycleMicroRNAsMiRNAsRNADNAMRNAVirusExpressionInteractionMinireviewDiscoveryStructural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix
Brown JA, Bulkley D, Wang J, Valenstein ML, Yario TA, Steitz TA, Steitz JA. Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix. Nature Structural & Molecular Biology 2014, 21: 633-640. PMID: 24952594, PMCID: PMC4096706, DOI: 10.1038/nsmb.2844.Peer-Reviewed Original Research3′-Biotin-tagged microRNA-27 does not associate with Argonaute proteins in cells
Guo YE, Steitz JA. 3′-Biotin-tagged microRNA-27 does not associate with Argonaute proteins in cells. RNA 2014, 20: 985-988. PMID: 24821854, PMCID: PMC4114695, DOI: 10.1261/rna.045054.114.Peer-Reviewed Original ResearchAlternative Capture of Noncoding RNAs or Protein-Coding Genes by Herpesviruses to Alter Host T Cell Function
Guo YE, Riley KJ, Iwasaki A, Steitz JA. Alternative Capture of Noncoding RNAs or Protein-Coding Genes by Herpesviruses to Alter Host T Cell Function. Molecular Cell 2014, 54: 67-79. PMID: 24725595, PMCID: PMC4039351, DOI: 10.1016/j.molcel.2014.03.025.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntigens, CDAntigens, Differentiation, T-LymphocyteBase SequenceCallithrixEnzyme ActivationGene Expression RegulationGPI-Linked ProteinsGRB2 Adaptor ProteinHEK293 CellsHerpesvirus 2, SaimiriineHigh-Throughput Nucleotide SequencingHost-Pathogen InteractionsHumansImmunoprecipitationInterferon-gammaJurkat CellsLectins, C-TypeLymphocyte ActivationMicroRNAsMitogen-Activated Protein KinasesMolecular Sequence DataReceptors, Antigen, T-CellRNA StabilityRNA, UntranslatedRNA, ViralSemaphorinsSequence Analysis, RNASignal TransductionT-LymphocytesTime FactorsTransfectionConceptsMitogen-activated protein kinaseMiR-27Protein coding genesHerpesvirus saimiriHigh-throughput sequencingTCR-induced activationCell functionHSUR 1Γ-herpesvirusesNoncoding RNAsProtein kinaseEctopic expressionOncogenic γ-herpesvirusesTarget genesInduction of CD69MicroRNA-27Key modulatorRNACommon targetAlHV-1GenesCell receptorDiverse strategiesHost T-cell functionCells
2013
RNA families in Epstein–Barr virus
Moss WN, Lee N, Pimienta G, Steitz JA. RNA families in Epstein–Barr virus. RNA Biology 2013, 11: 10-17. PMID: 24441309, PMCID: PMC3929418, DOI: 10.4161/rna.27488.Peer-Reviewed Original ResearchConceptsEpstein-Barr virusFunctional importanceSmall regulatory RNAsNovel Epstein-Barr virusSmall nucleolar RNAsLikely functional importanceInternal ribosomal entry siteRNA-seq studiesHuman γ-herpesvirusEvolutionary conservationNovel ncRNARegulatory RNAsShort intronsRecent bioinformaticsNucleolar RNAsOncogenic typesRNA familiesTumorigenic phenotypeStructured RNAsEBV genomeEBNA1 mRNARepetitive regionsViral latencyHigh abundanceLatency maintenanceMammalian 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 microRNAMiRNAsMicroRNAsPathwayMicroRNPsGenome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA
Moss WN, Steitz JA. Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA. BMC Genomics 2013, 14: 543. PMID: 23937650, PMCID: PMC3751371, DOI: 10.1186/1471-2164-14-543.Peer-Reviewed Original ResearchConceptsStable intronic sequence RNARNA structureSequence RNAComprehensive genome-wide surveyGenome-wide surveyGenome-wide analysisRNA-seq analysisComparative sequence analysisNon-coding RNAsSecondary structure modelRNA-seq dataRNAz programFunctional RNAsGenomic sequencesImportant human pathogenSequence analysisRNAEBV transcriptomeHuman pathogensHerpesvirus 4Future experimental analysisPotential functionTranscriptomeGenomeEBV genome
2012
Formation of triple-helical structures by the 3′-end sequences of MALAT1 and MENβ noncoding RNAs
Brown JA, Valenstein ML, Yario TA, Tycowski KT, Steitz JA. Formation of triple-helical structures by the 3′-end sequences of MALAT1 and MENβ noncoding RNAs. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 19202-19207. PMID: 23129630, PMCID: PMC3511071, DOI: 10.1073/pnas.1217338109.Peer-Reviewed Original ResearchConceptsRich internal loopMetastasis-associated lung adenocarcinoma transcript 1Rich tractSarcoma-associated herpesvirusDuplex-triplex junctionsTriple helical structureCellular noncoding RNAsNuclear retention elementBase triplesInternal loopKaposi's sarcoma-associated herpesvirusU base triplesPAN RNATriple helixNoncoding RNAsNuclear RNAThermal denaturation profilesReporter RNALung adenocarcinoma transcript 1C nucleotidesC base pairsMolecular mechanismsUnpaired nucleotidesBase pairsRNAConservation of a Triple-Helix-Forming RNA Stability Element in Noncoding and Genomic RNAs of Diverse Viruses
Tycowski KT, Shu MD, Borah S, Shi M, Steitz JA. Conservation of a Triple-Helix-Forming RNA Stability Element in Noncoding and Genomic RNAs of Diverse Viruses. Cell Reports 2012, 2: 26-32. PMID: 22840393, PMCID: PMC3430378, DOI: 10.1016/j.celrep.2012.05.020.Peer-Reviewed Original ResearchConceptsPAN RNAKaposi's sarcoma-associated herpesvirusSarcoma-associated herpesvirusStructure-based bioinformaticsRNA decay pathwaysDiverse viral genomesRNA stability elementNuclear retention elementPositive-strand RNA virusesReporter transcriptMammalian herpesvirusesGenomic RNAStability elementDNA virusesHuman cellsTriple helix formationRNA virusesDiverse virusesViral genomeRNAAbundant expressionDecay pathwaysTriple helixRetention elementsRapid identification
2011
A Primate Herpesvirus Uses the Integrator Complex to Generate Viral MicroRNAs
Cazalla D, Xie M, Steitz JA. A Primate Herpesvirus Uses the Integrator Complex to Generate Viral MicroRNAs. Molecular Cell 2011, 43: 982-992. PMID: 21925386, PMCID: PMC3176678, DOI: 10.1016/j.molcel.2011.07.025.Peer-Reviewed Original ResearchConceptsEnd processing signalsHerpesvirus saimiriMature viral miRNAsPre-miRNA hairpinsCis-acting elementsMarmoset T cellsIntegrator complexAGO proteinsMiRNA biogenesisMicroprocessor complexU RNAExportin-5Noncoding RNAsViral miRNAsProcessing assaysHost miRNAsDeep sequencingViral noncoding RNAsProtein componentsComplex cleavesHairpin structureHSURsPrimate herpesvirusesMiRNAsRNA
2010
miR-29 and miR-30 regulate B-Myb expression during cellular senescence
Martinez I, Cazalla D, Almstead LL, Steitz JA, DiMaio D. miR-29 and miR-30 regulate B-Myb expression during cellular senescence. Proceedings Of The National Academy Of Sciences Of The United States Of America 2010, 108: 522-527. PMID: 21187425, PMCID: PMC3021067, DOI: 10.1073/pnas.1017346108.Peer-Reviewed Original ResearchConceptsB-myb expressionCellular senescenceMiR-30MiR-29Reporter constructsEndogenous B-MybMajor tumor suppressor mechanismTumor suppressor mechanismIrreversible growth arrestMicroRNA familiesMutant 3'UTRCellular DNA synthesisB-MybReplicative senescenceCompensatory mutationsGrowth arrestMutant sitesRb pathwaySenescenceSuppressor mechanismDNA synthesisRepressionInhibits senescenceExpressionMutationsDown-Regulation of a Host microRNA by a Viral Noncoding RNA
Cazalla D, Steitz JA. Down-Regulation of a Host microRNA by a Viral Noncoding RNA. Cold Spring Harbor Symposia On Quantitative Biology 2010, 75: 321-324. PMID: 21139068, PMCID: PMC5647998, DOI: 10.1101/sqb.2010.75.009.Peer-Reviewed Original ResearchConceptsHerpesvirus saimiriNoncoding RNAsHost cell gene expressionMiR-27Binding-dependent mannerAU-rich elementsViral noncoding RNAMarmoset T cellsMiRNA pathwayHost cell microRNAsViral life cycleConserved sequencesEctopic expressionMammalian virusesTarget genesTransient knockdownMutational analysisGene expressionHost microRNAsHSUR1Viral strategiesBase pairingDown regulationPrimate herpesvirusesLytic phase
2009
A Conserved WD40 Protein Binds the Cajal Body Localization Signal of scaRNP Particles
Tycowski KT, Shu MD, Kukoyi A, Steitz JA. A Conserved WD40 Protein Binds the Cajal Body Localization Signal of scaRNP Particles. Molecular Cell 2009, 34: 47-57. PMID: 19285445, PMCID: PMC2700737, DOI: 10.1016/j.molcel.2009.02.020.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAnimalsBase SequenceCell LineChromatography, AffinityCoiled BodiesDrosophila melanogasterDrosophila ProteinsHeLa CellsHumansMolecular Sequence DataNucleic Acid ConformationRecombinant Fusion ProteinsRegulatory Sequences, Ribonucleic AcidRibonucleoproteinsRNA-Binding ProteinsSequence AlignmentConceptsCAB boxCB localizationSmall Cajal bodyWD40 proteinsRNP functionCajal bodiesLocalization signalACA motifDomain RNATelomerase RNAHuman homologPosttranscriptional modificationsSmall nuclearWDR79ScaRNAsRNA elementsCentral playerUV crosslinkNuclear RNPCore proteinRNAProteinAdditional interactionsBindingLocalization
2008
Conserved motifs in both CPSF73 and CPSF100 are required to assemble the active endonuclease for histone mRNA 3′‐end maturation
Kolev NG, Yario TA, Benson E, Steitz JA. Conserved motifs in both CPSF73 and CPSF100 are required to assemble the active endonuclease for histone mRNA 3′‐end maturation. EMBO Reports 2008, 9: 1013-1018. PMID: 18688255, PMCID: PMC2572124, DOI: 10.1038/embor.2008.146.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAmino Acid SequenceBase SequenceCell LineCleavage And Polyadenylation Specificity FactorConserved SequenceEndonucleasesEnzyme ActivationHeLa CellsHistonesHumansMolecular Sequence DataProtein Structure, TertiaryProtein SubunitsRNA 3' End ProcessingRNA PrecursorsRNA, MessengerConceptsPre-messenger RNAPolyadenylation specificity factorMammalian proteinsRNase ZConserved motifsHistone mRNASpecificity factorEndonucleolytic cleavageActive endonucleaseEndonuclease activityMBL familyComplex machineryMessenger RNAPoint mutationsCPSF73CPSF100Process of maturationMaturation processRNAProteinMotifMRNAMaturationEukaryotesCleavage
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 laevisMutational analysis of a viral RNA element that counteracts rapid RNA decay by interaction with the polyadenylate tail
Conrad NK, Shu MD, Uyhazi KE, Steitz JA. Mutational analysis of a viral RNA element that counteracts rapid RNA decay by interaction with the polyadenylate tail. Proceedings Of The National Academy Of Sciences Of The United States Of America 2007, 104: 10412-10417. PMID: 17563387, PMCID: PMC1965527, DOI: 10.1073/pnas.0704187104.Peer-Reviewed Original ResearchTarget mRNAs are repressed as efficiently by microRNA-binding sites in the 5′ UTR as in the 3′ UTR
Lytle JR, Yario TA, Steitz JA. Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5′ UTR as in the 3′ UTR. Proceedings Of The National Academy Of Sciences Of The United States Of America 2007, 104: 9667-9672. PMID: 17535905, PMCID: PMC1887587, DOI: 10.1073/pnas.0703820104.Peer-Reviewed Original ResearchConceptsInternal ribosome entry siteTarget mRNAsMiRNA-mediated repressionRepression of translationLuciferase reporter mRNAMiRNA target sitesInitiation of translationMiRNA-binding sitesHuman HeLa cellsRibosome entry siteMicroRNA-binding sitesLet-7 complementary sitesHuman Ago2Reporter mRNAMicroRNAs (miRNAs) bindEndogenous mRNATranslational efficiencyLet-7a miRNAUTRProtein synthesisDNA transfectionComplementary sitesHeLa cellsEntry siteTarget site