2019
Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins
Shao W, Guo T, Toussaint N, Xue P, Wagner U, Li L, Charmpi K, Zhu Y, Wu J, Buljan M, Sun R, Rutishauser D, Hermanns T, Fankhauser C, Poyet C, Ljubicic J, Rupp N, Rüschoff J, Zhong Q, Beyer A, Ji J, Collins B, Liu Y, Rätsch G, Wild P, Aebersold R. Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins. Nature Communications 2019, 10: 2524. PMID: 31175306, PMCID: PMC6555818, DOI: 10.1038/s41467-019-10513-5.Peer-Reviewed Original ResearchConceptsProtein degradationMass spectrometric methodDegradation of mRNAAnalysis of mRNASpectrometric methodStability of proteinsMass spectrometryRNA-seqIndicator of sample qualitySWATH mass spectrometryDegree of protein degradationMRNA degradationClinical sample cohortsProteomic analysisClinical tissuesProteinMRNAMolecular measurementsConfounding conclusions
2018
RNA tales – how embryos read and discard messages from mom
Despic V, Neugebauer KM. RNA tales – how embryos read and discard messages from mom. Journal Of Cell Science 2018, 131: jcs201996. PMID: 29467249, DOI: 10.1242/jcs.201996.Peer-Reviewed Original ResearchConceptsZygotic genomePost-transcriptional regulatory pathwaysMaternal mRNA clearanceMaternal mRNA degradationEarly developmentContribution of microRNAsZygotic transitionMRNA clearanceRNA regulationMRNA decayCellular contextHigh-throughput methodZebrafish embryosFemale gametesMaternal mRNAsMolecular playersMRNA degradationRNA modificationsMolecular principlesRegulatory pathwaysGenomeLater stepsMZTSilent genomeEmbryos
2017
The Role of mRNA Degradation in Dynamic Nitrogen Environments in Saccharomyces cerevisiae
Rodriguez‐Tirado C, Gresham D, Abdul‐Rahman F. The Role of mRNA Degradation in Dynamic Nitrogen Environments in Saccharomyces cerevisiae. The FASEB Journal 2017, 31 DOI: 10.1096/fasebj.31.1_supplement.596.4.Peer-Reviewed Original ResearchNitrogen catabolite repressionReprogramming of gene expressionNitrogen-poor conditionsMRNA degradationUntranslated regionGene expressionAmino acid permeaseNitrogen-rich conditionsSaccharomyces cerevisiae cellsNitrogen-poor environmentsKnock-outAmino acid substratesNitrogen-rich environmentCatabolite repressionSaccharomyces cerevisiaeIdentified mutantsGrowth defectRegulates localizationGAP1MutantsStem cell differentiationAccelerated degradationGrowth rateAcid substratesPlasma membraneChapter 15 Comparative Functions of miRNAs in Embryonic Neurogenesis and Neuronal Network Formation
Ristori E, Nicoli S. Chapter 15 Comparative Functions of miRNAs in Embryonic Neurogenesis and Neuronal Network Formation. 2017, 265-282. DOI: 10.1016/b978-0-12-804402-5.00015-7.Peer-Reviewed Original ResearchTarget mRNA degradationCell fate determinationGene regulatory pathwaysDynamic spatiotemporal expressionImportance of miRNAsSmall noncoding RNAsStem cell proliferationMulticellular organismsFate determinationMost miRNAsNeuronal network formationTranslational repressionModel organismsNeural stem cell proliferationMRNA degradationPosttranscriptional regulatorsNoncoding RNAsRegulatory pathwaysDevelopmental processesEmbryonic neurogenesisGene expressionSpatiotemporal expressionNovel roleNeuronal differentiationMiRNAs
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 factorsCellsCRISPRCodonHomologySTarMir Tools for Prediction of microRNA Binding Sites
Kanoria S, Rennie W, Liu C, Carmack CS, Lu J, Ding Y. STarMir Tools for Prediction of microRNA Binding Sites. Methods In Molecular Biology 2016, 1490: 73-82. PMID: 27665594, PMCID: PMC5353976, DOI: 10.1007/978-1-4939-6433-8_6.Peer-Reviewed Original ResearchConceptsMessenger RNAEndogenous short noncoding RNAsGene expressionMammalian biological processesHigh-throughput miRNATarget messenger RNAsShort noncoding RNAsMicroRNA Binding SitesCertain human diseasesCross-species validationTranslational repressionMiRNA functionGene regulationSeedless sitesMRNA degradationNoncoding RNAsRegulatory moleculesBiological processesSequence featuresHuman diseasesImmunoprecipitation studiesMiRNAComputational predictionsBinding sitesMiRNAs
2012
The Prolyl Isomerase Pin1 Targets Stem-Loop Binding Protein (SLBP) To Dissociate the SLBP-Histone mRNA Complex Linking Histone mRNA Decay with SLBP Ubiquitination
Krishnan N, Lam TT, Fritz A, Rempinski D, O'Loughlin K, Minderman H, Berezney R, Marzluff WF, Thapar R. The Prolyl Isomerase Pin1 Targets Stem-Loop Binding Protein (SLBP) To Dissociate the SLBP-Histone mRNA Complex Linking Histone mRNA Decay with SLBP Ubiquitination. Molecular And Cellular Biology 2012, 32: 4306-4322. PMID: 22907757, PMCID: PMC3486140, DOI: 10.1128/mcb.00382-12.Peer-Reviewed Original ResearchMeSH KeywordsCell CycleCell Line, TumorCell NucleusDown-RegulationHEK293 CellsHeLa CellsHistonesHumansmRNA Cleavage and Polyadenylation FactorsNIMA-Interacting Peptidylprolyl IsomeraseNuclear ProteinsPeptidylprolyl IsomeraseProtein Phosphatase 2RNA InterferenceRNA StabilityRNA-Binding ProteinsRNA, MessengerRNA, Small InterferingUbiquitinationConceptsStem-loop binding proteinHistone mRNADegradation of SLBPMRNA stabilityBinding proteinHistone mRNA stabilityRNA degradation machineryHistone mRNA decayS phaseProtein phosphatase 2AHistone mRNA degradationCore histone mRNAsExosome-mediated degradationDownregulation of Pin1Ubiquitin-proteasome systemMRNA 3' endsProlyl isomerase Pin1Phosphatase 2ADegradation machineryMRNA decayMRNA degradationProteasome systemIsomerase Pin1MRNA complexesUntranslated region
2000
Genetic interference in Trypanosoma brucei by heritable and inducible double-stranded RNA.
Shi H, Djikeng A, Mark T, Wirtz E, Tschudi C, Ullu E. Genetic interference in Trypanosoma brucei by heritable and inducible double-stranded RNA. RNA 2000, 6: 1069-76. PMID: 10917601, PMCID: PMC1369981, DOI: 10.1017/s1355838200000297.Peer-Reviewed Original ResearchMeSH KeywordsActinsAnimalsDNA-Directed RNA PolymerasesDose-Response Relationship, DrugDown-RegulationElectroporationGene ExpressionGenetic EngineeringPhenotypePlasmidsPromoter Regions, GeneticProtein Synthesis InhibitorsProteinsRNA, Double-StrandedTetracyclineTime FactorsTransfectionTrypanosoma brucei bruceiTubulinViral ProteinsConceptsDouble-stranded RNARNA interferenceGenetic interferenceExpression of dsRNAActin mRNAT7 RNA polymerase systemRNA polymerase systemSpecific mRNA degradationStem-loop structureStable cell linesTetracycline-inducible promoterRNAi responseMolecular dissectionMRNA degradationInducible fashionPolymerase systemCellular divisionGene expressionTransfection efficiencyTransient interferenceCell generationCell linesRNAOrganismsInterference
1998
Double-stranded RNA induces mRNA degradation in Trypanosoma brucei
Ngô H, Tschudi C, Gull K, Ullu E. Double-stranded RNA induces mRNA degradation in Trypanosoma brucei. Proceedings Of The National Academy Of Sciences Of The United States Of America 1998, 95: 14687-14692. PMID: 9843950, PMCID: PMC24510, DOI: 10.1073/pnas.95.25.14687.Peer-Reviewed Original ResearchConceptsMRNA degradationUntranslated regionFlagellar attachment zoneMRNA 5' untranslated regionAlpha-tubulin synthesisImportant protozoan parasitesCaenorhabditis elegansAlpha-tubulin mRNACellular mRNAsTrypanosome cellsGenetic interferenceCytoskeletal structuresCleavage furrowDsRNA transfectionSame phenotypeCytokinesisComplex cortical structureFlagellar axonemeTubulin mRNAPlasmid vectorProtozoan parasiteVivo expressionAttachment zoneMRNADsRNAPosttranscriptional regulation of urokinase plasminogen activator receptor messenger RNA levels by leukocyte integrin engagement
Wang G, Collinge M, Blasi F, Pardi R, Bender J. Posttranscriptional regulation of urokinase plasminogen activator receptor messenger RNA levels by leukocyte integrin engagement. Proceedings Of The National Academy Of Sciences Of The United States Of America 1998, 95: 6296-6301. PMID: 9600959, PMCID: PMC27663, DOI: 10.1073/pnas.95.11.6296.Peer-Reviewed Original ResearchConceptsAU-rich elementsLFA-1 activationMRNA degradationReporter constructsUrokinase plasminogen activator receptorT cell activationCrucial cis-acting elementsCis-acting elementsLymphocyte function-associated antigen-1Integrin lymphocyte function-associated antigen-1Jurkat T cellsLFA-1 engagementUPAR cDNAReceptor-mediated signalingPosttranscriptional regulationTransmembrane signalingReporter mRNAIntegrin engagementCell activationInhibitor 5Adhesion receptorsSecond messengerMessenger RNA levelsPlasminogen activator receptorFunction-associated antigen-1
1997
Identification of HuR as a protein implicated in AUUUA‐mediated mRNA decay
Myer V, Fan X, Steitz J. Identification of HuR as a protein implicated in AUUUA‐mediated mRNA decay. The EMBO Journal 1997, 16: 2130-2139. PMID: 9155038, PMCID: PMC1169815, DOI: 10.1093/emboj/16.8.2130.Peer-Reviewed Original ResearchMeSH Keywords3T3 CellsAmino Acid SequenceAnimalsAntigens, SurfaceBase CompositionCell ExtractsCross-Linking ReagentsELAV ProteinsELAV-Like Protein 1Gene Expression RegulationHeLa CellsHumansMiceMolecular Sequence DataMolecular WeightRegulatory Sequences, Nucleic AcidRNA, MessengerRNA-Binding ProteinsUltraviolet RaysConceptsAU-rich elementsMRNA decayUntranslated regionRNA-binding specificityARE-binding proteinsHeLa nuclear extractsGene familyMRNA degradationNuclear extractsEssential signalMessenger RNAProteinSequence's abilityHuRAUUUARapid degradationCritical roleHuR.RNAMachineryMRNADegradationRegulationSubsequent analysisExpression
1990
Reductions in γ-GIobin mRNA Levels Restricted to the Cytoplasm of 5-Fluorouridine Treated K-562 Human Erythroleukemia Cells
Heimer R, Sartorelli A. Reductions in γ-GIobin mRNA Levels Restricted to the Cytoplasm of 5-Fluorouridine Treated K-562 Human Erythroleukemia Cells. Oncology Research Featuring Preclinical And Clinical Cancer Therapeutics 1990, 2: 45-53. PMID: 2369550, DOI: 10.3727/095535490820874759.Peer-Reviewed Original ResearchConceptsGamma-globin mRNAHuman erythroleukemia cellsErythroleukemia cellsRNA synthesisRibosomal RNA synthesisNuclease protection analysisMRNA levelsMRNA degradationSteady-state levelsCytoplasmic mRNAMRNA speciesCytoplasmic rRNACytoplasmic endonucleaseMRNA synthesisBeta-actin mRNANorthern blottingProtection analysisUntreated control cellsProtein levelsMRNAControl cellsUntreated cellsUridine analogs
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