2021
Who let the DoGs out? – biogenesis of stress-induced readthrough transcripts
Rosa-Mercado NA, Steitz JA. Who let the DoGs out? – biogenesis of stress-induced readthrough transcripts. Trends In Biochemical Sciences 2021, 47: 206-217. PMID: 34489151, PMCID: PMC8840951, DOI: 10.1016/j.tibs.2021.08.003.Peer-Reviewed Original ResearchConceptsCellular stress responseHuman protein-coding genesStress responseProtein-coding genesDoG inductionNascent mRNAReadthrough transcriptionTranscriptional landscapeDifferent stress conditionsReadthrough transcriptsStress conditionsViral proteinsBiogenesisStress removalGenesTranscriptsCell exposureProduction playTranscriptionRNAProteinMRNAHostProductionHallmark
2019
Quantitative Fluorescence In Situ Hybridization (FISH) and Immunofluorescence (IF) of Specific Gene Products in KSHV-Infected Cells.
Vallery TK, Steitz JA. Quantitative Fluorescence In Situ Hybridization (FISH) and Immunofluorescence (IF) of Specific Gene Products in KSHV-Infected Cells. Journal Of Visualized Experiments 2019 PMID: 31524859, PMCID: PMC6750728, DOI: 10.3791/59697.Peer-Reviewed Original ResearchConceptsRNA FISHSarcoma-associated herpesvirusSpecific RNAViral replication compartmentsSpecific gene productsSitu hybridizationKaposi's sarcoma-associated herpesvirusMultiple cell typesReplication compartmentsGene productsViral genesHost cellsCell typesQuantitative fluorescenceNuclear factoriesFishCell morphologyHuman hostMechanistic insightsSpatiotemporal activityUninfected cellsBehavior of biomoleculesRNAProteinCellsStructural 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 ResearchConceptsTarget-directed miRNA degradationMiRNA 3' endMicroRNA degradationMiRNA degradationHuman Ago2MiRNA activityMiRNA stabilityStructural basisGene expressionTarget RNALinker flexibilityMiRNAsEnd displaysFlexible linkerRNAKey determinantArgonauteHAgo2Enzymatic attackAgo2DegradationDuplexMicroRNAsMiRNAIsoformsHow Complementary Targets Expose the microRNA 3′ End for Tailing and Trimming during Target-Directed microRNA Degradation
Pawlica P, Sheu-Gruttadauria J, MacRae IJ, Steitz JA. How Complementary Targets Expose the microRNA 3′ End for Tailing and Trimming during Target-Directed microRNA Degradation. Cold Spring Harbor Symposia On Quantitative Biology 2019, 84: 039321. PMID: 32019864, PMCID: PMC9161719, DOI: 10.1101/sqb.2019.84.039321.Peer-Reviewed Original ResearchTarget-directed miRNA degradationMiRNA 3' endCellular enzymesMiRNA seed sequencesMiRNA complementarityMiRNA decayArgonaute proteinsMicroRNA degradationMiRNA degradationMiRNA 5Posttranscriptional regulationMiRNA targetsCertain transcriptsSeed sequenceExtensive complementarityMolecular mechanismsMessenger RNATranscriptsEnzymeRegulationEnzymatic attackRecent advancesTargetMicroRNAsRNA
2018
Immunoprecipitation of Tri-methylated Capped RNA.
Hayes KE, Barr JA, Xie M, Steitz JA, Martinez I. Immunoprecipitation of Tri-methylated Capped RNA. Bio-protocol 2018, 8 PMID: 29527542, PMCID: PMC5842925, DOI: 10.21769/bioprotoc.2717.Peer-Reviewed Original ResearchPri-miRNAsCellular quiescenceAlternative miRNA biogenesis pathwaysMiRNA biogenesis pathwayNon-coding RNAsBiogenesis pathwayDNA replicationTotal RNA extractsRNA immunoprecipitationOrgan regenerationRNA extractsFibroblast cellsImmunoprecipitationRNASpecific isolationProteinQuiescenceWound healingImportant roleTrimethylguanosineMicroRNAsAutophagyCytoplasmP27Pathway
2017
Settling the m6A debate: methylation of mature mRNA is not dynamic but accelerates turnover
Rosa-Mercado NA, Withers JB, Steitz JA. Settling the m6A debate: methylation of mature mRNA is not dynamic but accelerates turnover. Genes & Development 2017, 31: 957-958. PMID: 28637691, PMCID: PMC5495124, DOI: 10.1101/gad.302695.117.Peer-Reviewed Original ResearchConceptsPre-mRNA splicing eventsPost-transcriptional modificationsMRNA biogenesisDifferent subcellular fractionsMRNA biologySplicing eventsMature mRNABiochemical approachesRNA transcriptsPivotal regulatorMethylation levelsHeLa cellsSubcellular fractionsRNA nucleosidesMethylationTranscriptsBiogenesisChromatinSplicingMethyladenosineExonsGenesRNABiologyRegulator
2016
A proximity-dependent assay for specific RNA–protein interactions in intact cells
Zhang W, Xie M, Shu MD, Steitz JA, DiMaio D. A proximity-dependent assay for specific RNA–protein interactions in intact cells. RNA 2016, 22: 1785-1792. PMID: 27659050, PMCID: PMC5066630, DOI: 10.1261/rna.058248.116.Peer-Reviewed Original ResearchConceptsRNA-protein interactionsSpecific RNA-protein interactionsProximity ligation assayTarget RNAProtein-protein interactionsSame cellular compartmentCellular compartmentsRNA targetsIntact cellsLigation assayRNADiscrete compartmentsProteinDNA oligonucleotideFluorescent signalOligonucleotide complementaryCellsCompartmentsAssaysColocalizationHigh specificityInteractionStaining methodOligonucleotideAdaptationHost miRNA degradation by Herpesvirus saimiri small nuclear RNA requires an unstructured interacting region
Pawlica P, Moss WN, Steitz JA. Host miRNA degradation by Herpesvirus saimiri small nuclear RNA requires an unstructured interacting region. RNA 2016, 22: 1181-1189. PMID: 27335146, PMCID: PMC4931111, DOI: 10.1261/rna.054817.115.Peer-Reviewed Original ResearchConceptsSmall nuclear RNAMiR-27Nuclear RNAVivo secondary structureBioinformatic structural analysisBinding site sequenceMiRNA degradationU RNARNA functionMutagenic analysisHSUR1Interacting regionsSite sequenceHost microRNAsSecondary structureHerpesvirus saimiriT cell activationOncogenic herpesvirusRNAStructural flexibilityDecreased levelsMutantsStructural analysisDegradationMicroRNAsMyriad 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 helixIntronlessGenomeEBV noncoding RNA EBER2 interacts with host RNA-binding proteins to regulate viral gene expression
Lee N, Yario TA, Gao JS, Steitz JA. EBV noncoding RNA EBER2 interacts with host RNA-binding proteins to regulate viral gene expression. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 3221-3226. PMID: 26951683, PMCID: PMC4812724, DOI: 10.1073/pnas.1601773113.Peer-Reviewed Original ResearchConceptsNon-POU domain-containing octamer-binding proteinGene expressionNoncoding RNAsHost RNAAbundant noncoding RNAsCellular noncoding RNAsRNA-protein crosslinkingOctamer-binding proteinHost gene expressionBox protein 5Viral gene expressionHost transcription factorsGlutamine richFactor prolineIntermediary proteinsNuclear bodiesTranscription factorsRNA 2Host proteinsRecombinant proteinsProtein resultsProtein componentsProtein 5Protein 14RNA
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 stoichiometryNoncoding RNA‐guided recruitment of transcription factors: A prevalent but undocumented mechanism?
Lee N, Steitz JA. Noncoding RNA‐guided recruitment of transcription factors: A prevalent but undocumented mechanism? BioEssays 2015, 37: 936-941. PMID: 26200477, PMCID: PMC4721591, DOI: 10.1002/bies.201500060.Peer-Reviewed Original ResearchConceptsTranscription factorsDomains of TFsCognate binding motifsDNA target sitesAssociated transcription factorsRNA-RNA interactionsTarget siteNascent transcriptsCell identityTarget lociCellular processesNoncoding RNAsBinding motifProper regulationViral genomeUndocumented mechanismGenomeDNAViral DNARNARecruitmentNcRNAsNcRNARNAsLociWidespread 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 studiesViral noncoding RNAs: more surprises
Tycowski KT, Guo YE, Lee N, Moss WN, Vallery TK, Xie M, Steitz JA. Viral noncoding RNAs: more surprises. Genes & Development 2015, 29: 567-584. PMID: 25792595, PMCID: PMC4378190, DOI: 10.1101/gad.259077.115.Peer-Reviewed Original ResearchConceptsDiverse biological rolesSmall noncoding RNAsMultitude of functionsHost immune evasionEukaryotic cellsCellular transformationNoncoding RNAsHost counterpartsAnimal virusesBiological roleNcRNAsRNA virusesViral ncRNAsMechanism of actionImmune evasionViral replicationMore surprisesBiogenesisViral persistenceRNAProteinDNAVirusRegulationReplicationEBV 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
RNA editing, epitranscriptomics, and processing in cancer progression
Witkin KL, Hanlon SE, Strasburger JA, Coffin JM, Jaffrey SR, Howcroft TK, Dedon PC, Steitz JA, Daschner PJ, Read-Connole E. RNA editing, epitranscriptomics, and processing in cancer progression. Cancer Biology & Therapy 2014, 16: 21-27. PMID: 25455629, PMCID: PMC4622672, DOI: 10.4161/15384047.2014.987555.Peer-Reviewed Original ResearchConceptsRNA modificationsRNA editingNetworks of RNAsTRNA base modificationsEpitranscriptomic RNA modificationsNuclear-cytoplasmic transportCancer progressionCellular stress pathwaysPrimary RNA sequenceRNA processingRNA splicingMRNA translationRNA interferenceRNA moleculesRegulated cleavageGene expressionCancer biologistsRNA sequencesBase modificationsCancer initiationCancer biologyStress pathwaysEnvironmental conditionsRNAEnzymatic pathwaysVirus 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 TransductionTime FactorsT-LymphocytesTransfectionConceptsMitogen-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