2024
Characterization and implementation of the MarathonRT template-switching reaction to expand the capabilities of RNA-Seq
Guo L, Grinko A, Olson S, Leipold A, Graveley B, Saliba A, Pyle A. Characterization and implementation of the MarathonRT template-switching reaction to expand the capabilities of RNA-Seq. RNA 2024, 30: rna.080032.124. PMID: 39174298, PMCID: PMC11482623, DOI: 10.1261/rna.080032.124.Peer-Reviewed Original ResearchNontemplated additionRNA-seqRNA sequencingGroup II self-splicing intronsTemplate-switching oligonucleotidesLong-read sequencingRNA-seq technologySelf-splicing intronsTemplate-switching reactionsLong RNA transcriptsRNA sequencing methodsWell-characterized enzymesPoly(A)-enriched RNART enzymeRNA identityNucleotide specificityEnzymatic specificityRNA librariesRNA transcriptsLong RNAsHuman RNARNA moleculesRNA referenceAccurate sequencingBinding specificity
2022
The In Vivo and In Vitro Architecture of the Hepatitis C Virus RNA Genome Uncovers Functional RNA Secondary and Tertiary Structures
Wan H, Adams RL, Lindenbach BD, Pyle AM. The In Vivo and In Vitro Architecture of the Hepatitis C Virus RNA Genome Uncovers Functional RNA Secondary and Tertiary Structures. Journal Of Virology 2022, 96: e01946-21. PMID: 35353000, PMCID: PMC9044954, DOI: 10.1128/jvi.01946-21.Peer-Reviewed Original ResearchConceptsSecondary structure mapRNA genomeRNA structureTertiary structureProtein-coding genesPositive-strand RNA virusesRegulatory RNA structuresFull-length structureHCV RNA genomeValuable model systemRNA structural motifsSecondary structural elementsEvolutionary functional analysisLife cycleVirus life cycleCellular contextCorresponding transcriptsImportant human pathogenLong RNAsGenomeSame RNAGenomic RNAComprehensive atlasFunctional analysisFunctional importance
2020
Sequencing and Structure Probing of Long RNAs Using MarathonRT: A Next-Generation Reverse Transcriptase
Guo LT, Adams RL, Wan H, Huston NC, Potapova O, Olson S, Gallardo CM, Graveley BR, Torbett BE, Pyle AM. Sequencing and Structure Probing of Long RNAs Using MarathonRT: A Next-Generation Reverse Transcriptase. Journal Of Molecular Biology 2020, 432: 3338-3352. PMID: 32259542, PMCID: PMC7556701, DOI: 10.1016/j.jmb.2020.03.022.Peer-Reviewed Original ResearchConceptsLong RNA moleculesLong RNAsRNA moleculesRNA base modificationsGroup II intronsMutational profilingTranscriptome compositionRNA metabolismRNA researchBase modificationsPrimer extensionTool enzymeDiverse aspectsMixed populationEnzymeReverse transcriptionRNAStructural complexityReverse transcriptaseProfilingTranscriptase enzymeIntronsTranscription
2018
A Regulatory Circuitry Between Gria2, miR-409, and miR-495 Is Affected by ALS FUS Mutation in ESC-Derived Motor Neurons
Capauto D, Colantoni A, Lu L, Santini T, Peruzzi G, Biscarini S, Morlando M, Shneider NA, Caffarelli E, Laneve P, Bozzoni I. A Regulatory Circuitry Between Gria2, miR-409, and miR-495 Is Affected by ALS FUS Mutation in ESC-Derived Motor Neurons. Molecular Neurobiology 2018, 55: 7635-7651. PMID: 29430619, PMCID: PMC6132778, DOI: 10.1007/s12035-018-0884-4.Peer-Reviewed Original ResearchConceptsAmyotrophic lateral sclerosisMotor neuronsFUS mutationsMouse embryonic stem cellsPathogenesis of ALSMiRNA-dependent regulationCorresponding mRNA targetsNeuron-specific RNATypes of RNAEmbryonic stem cellsCross talkGlutamate α-aminoIsoxazole propionic acidDisease-associated mutationsMolecular cross talkDisturbance of Ca2Juvenile-onset formMiRNA repressionRegulatory circuitryTranscriptome profilingMRNA targetsMultifunctional proteinLong RNAsMN degenerationExcitatory neurotransmission
2000
[10] Using DNAzylnes to cut, process, and map RNA molecules for structural studies or modification
Pyle AM, Chu VT, Jankowsky E, Boudvillain M. [10] Using DNAzylnes to cut, process, and map RNA molecules for structural studies or modification. Methods In Enzymology 2000, 317: 140-146. PMID: 10829278, DOI: 10.1016/s0076-6879(00)17012-0.Peer-Reviewed Original ResearchConceptsStructural studiesTypes of DNAzymeTemplate-directed ligationDNAzyme reactionDNAzyme moleculesSimple DNA moleculesDNAzymeDivalent ionsAnalytical scaleMoleculesDNA moleculesAddition of Mg2Crystallographic applicationsRNA targetsRNA moleculesCatalytic coreIonsLong RNAsReactionModificationDifferent applicationsInexpensive wayRNA fragmentsMg2Incorporation
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