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 ResearchMeSH KeywordsAnimalsGene Expression RegulationHigh-Throughput Nucleotide SequencingMiceNIH 3T3 CellsPromoter Regions, GeneticRNA, Small NucleolarStress, PhysiologicalTranscription Initiation SiteTranscriptomeConceptsTranscription 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
2015
Herpesvirus saimiri MicroRNAs Preferentially Target Host Cell Cycle Regulators
Guo YE, Oei T, Steitz JA. Herpesvirus saimiri MicroRNAs Preferentially Target Host Cell Cycle Regulators. Journal Of Virology 2015, 89: 10901-10911. PMID: 26292323, PMCID: PMC4621106, DOI: 10.1128/jvi.01884-15.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBinding SitesBlotting, WesternCallithrixCDC2 Protein KinaseCell Cycle ProteinsEndoplasmic Reticulum Chaperone BiPHeat-Shock ProteinsHEK293 CellsHerpesvirus 2, SaimiriineHigh-Throughput Nucleotide SequencingHumansImmunoprecipitationLuciferasesMicroRNAsPhosphorylationRNA, MessengerT-LymphocytesConceptsHost cell cycle regulatorsViral miRNAsCell cycle regulatorsHerpesvirus saimiriMRNA targetsCycle regulatorsProtein-coding genesPre-miRNA hairpinsCross-linking immunoprecipitationGene ontology analysisHigh-throughput sequencingOpen reading frameOncogenic Herpesvirus saimiriCyclin-dependent kinasesP300 transcriptional coactivatorCell cycle progressionKey negative regulatorMarmoset T cellsHITS-CLIPRepresses expressionOntology analysisTranscriptional coactivatorViral life cyclePrimary transcriptCellular transformation
2014
Alternative 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 TransductionT-LymphocytesTime FactorsTransfectionConceptsMitogen-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