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 ResearchRNA stabilization by a poly(A) tail 3′-end binding pocket and other modes of poly(A)-RNA interaction
Torabi SF, Vaidya AT, Tycowski KT, DeGregorio SJ, Wang J, Shu MD, Steitz TA, Steitz JA. RNA stabilization by a poly(A) tail 3′-end binding pocket and other modes of poly(A)-RNA interaction. Science 2021, 371 PMID: 33414189, PMCID: PMC9491362, DOI: 10.1126/science.abe6523.Peer-Reviewed Original ResearchMeSH KeywordsCrystallizationNucleic Acid ConformationOryzaPoly APolyadenylationRNA StabilityRNA, Messenger
2019
Structural Basis for Target-Directed MicroRNA Degradation
Sheu-Gruttadauria J, Pawlica P, Klum SM, Wang S, Yario TA, Schirle Oakdale NT, Steitz JA, MacRae IJ. Structural Basis for Target-Directed MicroRNA Degradation. Molecular Cell 2019, 75: 1243-1255.e7. PMID: 31353209, PMCID: PMC6754277, DOI: 10.1016/j.molcel.2019.06.019.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsArgonaute ProteinsHEK293 CellsHumansMicroRNAsNucleic Acid ConformationRNA StabilitySf9 CellsSpodopteraConceptsTarget-directed miRNA degradationMiRNA 3' endMicroRNA degradationMiRNA degradationHuman Ago2MiRNA activityMiRNA stabilityStructural basisGene expressionTarget RNALinker flexibilityMiRNAsEnd displaysFlexible linkerRNAKey determinantArgonauteHAgo2Enzymatic attackAgo2DegradationDuplexMicroRNAsMiRNAIsoforms
2016
Methyltransferase-like protein 16 binds the 3′-terminal triple helix of MALAT1 long noncoding RNA
Brown JA, Kinzig CG, DeGregorio SJ, Steitz JA. Methyltransferase-like protein 16 binds the 3′-terminal triple helix of MALAT1 long noncoding RNA. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 14013-14018. PMID: 27872311, PMCID: PMC5150381, DOI: 10.1073/pnas.1614759113.Peer-Reviewed Original ResearchMeSH KeywordsHEK293 CellsHeLa CellsHumansMethyltransferasesNucleic Acid ConformationRNA FoldingRNA StabilityRNA, Long NoncodingConceptsGel shift assaysMetastasis-associated lung adenocarcinoma transcript 1RNA triple helicesPutative RNA methyltransferaseCompetitive gel shift assaysRNA-protein interactionsRNA stability elementAbundant nuclear proteinNative gel shift assaysRich internal loopSitu proximity ligation assayTriple helixHEK293T cell lysatesStem-loop structureProximity ligation assayT cell lysatesRNA methyltransferaseVivo UVNucleotide compositionNuclear proteinsLung adenocarcinoma transcript 1RNA immunoprecipitationStability elementMETTL16Rich tractIntronless β-Globin Reporter: A Tool for Studying Nuclear RNA Stability Elements
Brown JA, Steitz JA. Intronless β-Globin Reporter: A Tool for Studying Nuclear RNA Stability Elements. Methods In Molecular Biology 2016, 1428: 77-92. PMID: 27236793, PMCID: PMC5547891, DOI: 10.1007/978-1-4939-3625-0_5.Peer-Reviewed Original ResearchMeSH KeywordsBeta-GlobinsCell NucleusCloning, MolecularGenes, ReporterHEK293 CellsHumansIntronsNucleic Acid ConformationRNA StabilityRNA, MessengerMyriad 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
A heterotrimer model of the complete Microprocessor complex revealed by single-molecule subunit counting
Herbert KM, Sarkar SK, Mills M, De la Herran H, Neuman KC, Steitz JA. A heterotrimer model of the complete Microprocessor complex revealed by single-molecule subunit counting. RNA 2015, 22: 175-183. PMID: 26683315, PMCID: PMC4712668, DOI: 10.1261/rna.054684.115.Peer-Reviewed Original ResearchConceptsPri-miRNA substratesMicroprocessor complexHeterotrimeric complexDeletion constructsSingle-molecule subunit countingRNA-binding proteinFull-length proteinAbsence of RNAStem-loop structureSingle-molecule photobleachingSize exclusion chromatographyPresence of RNARNaseIII enzymesPhotobleaching assaysMicroRNA biogenesisSubunit countingMammalian cellsDroshaDGCR8Fluorescent proteinHuman cellsMultiple copiesRNAProteinExact stoichiometryIn silico discovery and modeling of non-coding RNA structure in viruses
Moss WN, Steitz JA. In silico discovery and modeling of non-coding RNA structure in viruses. Methods 2015, 91: 48-56. PMID: 26116541, PMCID: PMC4684774, DOI: 10.1016/j.ymeth.2015.06.015.Peer-Reviewed Original ResearchMeSH KeywordsComputer SimulationHerpesvirus 4, HumanInfluenza A virusNucleic Acid ConformationRNA, UntranslatedRNA, ViralEBV 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
Structural 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 ResearchMeSH KeywordsBase PairingBase SequenceCrystallography, X-RayHumansHydrogen BondingMolecular Sequence DataNucleic Acid ConformationRNA StabilityRNA, Long Noncoding
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
Poly(A) Tail Recognition by a Viral RNA Element Through Assembly of a Triple Helix
Mitton-Fry RM, DeGregorio SJ, Wang J, Steitz TA, Steitz JA. Poly(A) Tail Recognition by a Viral RNA Element Through Assembly of a Triple Helix. Science 2010, 330: 1244-1247. PMID: 21109672, PMCID: PMC3074936, DOI: 10.1126/science.1195858.Peer-Reviewed Original ResearchConceptsSarcoma-associated herpesvirusBox H/ACA small nucleolar RNAsMajor-groove triple helixNuclear noncoding RNANuclear retention elementSmall nucleolar RNAsViral RNA elementsRich internal loopTriple helixKaposi's sarcoma-associated herpesvirusPAN RNADeadenylation assaysRNA decayRNA clampNucleolar RNAsNoncoding RNAsNuclear RNATail recognitionRNA elementsFunctional importanceAngstrom resolutionRich loopSecondary structureRNAEne coreNoncoding RNPs of Viral Origin
Steitz J, Borah S, Cazalla D, Fok V, Lytle R, Mitton-Fry R, Riley K, Samji T. Noncoding RNPs of Viral Origin. Cold Spring Harbor Perspectives In Biology 2010, 3: a005165. PMID: 20719877, PMCID: PMC3039937, DOI: 10.1101/cshperspect.a005165.Peer-Reviewed Original ResearchMeSH KeywordsAdenoviridaeBase PairingHerpesvirus 2, SaimiriineHerpesvirus 4, HumanHerpesvirus 8, HumanMicroRNAsNucleic Acid ConformationRibonucleoproteinsRNA, UntranslatedRNA, Viral
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 interactionsBindingLocalizationSubnuclear compartmentalization of transiently expressed polyadenylated pri-microRNAs: Processing at transcription sites or accumulation in SC35 foci
Pawlicki JM, Steitz JA. Subnuclear compartmentalization of transiently expressed polyadenylated pri-microRNAs: Processing at transcription sites or accumulation in SC35 foci. Cell Cycle 2009, 8: 345-356. PMID: 19177009, PMCID: PMC3004524, DOI: 10.4161/cc.8.3.7494.Peer-Reviewed Original ResearchConceptsPri-miRNA processingPri-miRNAsTranscription sitesPrimary miRNA transcriptsPri-miRNA transcriptsPre-miRNA hairpinsRNA polymerase IIASF/SF2Splicing factor SC35Target messenger RNAsNumber of proteinsMiRNA biogenesisMiRNA transcriptsNuclear organizationMRNA metabolismPolymerase IINuclear fociProlyl isomeraseFactor SC35Subnuclear compartmentalizationPri-microRNAsMammalian cellsSC35 domainsGene expressionSC35
2008
Flexibility in the site of exon junction complex deposition revealed by functional group and RNA secondary structure alterations in the splicing substrate
Mishler DM, Christ AB, Steitz JA. Flexibility in the site of exon junction complex deposition revealed by functional group and RNA secondary structure alterations in the splicing substrate. RNA 2008, 14: 2657-2670. PMID: 18952819, PMCID: PMC2590960, DOI: 10.1261/rna.1312808.Peer-Reviewed Original ResearchMeSH KeywordsEukaryotic Initiation Factor-4AHeLa CellsHumansNucleic Acid ConformationRiboseRNA Splice SitesRNA SplicingRNA, MessengerConceptsExon junction complexRNA secondary structureEJC depositionSplicing substrateMammalian nonsense-mediated mRNA decayNonsense-mediated mRNA decaySecondary structureStretches of DNATranslational regulationMRNA decayCoimmunoprecipitation assaysJunction complexSecondary structure alterationsDNA nucleotidesStructure alterationsH protectionUpstream shiftToeprintingExonsSitesNucleotidesDNACrystal structureDeposition sitesMRNA
2007
Mutational 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 Research
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 Research