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 signaturesPathogensGenomeCofactorDiversityTarget
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 ResearchConceptsLong 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 ResearchConceptsFunctional 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