2021
Structural analyses of an RNA stability element interacting with poly(A)
Torabi SF, Chen YL, Zhang K, Wang J, DeGregorio SJ, Vaidya AT, Su Z, Pabit SA, Chiu W, Pollack L, Steitz JA. Structural analyses of an RNA stability element interacting with poly(A). Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2026656118. PMID: 33785601, PMCID: PMC8040590, DOI: 10.1073/pnas.2026656118.Peer-Reviewed Original ResearchConceptsRNA stability elementCis-acting RNA elementsGlobal conformational changesRich internal loopCryo-electron microscopyRice transposable elementsDiverse genomesDouble-helical regionsSmall-angle X-ray scatteringEne motifTransposable elementsGlobal structural changesRNA interactionsRNA stabilityBioinformatics studiesRNA elementsStability elementShort helixConformational changesDecay pathwaysInternal loopBiochemical structureTriplex structureBindingMotif
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 tract
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 pairsRNA
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