2023
Genome-Wide Association Study Points to Novel Locus for Gilles de la Tourette Syndrome
Tsetsos F, Topaloudi A, Jain P, Yang Z, Yu D, Kolovos P, Tumer Z, Rizzo R, Hartmann A, Depienne C, Worbe Y, Müller-Vahl K, Cath D, Boomsma D, Wolanczyk T, Zekanowski C, Barta C, Nemoda Z, Tarnok Z, Padmanabhuni S, Buxbaum J, Grice D, Glennon J, Stefansson H, Hengerer B, Yannaki E, Stamatoyannopoulos J, Benaroya-Milshtein N, Cardona F, Hedderly T, Heyman I, Huyser C, Mir P, Morer A, Mueller N, Munchau A, Plessen K, Porcelli C, Roessner V, Walitza S, Schrag A, Martino D, Group T, TSAICG T, Barr C, Batterson J, Berlin C, Budman C, Coppola G, Cox N, Darrow S, Dion Y, Freimer N, Grados M, Greenberg E, Hirschtritt M, Huang A, Illmann C, King R, Kurlan R, Leckman J, Lyon G, Malaty I, McMahon W, Neale B, Okun M, Osiecki L, Robertson M, Rouleau G, Sandor P, Singer H, Smit J, Sul J, Initiative T, Androutsos C, Basha E, Farkas L, Fichna J, Janik P, Kapisyzi M, Karagiannidis I, Koumoula A, Nagy P, Puchala J, Szejko N, Szymanska U, Tsironi V, Group T, Apter A, Ball J, Bodmer B, Bognar E, Buse J, Vela M, Fremer C, Garcia-Delgar B, Gulisano M, Hagen A, Hagstrøm J, Madruga-Garrido M, Pellico A, Ruhrman D, Schnell J, Silvestri P, Skov L, Steinberg T, Gloor F, Turner V, Weidinger E, Network T, Alexander J, Aranyi T, Buisman W, Buitelaar J, Driessen N, Drineas P, Fan S, Forde N, Gerasch S, van den Heuvel O, Jespersgaard C, Kanaan A, Möller H, Nawaz M, Nespoli E, Pagliaroli L, Poelmans G, Pouwels P, Rizzo F, Veltman D, van der Werf Y, Widomska J, Zilhäo N, Group T, Brown L, Cheon K, Coffey B, Fernandez T, Gilbert D, Hong H, Ibanez-Gomez L, Kim E, Kim Y, Kim Y, Koh Y, Kook S, Kuperman S, Leventhal B, Maras A, Murphy T, Shin E, Song D, Song J, State M, Visscher F, Wang S, Zinner S, Tischfield J, Heiman G, Willsey A, Dietrich A, Davis L, Crowley J, Mathews C, Scharf J, Georgitsi M, Hoekstra P, Paschou P. Genome-Wide Association Study Points to Novel Locus for Gilles de la Tourette Syndrome. Biological Psychiatry 2023, 96: 114-124. PMID: 36738982, PMCID: PMC10783199, DOI: 10.1016/j.biopsych.2023.01.023.Peer-Reviewed Original ResearchExpression quantitative trait lociGenome-wide significant lociWide association study dataComplex genetic architectureQuantitative trait lociAssociation study dataGenetic architectureTrait lociChromosome 5q15Significant lociSignificant enrichmentLociNovel insightsNeurodevelopmental disordersChildhood-onset neurodevelopmental disorderHistonesRNAsGenesPolygenic riskFuture studiesEnrichment
2021
Noncoding RNAs: biology and applications—a Keystone Symposia report
Cable J, Heard E, Hirose T, Prasanth KV, Chen L, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, Chen C, Wilusz JE, Lempradl A, McGeary SE, Wahba L, Pyle AM, Hargrove AE, Simon MD, Marcia M, Przanowska RK, Chang HY, Jaffrey SR, Contreras LM, Chen Q, Shi J, Mendell JT, He L, Song E, Rinn JL, Lalwani MK, Kalem MC, Chuong EB, Maquat LE, Liu X. Noncoding RNAs: biology and applications—a Keystone Symposia report. Annals Of The New York Academy Of Sciences 2021, 1506: 118-141. PMID: 34791665, PMCID: PMC9808899, DOI: 10.1111/nyas.14713.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsKeystone Symposia reportPotential drug targetsRNA biologyHuman transcriptomeEpigenetic modificationsKeystone eSymposiumNoncoding RNAsCell signalingBasic biologyDrug targetsRNABiologyDisease mechanismsNucleotidesSpeciesTranscriptomeImportant roleRNAsTranscriptionSymposium reportSignalingTranslationRoleTarget
2018
Bacterial Y RNAs: Gates, Tethers, and tRNA Mimics
Sim S, Wolin S. Bacterial Y RNAs: Gates, Tethers, and tRNA Mimics. 2018, 369-381. DOI: 10.1128/9781683670247.ch21.Peer-Reviewed Original ResearchY RNAsBacterial Y RNAsRing-shaped proteinSubset of bacteriaCharacterized organismsProtein partnersNoncoding RNAsTRNA mimicAnimal cellsHomology searchHuman RNAHuman cellsRNANucleotidesImportant targetBacteriaSystemic autoimmune rheumatic diseasesAutoimmune rheumatic diseasesSystemic lupus erythematosusCellsRNAsOrganismsSpeciesProteinLupus erythematosusTissue-specific miRNA Expression Profiling in Mouse Heart Sections Using In Situ Hybridization.
Memi F, Tirziu D, Papangeli I. Tissue-specific miRNA Expression Profiling in Mouse Heart Sections Using In Situ Hybridization. Journal Of Visualized Experiments 2018 PMID: 30272664, PMCID: PMC6235194, DOI: 10.3791/57920.Peer-Reviewed Original ResearchConceptsMouse heart sectionsMiRNA expression profilingMiRNA-182Relevant protein expressionMiRNAs of interestMiRNA transcriptsT proteinRNA transcriptsExpression profilingMicro-RNAsDetailed protocolSitu hybridization techniqueCardiac troponin T proteinsSitu hybridizationLNA probesProtein expressionTroponin T proteinsTranscriptsHybridization techniqueCardiomyocyte cellsProteinExpressionFluorescent stainingMiRNA detectionRNAs
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 featureProspects for Noncoding RNA Discovery in Bacteria
Breaker R. Prospects for Noncoding RNA Discovery in Bacteria. The FASEB Journal 2016, 30 DOI: 10.1096/fasebj.30.1_supplement.386.1.Peer-Reviewed Original ResearchNoncoding RNAsNovel biochemical functionLarge noncoding RNAsBacterial noncoding RNAsRNA world organismsSelf-cleaving ribozymesRiboswitch candidatesRNA discoveryBiological validation studiesBiochemical functionsBioinformatics analysisModern cellsWorld organismsRNAGreat diversityStructural diversityNovel ribozymesRibozymeDiversityBacteriaDiscoveryRiboswitchRNAsOrganismsCells
2015
Noncoding RNA‐guided recruitment of transcription factors: A prevalent but undocumented mechanism?
Lee N, Steitz JA. Noncoding RNA‐guided recruitment of transcription factors: A prevalent but undocumented mechanism? BioEssays 2015, 37: 936-941. PMID: 26200477, PMCID: PMC4721591, DOI: 10.1002/bies.201500060.Peer-Reviewed Original ResearchConceptsTranscription factorsDomains of TFsCognate binding motifsDNA target sitesAssociated transcription factorsRNA-RNA interactionsTarget siteNascent transcriptsCell identityTarget lociCellular processesNoncoding RNAsBinding motifProper regulationViral genomeUndocumented mechanismGenomeDNAViral DNARNARecruitmentNcRNAsNcRNARNAsLociA retrovirus packages nascent host noncoding RNAs from a novel surveillance pathway
Eckwahl MJ, Sim S, Smith D, Telesnitsky A, Wolin SL. A retrovirus packages nascent host noncoding RNAs from a novel surveillance pathway. Genes & Development 2015, 29: 646-657. PMID: 25792599, PMCID: PMC4378196, DOI: 10.1101/gad.258731.115.Peer-Reviewed Original ResearchConceptsSmall nuclear RNAMoloney leukemia virusSurveillance pathwayU6 small nuclear RNASmall nucleolar RNAsHigh-throughput sequencingHost cell RNAExoribonuclease DIS3L2RNA exosomeLeukemia virusExportin-5Nucleolar RNAsNuclear RNAHost RNASpecific tRNAsCytoplasmic recruitmentMurine leukemia virusCell RNAEndogenous retrovirusesRNAModel retrovirusRNAsVirionsCytoplasmPathway
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 autoantigenRNAOrthologsNcRNAsSpeciesBacteriaExoribonucleaseRNAsRadioduransProteinRo60EnzymePhysiologyPhosphorylaseNoncoding RNAs in the regulation of DNA replication
Ge XQ, Lin H. Noncoding RNAs in the regulation of DNA replication. Trends In Biochemical Sciences 2014, 39: 341-343. PMID: 25027733, PMCID: PMC4265214, DOI: 10.1016/j.tibs.2014.06.003.Peer-Reviewed Original ResearchThe Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones
Cech TR, Steitz JA. The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones. Cell 2014, 157: 77-94. PMID: 24679528, DOI: 10.1016/j.cell.2014.03.008.Peer-Reviewed Original ResearchConceptsBiological functionsRNA-protein complexesLevel of transcriptionForeign nucleic acidsMost ncRNAsLong ncRNAsNcRNA researchRNA processingGenome rearrangementsNucleic acidsNoncoding RNAsGene expressionRNA structureNcRNAsBase pairingDNA synthesisRemarkable varietySnoRNPsRiboswitchGenomeSnRNPsRNAsRibosomesTranscriptionTelomerase
2010
Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data
Lu ZJ, Yip KY, Wang G, Shou C, Hillier LW, Khurana E, Agarwal A, Auerbach R, Rozowsky J, Cheng C, Kato M, Miller DM, Slack F, Snyder M, Waterston RH, Reinke V, Gerstein MB. Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. Genome Research 2010, 21: 276-285. PMID: 21177971, PMCID: PMC3032931, DOI: 10.1101/gr.110189.110.Peer-Reviewed Original ResearchConceptsNovel ncRNA candidatesNcRNA candidatesC. elegansC. elegans genomeWhole-genome identificationSpecific transcription factorsHigh-throughput sequencingDistinct expression patternsSecondary structure stabilityEvolutionary conservationGenomic elementsModENCODE consortiumNucleic acid levelIntergenic regionTranscription factorsPotential ncRNAsExpression patternsExpression dataDevelopmental stagesSecondary structureElegansNcRNAsRNAsStructural familyArray data
2009
A Cytidine Deaminase Edits C to U in Transfer RNAs in Archaea
Randau L, Stanley BJ, Kohlway A, Mechta S, Xiong Y, Söll D. A Cytidine Deaminase Edits C to U in Transfer RNAs in Archaea. Science 2009, 324: 657-659. PMID: 19407206, PMCID: PMC2857566, DOI: 10.1126/science.1170123.Peer-Reviewed Original ResearchConceptsTransfer RNAArchaeon Methanopyrus kandleriTertiary coreCytidine deaminase domainsTRNA genesTransfer RNAsTHUMP domainProper foldingU editingC deaminationMethanopyrus kandleriTRNA tertiary structureDeaminase domainTertiary structureTRNA tertiary corePosition 8Cytidine deaminaseUnique familyArchaeaRNAsGenesRNAFoldingDomainCrystal structure
2006
The 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
2004
Prediction of functional tertiary interactions and intermolecular interfaces from primary sequence data
Pang PS, Jankowsky E, Wadley LM, Pyle AM. Prediction of functional tertiary interactions and intermolecular interfaces from primary sequence data. Journal Of Experimental Zoology Part B Molecular And Developmental Evolution 2004, 304B: 50-63. PMID: 15595717, DOI: 10.1002/jez.b.21024.Peer-Reviewed Original ResearchConceptsRNA-protein complexesPattern of conservationProtein-protein interactionsPrimary sequence dataRNA-proteinDifferent organismsSequence dataSequence informationIntermolecular interfaceEnergetic couplingTertiary interactionsMacromolecular interactionsRNAsGenesImportant intramolecular interactionsProteinSequenceIntramolecular interactionsRNAOrganismsSpeciesInteractionMutationsNumber of predictionsConservation
2001
HuR and mRNA stability
Brennan CM, Steitz* J. HuR and mRNA stability. Cellular And Molecular Life Sciences 2001, 58: 266-277. PMID: 11289308, PMCID: PMC11146503, DOI: 10.1007/pl00000854.Peer-Reviewed Original ResearchConceptsAU-rich elementsMessenger RNAsGene regulationMRNA decayPosttranscriptional gene regulationMRNA degradation pathwayDrosophila ELAVMammalian cellsHu familyHuR functionMRNA stabilityUntranslated regionStressed cellsProtein ligandsRole of HuRCultured cellsEnvironmental changesHuRDegradation pathwayRapid degradationImportant mechanismRegulationCellsELAVRNAs
1996
Length suppression in histone messenger RNA 3′-end maturation: Processing defects of insertion mutant premessenger RNAs can be compensated by insertions into the U7 small nuclear RNA
Scharl E, Steitz J. Length suppression in histone messenger RNA 3′-end maturation: Processing defects of insertion mutant premessenger RNAs can be compensated by insertions into the U7 small nuclear RNA. Proceedings Of The National Academy Of Sciences Of The United States Of America 1996, 93: 14659-14664. PMID: 8962110, PMCID: PMC26191, DOI: 10.1073/pnas.93.25.14659.Peer-Reviewed Original ResearchConceptsHistone downstream elementU7 RNAHistone messenger RNASmall nuclear RNARNA processing systemSmall ribonucleoproteinPremessenger RNANuclear RNAPre-mRNAU7 small nuclear RNADownstream elementsCleavage siteRNAMessenger RNAXenopus oocytesBase pairingProcessing defectsU7First demonstrationHistonesRNAsRibonucleoproteinInsertionMRNASites
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
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
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