2024
The West Nile virus genome harbors essential riboregulatory elements with conserved and host-specific functional roles
Huston N, Tsao L, Brackney D, Pyle A. The West Nile virus genome harbors essential riboregulatory elements with conserved and host-specific functional roles. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2312080121. PMID: 38985757, PMCID: PMC11260092, DOI: 10.1073/pnas.2312080121.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell LineGenome, ViralHost SpecificityHost-Pathogen InteractionsHumansNucleic Acid ConformationRNA, ViralWest Nile FeverWest Nile virusConceptsWest Nile virus genomeWest Nile virusPositive-sense RNA virusesFunctional roleArthropod cell linesRiboregulatory elementsGenome foldingFlaviviral genomeRNA genomeIncreasing global threatVirus genomeGenomeRNA virusesStructural homologyHost-dependentSecondary structureLack of effective therapeuticsFunctional validationLocked nucleic acidStructural insightsRNA drugsCell linesArthropod-borneNucleic acidsAntisense locked nucleic acid
2023
Structural insights into intron catalysis and dynamics during splicing
Xu L, Liu T, Chung K, Pyle A. Structural insights into intron catalysis and dynamics during splicing. Nature 2023, 624: 682-688. PMID: 37993708, PMCID: PMC10733145, DOI: 10.1038/s41586-023-06746-6.Peer-Reviewed Original ResearchAdenosineBiocatalysisCryoelectron MicroscopyExonsIntronsNucleic Acid ConformationRNA PrecursorsRNA Splice SitesRNA Splicing
2022
AMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids
Shine M, Zhang C, Pyle AM. AMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids. Bioinformatics 2022, 38: 2937-2939. PMID: 35561202, PMCID: PMC9113296, DOI: 10.1093/bioinformatics/btac207.Peer-Reviewed Original ResearchCSSR: assignment of secondary structure to coarse‐grained RNA tertiary structures
Zhang C, Pyle AM. CSSR: assignment of secondary structure to coarse‐grained RNA tertiary structures. Acta Crystallographica Section D, Structural Biology 2022, 78: 466-471. PMID: 35362469, PMCID: PMC8972804, DOI: 10.1107/s2059798322001292.Peer-Reviewed Original Research
2021
Discovery of highly reactive self-splicing group II introns within the mitochondrial genomes of human pathogenic fungi
Liu T, Pyle AM. Discovery of highly reactive self-splicing group II introns within the mitochondrial genomes of human pathogenic fungi. Nucleic Acids Research 2021, 49: 12422-12432. PMID: 34850132, PMCID: PMC8643640, DOI: 10.1093/nar/gkab1077.Peer-Reviewed Original ResearchConceptsGroup II intronsSelf-splicing group II intronsPathogenic fungiDrug targetsAntifungal drug targetsSelf-splicing intronsHuman pathogenic fungiMitochondrial genomeNear-physiological conditionsPromising drug targetProtein cofactorsStriking diversitySequence dataIntronsFungal pathogensInformatics searchBioinformatics workflowsFungiDimorphic fungusStructural signaturesPathogensGenomeCofactorDiversityTargetComprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms
Huston NC, Wan H, Strine MS, de Cesaris Araujo Tavares R, Wilen CB, Pyle AM. Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms. Molecular Cell 2021, 81: 584-598.e5. PMID: 33444546, PMCID: PMC7775661, DOI: 10.1016/j.molcel.2020.12.041.Peer-Reviewed Original ResearchMeSH KeywordsCell Line, TumorCOVID-19Genome, ViralHumansNucleic Acid ConformationResponse ElementsRNA, ViralSARS-CoV-2ConceptsRNA structureSecondary structureRNA virusesSARS-CoV-2 RNA genomeNovel regulatory motifsSingle-nucleotide resolutionDownstream functional analysisRNA drug targetsPositive-sense RNA virusesGenome architectureGenomic structureEvolutionary analysisRegulatory motifsSARS-CoV-2 genomeViral life cycleRNA genomeFunctional analysisGenomeDrug targetsPrimer designInfected cellsViral RNADepth structural analysisLife cycleΒ-coronavirus
2020
Visualizing group II intron dynamics between the first and second steps of splicing
Manigrasso J, Chillón I, Genna V, Vidossich P, Somarowthu S, Pyle AM, De Vivo M, Marcia M. Visualizing group II intron dynamics between the first and second steps of splicing. Nature Communications 2020, 11: 2837. PMID: 32503992, PMCID: PMC7275048, DOI: 10.1038/s41467-020-16741-4.Peer-Reviewed Original ResearchConceptsGroup II intron splicingGroup II intronsSelf-splicing ribozymesGene-editing toolsIntron dynamicsEukaryotic spliceosomeActive site dynamicsIntron splicingRetrotransposable elementsCatalytic triadSplicingMolecular machinesConformational changesFirst residueMultiple conformationsSite dynamicsSpliceosomeIntronsStructural rearrangementsX-ray crystallographyEnzymatic assayStructural dataEnzymatic strategyFunctional dataActive siteSequencing 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 ResearchMeSH KeywordsBacteriaBacterial ProteinsCell LineComputational BiologyHigh-Throughput Nucleotide SequencingHumansNucleic Acid ConformationRNARNA-Directed DNA PolymeraseSequence Analysis, RNAConceptsLong RNA moleculesLong RNAsRNA moleculesRNA base modificationsGroup II intronsMutational profilingTranscriptome compositionRNA metabolismRNA researchBase modificationsPrimer extensionTool enzymeDiverse aspectsMixed populationEnzymeReverse transcriptionRNAStructural complexityReverse transcriptaseProfilingTranscriptase enzymeIntronsTranscription
2015
HOTAIR Forms an Intricate and Modular Secondary Structure
Somarowthu S, Legiewicz M, Chillón I, Marcia M, Liu F, Pyle AM. HOTAIR Forms an Intricate and Modular Secondary Structure. Molecular Cell 2015, 58: 353-361. PMID: 25866246, PMCID: PMC4406478, DOI: 10.1016/j.molcel.2015.03.006.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceConserved SequenceHumansIn Vitro TechniquesModels, MolecularNucleic Acid ConformationPhylogenyRNA, Long NoncodingConceptsFunctional secondary structureFundamental cellular processesSecondary structureProtein-binding motifsProtein-binding domainsGroup II intronsMetastasis suppressor geneSecondary structure elementsCellular processesPhylogenetic analysisLncRNA moleculesEpidermal developmentChemical probingMolecular mechanismsSuppressor geneCancer progressionStructural organizationKey playersLncRNA HOTAIRHOTAIRStructure elementsRNAHomogenous formReceptor activatorIntrons
2014
Principles of ion recognition in RNA: insights from the group II intron structures
Marcia M, Pyle AM. Principles of ion recognition in RNA: insights from the group II intron structures. RNA 2014, 20: 516-527. PMID: 24570483, PMCID: PMC3964913, DOI: 10.1261/rna.043414.113.Peer-Reviewed Original ResearchMeSH KeywordsBacillalesBinding SitesCatalytic DomainIntronsMetalsModels, MolecularNucleic Acid ConformationProtein ConformationRNA SplicingRNA, BacterialRNA, CatalyticRNA-Binding ProteinsConceptsActive siteSite-bound ionsIon recognitionMetal ionsOrganic ionsLatter ionIon-binding sitesCatalytic ionsCrystal structureGU wobble pairsMonovalent ionsLarge RNA moleculesIonsStructural ionsBiophysical methodsGroup II intron structureGA mismatchesLong-range tertiary contactsRNA structureRNA foldingTertiary contactsWobble pairStructureCatalysisHeteronuclear
2004
The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery
Wadley LM, Pyle AM. The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery. Nucleic Acids Research 2004, 32: 6650-6659. PMID: 15608296, PMCID: PMC545444, DOI: 10.1093/nar/gkh1002.Peer-Reviewed Original ResearchPeriodic cycles of RNA unwinding and pausing by hepatitis C virus NS3 helicase
Serebrov V, Pyle AM. Periodic cycles of RNA unwinding and pausing by hepatitis C virus NS3 helicase. Nature 2004, 430: 476-480. PMID: 15269774, DOI: 10.1038/nature02704.Peer-Reviewed Original ResearchSolution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif
Sigel RK, Sashital DG, Abramovitz DL, Palmer AG, Butcher SE, Pyle AM. Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif. Nature Structural & Molecular Biology 2004, 11: 187-192. PMID: 14745440, DOI: 10.1038/nsmb717.Peer-Reviewed Original ResearchConceptsGroup II intron ribozymeMetal ion titrationsSolution structureMetal ion bindingDivalent metal ionsMetal ion-binding sitesRibozyme active siteBackbone substituentsMetal ionsMajor groove faceIon-binding sitesIon titrationActive siteIon bindingSyn conformationIntron ribozymesMinor groove sideAGC triadNew RNA motifMajor grooveGroove faceStrong Mg2Catalytic triadGroove sideCentral core
2003
An Alternative Route for the Folding of Large RNAs: Apparent Two-state Folding by a Group II Intron Ribozyme
Su LJ, Brenowitz M, Pyle AM. An Alternative Route for the Folding of Large RNAs: Apparent Two-state Folding by a Group II Intron Ribozyme. Journal Of Molecular Biology 2003, 334: 639-652. PMID: 14636593, DOI: 10.1016/j.jmb.2003.09.071.Peer-Reviewed Original ResearchRNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space
Duarte CM, Wadley LM, Pyle AM. RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space. Nucleic Acids Research 2003, 31: 4755-4761. PMID: 12907716, PMCID: PMC169959, DOI: 10.1093/nar/gkg682.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsBase SequenceNucleic Acid ConformationRNARNA, MessengerRNA, RibosomalSoftwareConceptsRNA structureRepertoire of RNANovel RNA structuresNew RNA structuresStructural genomicsRNA functionRNA conformational spaceRibosomal subunitRNA researchRNA moleculesRNA motifsRNA structure comparisonMotif searchTertiary structureConformational changesStructure comparisonNew motifMotifReduced representationConformational spaceMacromolecular structureFuture adaptationGenomicsMajor regionsSubunitsDomains 2 and 3 Interact to Form Critical Elements of the Group II Intron Active Site
Fedorova O, Mitros T, Pyle AM. Domains 2 and 3 Interact to Form Critical Elements of the Group II Intron Active Site. Journal Of Molecular Biology 2003, 330: 197-209. PMID: 12823961, DOI: 10.1016/s0022-2836(03)00594-1.Peer-Reviewed Original ResearchA Group II Intron Inserted into a Bacterial Heat-Shock Operon Shows Autocatalytic Activity and Unusual Thermostability †
Adamidi C, Fedorova O, Pyle AM. A Group II Intron Inserted into a Bacterial Heat-Shock Operon Shows Autocatalytic Activity and Unusual Thermostability †. Biochemistry 2003, 42: 3409-3418. PMID: 12653544, DOI: 10.1021/bi027330b.Peer-Reviewed Original ResearchLanthanide ions as probes for metal ions in the structure and catalytic mechanism of ribozymes.
Sigel RK, Pyle AM. Lanthanide ions as probes for metal ions in the structure and catalytic mechanism of ribozymes. 2003, 40: 477-512. PMID: 12723158.Peer-Reviewed Original Research
2002
Group II introns: highly specific endonucleases with modular structures and diverse catalytic functions
Fedorova O, Su LJ, Pyle AM. Group II introns: highly specific endonucleases with modular structures and diverse catalytic functions. Methods 2002, 28: 323-335. PMID: 12431436, DOI: 10.1016/s1046-2023(02)00239-6.Peer-Reviewed Original ResearchProductive folding to the native state by a group II intron ribozyme11Edited by D. Draper
Swisher JF, Su LJ, Brenowitz M, Anderson VE, Pyle AM. Productive folding to the native state by a group II intron ribozyme11Edited by D. Draper. Journal Of Molecular Biology 2002, 315: 297-310. PMID: 11786013, DOI: 10.1006/jmbi.2001.5233.Peer-Reviewed Original Research