2013
Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA
Moss WN, Steitz JA. Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA. BMC Genomics 2013, 14: 543. PMID: 23937650, PMCID: PMC3751371, DOI: 10.1186/1471-2164-14-543.Peer-Reviewed Original ResearchConceptsStable intronic sequence RNARNA structureSequence RNAComprehensive genome-wide surveyGenome-wide surveyGenome-wide analysisRNA-seq analysisComparative sequence analysisNon-coding RNAsSecondary structure modelRNA-seq dataRNAz programFunctional RNAsGenomic sequencesImportant human pathogenSequence analysisRNAEBV transcriptomeHuman pathogensHerpesvirus 4Future experimental analysisPotential functionTranscriptomeGenomeEBV genome
2008
Flexibility in the site of exon junction complex deposition revealed by functional group and RNA secondary structure alterations in the splicing substrate
Mishler DM, Christ AB, Steitz JA. Flexibility in the site of exon junction complex deposition revealed by functional group and RNA secondary structure alterations in the splicing substrate. RNA 2008, 14: 2657-2670. PMID: 18952819, PMCID: PMC2590960, DOI: 10.1261/rna.1312808.Peer-Reviewed Original ResearchMeSH KeywordsEukaryotic Initiation Factor-4AHeLa CellsHumansNucleic Acid ConformationRiboseRNA Splice SitesRNA SplicingRNA, MessengerConceptsExon junction complexRNA secondary structureEJC depositionSplicing substrateMammalian nonsense-mediated mRNA decayNonsense-mediated mRNA decaySecondary structureStretches of DNATranslational regulationMRNA decayCoimmunoprecipitation assaysJunction complexSecondary structure alterationsDNA nucleotidesStructure alterationsH protectionUpstream shiftToeprintingExonsSitesNucleotidesDNACrystal structureDeposition sitesMRNA
2006
Identification of a Rapid Mammalian Deadenylation-Dependent Decay Pathway and Its Inhibition by a Viral RNA Element
Conrad NK, Mili S, Marshall EL, Shu MD, Steitz JA. Identification of a Rapid Mammalian Deadenylation-Dependent Decay Pathway and Its Inhibition by a Viral RNA Element. Molecular Cell 2006, 24: 943-953. PMID: 17189195, DOI: 10.1016/j.molcel.2006.10.029.Peer-Reviewed Original ResearchConceptsQuality control pathwaysViral RNA elementsPAN RNAPolyadenylated transcriptsMammalian cellsNuclear RNASuch transcriptsRNA elementsCellular RNAGene expressionNuclear accumulationNuclear extractsNaked RNARNADecay pathwaysTranscriptsDeadenylationDependent fashionPathwayDeadenylaseIntronsAccumulationMRNAHybridizationIntramolecular hybridization
2003
Splicing-Dependent and -Independent Modes of Assembly for Intron-Encoded Box C/D snoRNPs in Mammalian Cells
Hirose T, Shu MD, Steitz JA. Splicing-Dependent and -Independent Modes of Assembly for Intron-Encoded Box C/D snoRNPs in Mammalian Cells. Molecular Cell 2003, 12: 113-123. PMID: 12887897, DOI: 10.1016/s1097-2765(03)00267-3.Peer-Reviewed Original ResearchConceptsBox C/D snoRNAsSplice siteSnoRNP proteinsD snoRNAsSnoRNP assemblyMammalian cellsHost intronBox C/D snoRNPsSmall nucleolar RNAsD snoRNPsRRNA modificationNucleolar RNAsHost genesActive splicingNts upstreamIntronsEfficient expressionSnoRNAsStable stemSplicingVivo analysisProteinAssemblyBlockage experimentsStem