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 tractA proximity-dependent assay for specific RNA–protein interactions in intact cells
Zhang W, Xie M, Shu MD, Steitz JA, DiMaio D. A proximity-dependent assay for specific RNA–protein interactions in intact cells. RNA 2016, 22: 1785-1792. PMID: 27659050, PMCID: PMC5066630, DOI: 10.1261/rna.058248.116.Peer-Reviewed Original ResearchConceptsRNA-protein interactionsSpecific RNA-protein interactionsProximity ligation assayTarget RNAProtein-protein interactionsSame cellular compartmentCellular compartmentsRNA targetsIntact cellsLigation assayRNADiscrete compartmentsProteinDNA oligonucleotideFluorescent signalOligonucleotide complementaryCellsCompartmentsAssaysColocalizationHigh specificityInteractionStaining methodOligonucleotideAdaptation
2015
The host Integrator complex acts in transcription-independent maturation of herpesvirus microRNA 3′ ends
Xie M, Zhang W, Shu MD, Xu A, Lenis DA, DiMaio D, Steitz JA. The host Integrator complex acts in transcription-independent maturation of herpesvirus microRNA 3′ ends. Genes & Development 2015, 29: 1552-1564. PMID: 26220997, PMCID: PMC4526738, DOI: 10.1101/gad.266973.115.Peer-Reviewed Original ResearchConceptsEnd processing signalsSmall nuclear RNAProximity ligation assayEnd processingPre-miRNAsHerpesvirus saimiriPre-miRNA hairpinsRNA-protein interactionsSitu proximity ligation assayIntegrator complexMiRNA 3MiRNA biogenesisSnRNA 3Primary miRNAMiRNA hairpinsIntegrator activityNuclear RNASequence downstreamOncogenic γ-herpesvirusesRescue experimentsLigation assayVivo knockdownComplex actsΓ-herpesvirusesHairpin