2018
The role of 3′ end uridylation in RNA metabolism and cellular physiology
Zigáčková D, Vaňáčová Š. The role of 3′ end uridylation in RNA metabolism and cellular physiology. Philosophical Transactions Of The Royal Society B Biological Sciences 2018, 373: 20180171. PMID: 30397107, PMCID: PMC6232591, DOI: 10.1098/rstb.2018.0171.Peer-Reviewed Original ResearchConceptsRNA metabolismRegulation of stabilityCell cycle regulationNumber of pathwaysRNA maturationEukaryotic RNAOrganismal levelCellular physiologyCycle regulationRNA degradationCellular RNADiverse rolesWidespread modificationCell deathUridylationRNAMajority of modificationsCurrent knowledgeLife cycleCritical roleTheme issueRegulationPathwayMetabolismEukaryotesMIWI2 targets RNAs transcribed from piRNA‐dependent regions to drive DNA methylation in mouse prospermatogonia
Watanabe T, Cui X, Yuan Z, Qi H, Lin H. MIWI2 targets RNAs transcribed from piRNA‐dependent regions to drive DNA methylation in mouse prospermatogonia. The EMBO Journal 2018, 37: embj201695329. PMID: 30108053, PMCID: PMC6138435, DOI: 10.15252/embj.201695329.Peer-Reviewed Original ResearchConceptsDNA methylationRetrotransposon sequencesSmall RNAsArgonaute/Piwi proteinsPiwi protein MIWI2Suppressive epigenetic marksMouse prospermatogoniaChromatin statePIWI proteinsUnderlying molecular mechanismsDiverse organismsEpigenetic marksPiRNA clustersNascent RNAEpigenetic regulationTranslational regulationMIWI2RNA degradationRepeat sequencesGene expressionMolecular mechanismsTarget RNAMethylationRNAPiRNAs
2016
TUT‐DIS3L2 is a mammalian surveillance pathway for aberrant structured non‐coding RNAs
Ustianenko D, Pasulka J, Feketova Z, Bednarik L, Zigackova D, Fortova A, Zavolan M, Vanacova S. TUT‐DIS3L2 is a mammalian surveillance pathway for aberrant structured non‐coding RNAs. The EMBO Journal 2016, 35: 2179-2191. PMID: 27647875, PMCID: PMC5069555, DOI: 10.15252/embj.201694857.Peer-Reviewed Original ResearchConceptsStructured non-coding RNAsCellular RNA speciesRNA polymerase IICytoplasmic quality controlNon-coding RNAsStable secondary structureExoribonuclease DIS3L2Y-RNAsPolymerase IIStructured ncRNAsSurveillance pathwayRNA speciesWilms tumor susceptibilityRNA degradationDIS3L2Human cellsSecondary structureImmunoprecipitation methodPerlman syndromeUridylationRNAAberrant processingRNAsTumor susceptibilityUnifying feature
2014
Bacterial noncoding Y RNAs are widespread and mimic tRNAs
Chen X, Sim S, Wurtmann EJ, Feke A, Wolin SL. Bacterial noncoding Y RNAs are widespread and mimic tRNAs. RNA 2014, 20: 1715-1724. PMID: 25232022, PMCID: PMC4201824, DOI: 10.1261/rna.047241.114.Peer-Reviewed Original ResearchConceptsY RNAsStructured RNA degradationRing-shaped proteinNoncoding Y RNAsBacterial physiologyAnimal cellsNucleotide modificationsDeinococcus radioduransPhage speciesRNA degradationTRNARo60 autoantigenRNAOrthologsNcRNAsSpeciesBacteriaExoribonucleaseRNAsRadioduransProteinRo60EnzymePhysiologyPhosphorylase
2006
Dynamical Determinants of Drug-Inducible Gene Expression in a Single Bacterium
Le TT, Emonet T, Harlepp S, Guet C, Cluzel P. Dynamical Determinants of Drug-Inducible Gene Expression in a Single Bacterium. Biophysical Journal 2006, 90: 3315-3321. PMID: 16461398, PMCID: PMC1432126, DOI: 10.1529/biophysj.105.073353.Peer-Reviewed Original ResearchMeSH KeywordsAnti-Bacterial AgentsCapsid ProteinsDrug Resistance, Multiple, BacterialEscherichia coliEscherichia coli ProteinsGene Expression Regulation, BacterialLevivirusLipoproteinsMembrane Transport ProteinsMultidrug Resistance-Associated ProteinsPromoter Regions, GeneticRNA, BacterialRNA, MessengerTetracyclineConceptsGene expressionDrug-inducible gene expressionAcrAB-TolC multidrug effluxTet promoterMultidrug effluxEfflux systemDrug-inducible systemSingle-cell experimentsTranscriptional pulsesSingle bacteriumMultidrug efflux systemsTranscriptional responseEnvironmental signalsGenetic systemRNA degradationFluorescence correlation spectroscopyCellular RNATranscription activityRate of synthesisPromoterInducer concentrationTranscriptionRNA levelsBacteriumPrimitive examplesThe Challenge of Viral snRNPs
CONRAD NK, FOK V, CAZALLA D, BORAH S, STEITZ JA. The Challenge of Viral snRNPs. Cold Spring Harbor Symposia On Quantitative Biology 2006, 71: 377-384. PMID: 17381320, DOI: 10.1101/sqb.2006.71.057.Peer-Reviewed Original ResearchConceptsNuclear noncoding RNAsHSURs 1Sarcoma-associated herpesvirusRibosomal protein L22Aggressive T-cell leukemiaT cell signalingViral gene expressionKaposi's sarcoma-associated herpesvirusHeterokaryon assayU RNADependent RNA degradationMammalian cellsNoncoding RNAsProtein L22Nuclear surveillanceRNA degradationHost mRNAsHost proteinsGene expressionMRNA transcriptsMutant virusHerpesvirus saimiriRNAImportant functionsRNAs
2005
GAS5 Gene
Hirose T, Steitz J. GAS5 Gene. 2005 DOI: 10.1038/npg.els.0005019.Peer-Reviewed Original Research
2001
RNA interference in Trypanosoma brucei: cloning of small interfering RNAs provides evidence for retroposon-derived 24-26-nucleotide RNAs.
Djikeng A, Shi H, Tschudi C, Ullu E. RNA interference in Trypanosoma brucei: cloning of small interfering RNAs provides evidence for retroposon-derived 24-26-nucleotide RNAs. RNA 2001, 7: 1522-30. PMID: 11720282, PMCID: PMC1370195.Peer-Reviewed Original ResearchConceptsDouble-stranded RNARNA interferenceGene-specific double-stranded RNAHigh-speed pellet fractionStrand-specific probesSmall interfering RNAsTarget RNA degradationDsRNA resultsHousekeeping functionsTrypanosoma bruceiRNA degradationCellular RNAInterfering RNAsNorthern hybridizationWeight complexesSequence analysisHigh-speed pelletRNALong fragmentSiRNAsPellet fractionEnrichment strategyCloningSupernatant fractionFragments
1989
[32] Immunoprecipitation of ribonucleoproteins using autoantibodies
Steitz J. [32] Immunoprecipitation of ribonucleoproteins using autoantibodies. Methods In Enzymology 1989, 180: 468-481. PMID: 2693908, DOI: 10.1016/0076-6879(89)80118-1.Peer-Reviewed Original ResearchConceptsSmall ribonucleoproteinImmunoprecipitation procedureTissue culture cellsRNP complexesRNA degradationLaemmli gelsRibonucleoproteinCulture cellsImmunoprecipitationWestern blottingProteinMouse ascitesRNAsCell culture supernatantsCulture supernatantsPhosphoproteinMonoclonal antibodiesRNAImmunoprecipitatesTissueRibonuclease levelsHigh backgroundMouse monoclonal autoantibodyBlottingMonoclonal autoantibodies
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