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
2016
Fluorescence Amplification Method for Forward Genetic Discovery of Factors in Human mRNA Degradation
Alexandrov A, Shu MD, Steitz JA. Fluorescence Amplification Method for Forward Genetic Discovery of Factors in Human mRNA Degradation. Molecular Cell 2016, 65: 191-201. PMID: 28017590, PMCID: PMC5301997, DOI: 10.1016/j.molcel.2016.11.032.Peer-Reviewed Original ResearchConceptsNonsense-mediated decayPremature termination codonNMD factorsNMD pathwayMRNA degradationHuman cellsForward genetic screeningGenetic screen identifiesHuman genetic diseasesHuman candidate genesNonsense suppression therapyModel organismsGenetic screeningScreen identifiesTermination codonCandidate genesGenetic discoveriesReporter fluorescenceGenetic diseasesPathwayAdditional key factorsCellsCRISPRCodonHomologyMyriad 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 stoichiometry
2014
3′-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 Research
2012
Conservation 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
Human eIF4AIII interacts with an eIF4G-like partner, NOM1, revealing an evolutionarily conserved function outside the exon junction complex
Alexandrov A, Colognori D, Steitz JA. Human eIF4AIII interacts with an eIF4G-like partner, NOM1, revealing an evolutionarily conserved function outside the exon junction complex. Genes & Development 2011, 25: 1078-1090. PMID: 21576267, PMCID: PMC3093123, DOI: 10.1101/gad.2045411.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsDEAD-box RNA HelicasesEukaryotic Initiation Factor-4AEukaryotic Initiation Factor-4GEvolution, MolecularExonsGene DeletionGenetic Complementation TestHumansModels, MolecularMolecular Sequence DataMutationNuclear ProteinsPhenotypeProtein Structure, TertiaryRNA, Ribosomal, 18SRNA-Binding ProteinsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSequence AlignmentConceptsExon junction complexEIF4GJunction complexDEAD-box helicasePre-rRNA processingDirect physical interactionEIF4G complexExtragenic suppressorsBiogenesis defectsLethal phenotypeGrowth defectTranslation initiationHuman orthologEIF4AIIISaccharomyces cerevisiaeHuman cellsNOM1Physical interactionComplex actsG complexX-ray structureMutationsResiduesComplexesOrthologs
1994
The Epstein-Barr virus (EBV) small RNA EBER1 binds and relocalizes ribosomal protein L22 in EBV-infected human B lymphocytes.
Toczyski DP, Matera AG, Ward DC, Steitz JA. The Epstein-Barr virus (EBV) small RNA EBER1 binds and relocalizes ribosomal protein L22 in EBV-infected human B lymphocytes. Proceedings Of The National Academy Of Sciences Of The United States Of America 1994, 91: 3463-3467. PMID: 8159770, PMCID: PMC43597, DOI: 10.1073/pnas.91.8.3463.Peer-Reviewed Original ResearchConceptsEpstein-Barr virusHuman B lymphocytesB lymphocytesEBV-positive lymphocytesEBV-positive cellsEBER1 RNAUninfected human cellsCertain patientsEBER1Ribosomal protein L22LymphocytesChromosomal translocationsOncogenic herpesvirusProtein L22Situ hybridizationUninfected cell extractsNucleoplasmic stainingVivoCell transformationHigh levelsHuman cellsCellsPatientsLeukemiaCellular proteins
1983
Genes for two small cytoplasmic Ro RNAs are adjacent and appear to be single-copy in the human genome
Wolin S, Steitz J. Genes for two small cytoplasmic Ro RNAs are adjacent and appear to be single-copy in the human genome. Cell 1983, 32: 735-744. PMID: 6187471, DOI: 10.1016/0092-8674(83)90059-4.Peer-Reviewed Original ResearchConceptsHuman genomeRo RNAsSecondary structure homologyRNA polymerase IIISmall cytoplasmic ribonucleoproteinsClass III genesGenomic clonesMammalian cellsPolymerase IIIRNA componentStructure homologySingle copyCytoplasmic ribonucleoproteinHY5 RNAMouse cellsHuman cellsHY1Cell extractsGenesRNAGenomeRNAsHY3CellsMY1
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 RNAsHuman cellsRNA polymerase III transcriptsNuclear transcription systemRNA polymerase IIIUninfected mammalian cellsPolymerase III transcriptsSmall cytoplasmic ribonucleoproteinsDifferent RNA moleculesSmall ribonucleic acidsProtein complexesSmall ribonucleoproteinTransfer RNAMammalian cellsRo RNPsPolymerase IIIRNA componentCytoplasmic ribonucleoproteinRNA moleculesTranscription systemMouse cellsReconstitution experimentsLa ribonucleoproteinsRibonucleoproteinRNARo 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 cytoplasmTranscriptionCellsRo small cytoplasmic ribonucleoproteins are a subclass of La ribonucleoproteins: further characterization of the Ro and La small ribonucleoproteins from uninfected mammalian cells.
Hendrick JP, Wolin SL, Rinke J, Lerner MR, Steitz JA. 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. PMID: 6180298, PMCID: PMC369740, DOI: 10.1128/mcb.1.12.1138.Peer-Reviewed Original ResearchConceptsLa RNAsHuman cellsRNA polymerase III transcriptsNuclear transcription systemRNA polymerase IIIUninfected mammalian cellsPolymerase III transcriptsSmall cytoplasmic ribonucleoproteinsDifferent RNA moleculesSmall ribonucleic acidsProtein complexesSmall ribonucleoproteinTransfer RNAMammalian cellsRo RNPsPolymerase IIIRNA componentCytoplasmic ribonucleoproteinRNA moleculesTranscription systemMouse cellsReconstitution experimentsRNARNA-like moleculesCell cytoplasm