2016
Methyltransferase-like protein 16 binds the 3′-terminal triple helix of MALAT1 long noncoding RNA
Brown JA, Kinzig CG, DeGregorio SJ, Steitz JA. Methyltransferase-like protein 16 binds the 3′-terminal triple helix of MALAT1 long noncoding RNA. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 14013-14018. PMID: 27872311, PMCID: PMC5150381, DOI: 10.1073/pnas.1614759113.Peer-Reviewed Original ResearchConceptsGel shift assaysMetastasis-associated lung adenocarcinoma transcript 1RNA triple helicesPutative RNA methyltransferaseCompetitive gel shift assaysRNA-protein interactionsRNA stability elementAbundant nuclear proteinNative gel shift assaysRich internal loopSitu proximity ligation assayTriple helixHEK293T cell lysatesStem-loop structureProximity ligation assayT cell lysatesRNA methyltransferaseVivo UVNucleotide compositionNuclear proteinsLung adenocarcinoma transcript 1RNA immunoprecipitationStability elementMETTL16Rich tractMyriad Triple-Helix-Forming Structures in the Transposable Element RNAs of Plants and Fungi
Tycowski KT, Shu MD, Steitz JA. Myriad Triple-Helix-Forming Structures in the Transposable Element RNAs of Plants and Fungi. Cell Reports 2016, 15: 1266-1276. PMID: 27134163, PMCID: PMC4864102, DOI: 10.1016/j.celrep.2016.04.010.Peer-Reviewed Original ResearchConceptsTransposable elementsCellular noncoding RNAsPotential evolutionary consequencesCis-acting RNA structuresIntron lossEvolutionary consequencesBioinformatic identificationTE transcriptsReporter transcriptFish speciesNoncoding RNAsElement RNAHorizontal transferRNA structureTransposase geneRich tractHuman cellsTriple helix formationBase triplesRNAEne coreTranscriptsTriple helixIntronlessGenomeHoogsteen-position pyrimidines promote the stability and function of the MALAT1 RNA triple helix
Brown JA, Kinzig CG, DeGregorio SJ, Steitz JA. Hoogsteen-position pyrimidines promote the stability and function of the MALAT1 RNA triple helix. RNA 2016, 22: 743-749. PMID: 26952103, PMCID: PMC4836648, DOI: 10.1261/rna.055707.115.Peer-Reviewed Original ResearchConceptsElectrophoretic mobility shift assaysRNA triple helicesBase triplesMetastasis-associated lung adenocarcinoma transcript 1RNA stability elementMobility shift assaysTriple helixHuman metastasis-associated lung adenocarcinoma transcript 1Small molecule bindingU base triplesNucleotide compositionCellular functionsTriple-helical stabilityShift assaysLung adenocarcinoma transcript 1Stability elementEMSA resultsBiological significanceMolecule bindingRNA catalysisHelixTranscript 1Triple helix stabilityC tripleReporter
2014
Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix
Brown JA, Bulkley D, Wang J, Valenstein ML, Yario TA, Steitz TA, Steitz JA. Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix. Nature Structural & Molecular Biology 2014, 21: 633-640. PMID: 24952594, PMCID: PMC4096706, DOI: 10.1038/nsmb.2844.Peer-Reviewed Original Research
2012
Formation of triple-helical structures by the 3′-end sequences of MALAT1 and MENβ noncoding RNAs
Brown JA, Valenstein ML, Yario TA, Tycowski KT, Steitz JA. Formation of triple-helical structures by the 3′-end sequences of MALAT1 and MENβ noncoding RNAs. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 19202-19207. PMID: 23129630, PMCID: PMC3511071, DOI: 10.1073/pnas.1217338109.Peer-Reviewed Original ResearchConceptsRich internal loopMetastasis-associated lung adenocarcinoma transcript 1Rich tractSarcoma-associated herpesvirusDuplex-triplex junctionsTriple helical structureCellular noncoding RNAsNuclear retention elementBase triplesInternal loopKaposi's sarcoma-associated herpesvirusU base triplesPAN RNATriple helixNoncoding RNAsNuclear RNAThermal denaturation profilesReporter RNALung adenocarcinoma transcript 1C nucleotidesC base pairsMolecular mechanismsUnpaired nucleotidesBase pairsRNAConservation of a Triple-Helix-Forming RNA Stability Element in Noncoding and Genomic RNAs of Diverse Viruses
Tycowski KT, Shu MD, Borah S, Shi M, Steitz JA. Conservation of a Triple-Helix-Forming RNA Stability Element in Noncoding and Genomic RNAs of Diverse Viruses. Cell Reports 2012, 2: 26-32. PMID: 22840393, PMCID: PMC3430378, DOI: 10.1016/j.celrep.2012.05.020.Peer-Reviewed Original ResearchConceptsPAN RNAKaposi's sarcoma-associated herpesvirusSarcoma-associated herpesvirusStructure-based bioinformaticsRNA decay pathwaysDiverse viral genomesRNA stability elementNuclear retention elementPositive-strand RNA virusesReporter transcriptMammalian herpesvirusesGenomic RNAStability elementDNA virusesHuman cellsTriple helix formationRNA virusesDiverse virusesViral genomeRNAAbundant expressionDecay pathwaysTriple helixRetention elementsRapid identification
2010
Poly(A) Tail Recognition by a Viral RNA Element Through Assembly of a Triple Helix
Mitton-Fry RM, DeGregorio SJ, Wang J, Steitz TA, Steitz JA. Poly(A) Tail Recognition by a Viral RNA Element Through Assembly of a Triple Helix. Science 2010, 330: 1244-1247. PMID: 21109672, PMCID: PMC3074936, DOI: 10.1126/science.1195858.Peer-Reviewed Original ResearchConceptsSarcoma-associated herpesvirusBox H/ACA small nucleolar RNAsMajor-groove triple helixNuclear noncoding RNANuclear retention elementSmall nucleolar RNAsViral RNA elementsRich internal loopTriple helixKaposi's sarcoma-associated herpesvirusPAN RNADeadenylation assaysRNA decayRNA clampNucleolar RNAsNoncoding RNAsNuclear RNATail recognitionRNA elementsFunctional importanceAngstrom resolutionRich loopSecondary structureRNAEne core