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
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 releaseReticulumMechanismCalcium signaling and transcription: elongation, DoGs, and eRNAs.
Vilborg A, Passarelli MC, Steitz JA. Calcium signaling and transcription: elongation, DoGs, and eRNAs. Receptors & Clinical Investigation 2016, 3 PMID: 29147672, PMCID: PMC5685190, DOI: 10.14800/rci.1169.Peer-Reviewed Original ResearchGene-specific transcription factorsPhases of transcriptionCertain stress conditionsTranscription terminationReadthrough transcriptionTranscription initiationAlternative splicingCellular processesTranscription factorsRegulated processKey intracellularSignaling cascadesTranscriptionCalcium signalingStress conditionsDiverse classSuch CaERNAsSplicingGenesTranscriptsSignalingCalcium ionsIntracellularCascade
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 studies
2014
The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones
Cech TR, Steitz JA. The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones. Cell 2014, 157: 77-94. PMID: 24679528, DOI: 10.1016/j.cell.2014.03.008.Peer-Reviewed Original ResearchConceptsBiological functionsRNA-protein complexesLevel of transcriptionForeign nucleic acidsMost ncRNAsLong ncRNAsNcRNA researchRNA processingGenome rearrangementsNucleic acidsNoncoding RNAsGene expressionRNA structureNcRNAsBase pairingDNA synthesisRemarkable varietySnoRNPsRiboswitchGenomeSnRNPsRNAsRibosomesTranscriptionTelomerase
2008
Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production
Pawlicki JM, Steitz JA. Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production. Journal Of Cell Biology 2008, 182: 61-76. PMID: 18625843, PMCID: PMC2447899, DOI: 10.1083/jcb.200803111.Peer-Reviewed Original ResearchMeSH KeywordsChromatinExonsHeLa CellsHumansIntronsMicroRNAsMRNA Cleavage and Polyadenylation FactorsNuclear ProteinsPolyadenylationRegulatory Sequences, Nucleic AcidRibonucleoproteinsRNA Polymerase IIIRNA Processing, Post-TranscriptionalRNA TransportRNA, MessengerRNA, ViralSequence DeletionSerine-Arginine Splicing FactorsSubcellular FractionsTranscription, GeneticConceptsPri-miRNAsTranscription sitesEndogenous pri-miRNAsPrimary miRNA transcriptsPri-miRNA processingSplicing factor SC35Viral RNA elementsHigh nuclear levelsMiRNA biogenesisMiRNA transcriptionMiRNA transcriptsNuclear stepsPrecursor miRNAsNuclear fociFactor SC35MicroRNA productionRNA elementsGene expressionTranscription leadNuclear fractionNuclear levelsTranscriptionMiRNAsProcessing signalsBiogenesis
1996
A 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
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 intermediatesTranscriptsTranscriptionProteinComplexesPolymeraseRegulatorAbsenceThe RNA binding protein La influences both the accuracy and the efficiency of RNA polymerase III transcription in vitro.
Gottlieb E, Steitz JA. The RNA binding protein La influences both the accuracy and the efficiency of RNA polymerase III transcription in vitro. The EMBO Journal 1989, 8: 841-850. PMID: 2498086, PMCID: PMC400883, DOI: 10.1002/j.1460-2075.1989.tb03445.x.Peer-Reviewed Original ResearchConceptsTranscription levelsNascent RNA polymerase III transcriptsRNA polymerase III transcriptionAbundant nuclear phosphoproteinRNA polymerase III transcriptsPolymerase III transcriptionPolymerase III transcriptsClass III genesHeLa cell extractsAction of LaTranscript lengthTermination signalNuclear phosphoproteinUridylate residuesLa proteinTranscription activityAutoantigen LaCell extractsTranscriptsRNAAbsence of LAMouse monoclonal antibodyTranscriptionPhosphoproteinGenes
1987
Structural analysis of the human U3 ribonucleoprotein particle reveal a conserved sequence available for base pairing with pre-rRNA.
Parker KA, Steitz JA. Structural analysis of the human U3 ribonucleoprotein particle reveal a conserved sequence available for base pairing with pre-rRNA. Molecular And Cellular Biology 1987, 7: 2899-2913. PMID: 2959855, PMCID: PMC367909, DOI: 10.1128/mcb.7.8.2899.Peer-Reviewed Original ResearchConceptsProtein-RNA interactionsSecondary structureSubsequent reverse transcriptionRNA secondary structureHuman U3Phosphorylated proteinsRibonucleoprotein particleProcessing eventsAlternative functionsBase pairsNucleotides -159Specific nucleasesHeLa cellsProtein constituentsRNase ARNPProteinNonphosphorylated proteinsRRNAReverse transcriptionSequenceKilodaltonsNucleotides 65Specific reagentsTranscription
1982
Nucleotide sequence of γδ resolvase gene and demonstration that its gene product acts as a repressor of transcription
Reed R, Shibuya G, Steitz J. Nucleotide sequence of γδ resolvase gene and demonstration that its gene product acts as a repressor of transcription. Nature 1982, 300: 381-383. PMID: 6292730, DOI: 10.1038/300381a0.Peer-Reviewed Original ResearchConceptsRepressor of transcriptionSite-specific recombination systemResolvase proteinAmino acid sequenceSite-specific recombinationElement-encoded proteinsIntercistronic regionGene initiatesFrequency of transpositionGene productsNucleotide sequenceAcid sequenceRecombination systemTranscription systemGenetic analysisΓδ resolvaseResolvaseGenesTranscriptionProteinResolvase geneRelated transposonsTransposaseModel substrateRecombination
1981
Ro Small Cytoplasmic Ribonucleoproteins Are a Subclass of La Ribonucleoproteins: Further Characterization of the Ro and La Small Ribonucleoproteins from Uninfected Mammalian Cells
Hendrick J, Wolin S, Rinke J, Lerner M, Steitz J. Ro Small Cytoplasmic Ribonucleoproteins Are a Subclass of La Ribonucleoproteins: Further Characterization of the Ro and La Small Ribonucleoproteins from Uninfected Mammalian Cells. Molecular And Cellular Biology 1981, 1: 1138-1149. DOI: 10.1128/mcb.1.12.1138-1149.1981.Peer-Reviewed Original ResearchLa RNAsRNA polymerase III transcriptionLa ribonucleoproteinsHuman cellsPolymerase III transcriptionRNA polymerase IIINuclear transcription systemIII transcriptionSmall ribonucleoproteinsPolymerase IIITransfer RNACytoplasmic ribonucleoproteinRNA-like moleculesRNA componentRNA moleculesTranscription systemRo ribonucleoproteinsRibonucleoproteinMouse cellsReconstitution experimentsRNAInternal modificationCell cytoplasmTranscriptionCellsArrangement of 30S Heterogeneous Nuclear Ribonucleoprotein on Polyoma Virus Late Nuclear Transcripts
Steitz J, Kamen R. Arrangement of 30S Heterogeneous Nuclear Ribonucleoprotein on Polyoma Virus Late Nuclear Transcripts. Molecular And Cellular Biology 1981, 1: 21-34. DOI: 10.1128/mcb.1.1.21-34.1981.Peer-Reviewed Original ResearchHeterogeneous nuclear ribonucleoproteinHeterogeneous nuclear ribonucleic acidNuclear ribonucleoproteinSegments of viral RNANuclear RNA sequencingVirus-specific RNAEucaryotic cell nucleiNuclear ribonucleic acidRNA biogenesisConserved proteinsLate transcriptionNuclear RNANuclear transcriptionRNA sequencingHybridization studiesViral RNARibonuclease treatmentRNATranscriptionFingerprint analysisCell nucleiRibonucleoproteinPolyomaRibonucleic acidRibonuclease
1975
F factor-mediated inhibition of bacteriophage T7 growth: Analysis of T7 RNA and protein synthesis In vivo and In vitro using male and female Escherichia coli
Condit RC, Steitz JA. F factor-mediated inhibition of bacteriophage T7 growth: Analysis of T7 RNA and protein synthesis In vivo and In vitro using male and female Escherichia coli. Journal Of Molecular Biology 1975, 98: 31-43. PMID: 1104867, DOI: 10.1016/s0022-2836(75)80099-4.Peer-Reviewed Original ResearchConceptsT7 growthProtein synthesisE. coliPolyacrylamide gel electrophoresisEscherichia coliPhage protein synthesisGel electrophoresisTranslation apparatusT7 proteinsPhage proteinsT7 infectionT7 DNAT7 RNAFaithful synthesisRNA synthesisProteinMale cellsRNAColiTranscriptionSimultaneous inhibitionSpecific modificationsT7InhibitionElectrophoresis