2016
Calcium 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
Proteomics and Transcriptomics of BJAB Cells Expressing the Epstein-Barr Virus Noncoding RNAs EBER1 and EBER2
Pimienta G, Fok V, Haslip M, Nagy M, Takyar S, Steitz JA. Proteomics and Transcriptomics of BJAB Cells Expressing the Epstein-Barr Virus Noncoding RNAs EBER1 and EBER2. PLOS ONE 2015, 10: e0124638. PMID: 26121143, PMCID: PMC4487896, DOI: 10.1371/journal.pone.0124638.Peer-Reviewed Original ResearchConceptsMRNA-seq dataHost cell nucleusBJAB cellsCell proliferationGene expression featuresPro-survival effectsProtein adaptersAlternative splicingMRNA transcriptomeUpregulated proteinsSILAC dataRich elementsAkt activationPI3K-AktBiochemical assaysCell nucleiEBV latencySwitch eventsProteinMaintenance of latencyCell linesVEGFA proteinMechanistic explanationUpregulated oncogenesPIK3AP1
2012
AUF1/hnRNP D is a novel protein partner of the EBER1 noncoding RNA of Epstein-Barr virus
Lee N, Pimienta G, Steitz JA. AUF1/hnRNP D is a novel protein partner of the EBER1 noncoding RNA of Epstein-Barr virus. RNA 2012, 18: 2073-2082. PMID: 23012480, PMCID: PMC3479396, DOI: 10.1261/rna.034900.112.Peer-Reviewed Original ResearchMeSH Keywords3' Untranslated RegionsAptamers, NucleotideAU Rich ElementsBinding, CompetitiveCell Line, TumorHerpesvirus 4, HumanHeterogeneous Nuclear Ribonucleoprotein D0Heterogeneous-Nuclear Ribonucleoprotein DHost-Pathogen InteractionsHumansImmunoprecipitationMutagenesis, InsertionalProtein BindingProtein IsoformsRNA StabilityRNA, ViralConceptsAU-rich elementsProtein partnersAUF1/hnRNP DUntranslated regionBacteriophage MS2 coat proteinNovel protein partnersHigh abundanceElectrophoretic mobility shift assaysEpstein-Barr virusMS2 coat proteinStable isotope labelingMobility shift assaysInteracting proteinMolecular functionsHnRNP DAlternative splicingNoncoding RNAsShift assaysCoat proteinIsotope labelingP40 isoformRNA aptamersRNA 1AUF1UV crosslinking
2009
Drosophila hnRNP A1 homologs Hrp36/Hrp38 enhance U2-type versus U12-type splicing to regulate alternative splicing of the prospero twintron
Borah S, Wong AC, Steitz JA. Drosophila hnRNP A1 homologs Hrp36/Hrp38 enhance U2-type versus U12-type splicing to regulate alternative splicing of the prospero twintron. Proceedings Of The National Academy Of Sciences Of The United States Of America 2009, 106: 2577-2582. PMID: 19196985, PMCID: PMC2636732, DOI: 10.1073/pnas.0812826106.Peer-Reviewed Original ResearchConceptsU12-type splicingPurine-rich elementAlternative splicingMRNA undergoes alternative splicingTranscription factor ProsperoU12-type spliceosomeHeterogeneous nuclear ribonucleoprotein A1Undergoes alternative splicingU2-type spliceosomeDrosophila homologDrosophila embryogenesisS2 cellsHnRNP A1TwintronSplicingNeuronal differentiationHrp38SpliceosomeIntronsEmbryogenesisProteinAxonal outgrowthHrp36HnRNPsHomolog
2004
An Intronic Enhancer Regulates Splicing of the Twintron of Drosophila melanogaster prospero Pre-mRNA by Two Different Spliceosomes
Scamborova P, Wong A, Steitz JA. An Intronic Enhancer Regulates Splicing of the Twintron of Drosophila melanogaster prospero Pre-mRNA by Two Different Spliceosomes. Molecular And Cellular Biology 2004, 24: 1855-1869. PMID: 14966268, PMCID: PMC350559, DOI: 10.1128/mcb.24.5.1855-1869.2004.Peer-Reviewed Original ResearchConceptsPurine-rich elementSplicing pathwaySplice siteU12-type spliceosomeU12-type splicingVitro splicing systemForms of mRNAAlternative splicingEarly embryogenesisKc cellsIntron sequencesPre-mRNASystematic deletionIntronic enhancerSplicingSequence requirementsIntron regionsEnhancer elementsNucleotides downstreamMolecular mechanismsTwintronSpliceosomeSplicing systemMutation analysisPathway
2003
Splicing double: insights from the second spliceosome
Patel AA, Steitz JA. Splicing double: insights from the second spliceosome. Nature Reviews Molecular Cell Biology 2003, 4: 960-970. PMID: 14685174, DOI: 10.1038/nrm1259.Peer-Reviewed Original ResearchConceptsMinor class intronsPhylogenetic analysisU12-type intronsMost multicellular organismsSmall nuclear RNASmall nuclear ribonucleoproteinParticular functional classNon-homologous positionsMessenger RNA interactionsMost metazoan taxaParalogous genesMulticellular organismsSpliceosomal factorsHomologous genesEvolutionary historyMetazoan taxaU5 snRNPSplicing machineryAcceptor splice siteAlternative splicingRNA interactionsU6 snRNPsNuclear RNANuclear ribonucleoproteinSplicing reaction
1992
Three Novel Functional Variants of Human U5 Small Nuclear RNA
Sontheimer E, Steitz J. Three Novel Functional Variants of Human U5 Small Nuclear RNA. Molecular And Cellular Biology 1992, 12: 734-746. DOI: 10.1128/mcb.12.2.734-746.1992.Peer-Reviewed Original ResearchU5 small nuclear RNASmall nuclear RNAHeLa cellsNuclear RNAAffinity-purified spliceosomesSmall nuclear ribonucleoproteinTri-snRNP complexFull-length speciesSaccharomyces cerevisiaeSplicing extractsPrimer extensionUS variantsHeLa extractsAlternative splicingRNA blotsShort speciesNuclear ribonucleoproteinBase changesMinimal domainHigher abundanceNorthern blottingRNAHeLaAbundant formSplicingThree Novel Functional Variants of Human U5 Small Nuclear RNA
Sontheimer E, Steitz J. Three Novel Functional Variants of Human U5 Small Nuclear RNA. Molecular And Cellular Biology 1992, 12: 734-746. DOI: 10.1128/mcb.12.2.734-746.1992.Peer-Reviewed Original ResearchU5 small nuclear RNASmall nuclear RNANuclear RNAHeLa cellsSmall nuclear ribonucleoprotein particleTri-snRNP complexOligonucleotide-directed RNase H cleavageNuclear ribonucleoprotein particleNovel functional variantsFull-length speciesAffinity-purified spliceosomesTrimethylguanosine capAlternative splicingShorter speciesRibonucleoprotein particleMinimal domainHeLa extractsPrimer extensionFunctional variantsHigh abundanceBase changesNorthern blottingAbundant formUS variantsRNAThree novel functional variants of human U5 small nuclear RNA.
Sontheimer EJ, Steitz JA. Three novel functional variants of human U5 small nuclear RNA. Molecular And Cellular Biology 1992, 12: 734-746. PMID: 1310151, PMCID: PMC364287, DOI: 10.1128/mcb.12.2.734.Peer-Reviewed Original ResearchConceptsU5 small nuclear RNASmall nuclear RNANuclear RNAHeLa cellsSmall nuclear ribonucleoprotein particleTri-snRNP complexOligonucleotide-directed RNase H cleavageNuclear ribonucleoprotein particleNovel functional variantsFull-length speciesAffinity-purified spliceosomesTrimethylguanosine capAlternative splicingShorter speciesRibonucleoprotein particleMinimal domainHeLa extractsPrimer extensionFunctional variantsHigh abundanceBase changesNorthern blottingAbundant formRNASpecies