2025
Structural insights into RNA targeting with de novo small molecule
Xu L, Chung K, Liu T, Pyle A. Structural insights into RNA targeting with de novo small molecule. Structural Dynamics 2025, 12: a41-a41. DOI: 10.1063/4.0000350.Peer-Reviewed Original ResearchRNA-small molecule interactionsChemical space explorationRNA-ligand recognitionMedicinal chemistry campaignHigh-throughput screening assayChemistry campaignSelf-splicing intronsInhibitor discoveryNon-coding genesMolecule interactionsCryo-EM structureSmall moleculesAtomic detailRNA bindersStructural insightsMolecular interactionsC. albicansTarget RNASplicing inhibitorsGene productsRNA moleculesRNA targetsDruggable genomeDrug developmentMolecules
2024
An RNA-centric view of transcription and genome organization
Henninger J, Young R. An RNA-centric view of transcription and genome organization. Molecular Cell 2024, 84: 3627-3643. PMID: 39366351, PMCID: PMC11495847, DOI: 10.1016/j.molcel.2024.08.021.Peer-Reviewed Original ResearchConceptsGene regulationGenome architectureTranscriptional regulationModel of transcriptional regulationAssembly of protein complexesAssembly of transcription complexesLocal genome architectureSilencing of genesGenomic compartmentsGenome organizationGenomic structureRNA polymeraseChromatin regulationTranscription complexActive genesProtein complexesRNA moleculesTranscription factorsGenomeProtein kinaseSpecific genesGenesFeedback regulationRNASpatial compartmentsRNA and condensates: Disease implications and therapeutic opportunities
Han T, Portz B, Young R, Boija A, Klein I. RNA and condensates: Disease implications and therapeutic opportunities. Cell Chemical Biology 2024, 31: 1593-1609. PMID: 39303698, DOI: 10.1016/j.chembiol.2024.08.009.Peer-Reviewed Original ResearchConceptsRegulate key cellular processesDiverse RNA speciesRNA speciesTarget RNACompartmentalizing proteinsCellular processesRNA moleculesMembraneless organellesRNA roleBiomolecular condensatesRNA-based therapiesComplex diseasesRNA abnormalitiesRNADisease pathogenesisCondensate formationProperties of condensatesTherapeutic strategiesSmall moleculesOrganellesMislocalizationOverexpressionProteinSpeciesNeurological disordersCharacterization 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 specificityThe physiological and pathological roles of RNA modifications in T cells
Deng Y, Zhou J, Li H. The physiological and pathological roles of RNA modifications in T cells. Cell Chemical Biology 2024, 31: 1578-1592. PMID: 38986618, DOI: 10.1016/j.chembiol.2024.06.003.Peer-Reviewed Original ResearchRNA modificationsDynamic chemical modificationsInternal RNA modificationFunctions of mammalian cellsT cell developmentPathological roleRNA transcriptsCellular stimuliMammalian cellsRNA moleculesPost-transcriptionallyT cell biologyT cell survivalT cellsCell developmentCell survivalCell biologyRNAT cell-based immunotherapyCell-based immunotherapyT cell immunityAdaptive immunityCellsDifferentiationCell immunityCoupling clearing and hybridization chain reaction approaches to investigate gene expression in organs inside intact insect heads
Cayrol B, Colella S, Uzest M. Coupling clearing and hybridization chain reaction approaches to investigate gene expression in organs inside intact insect heads. Microscopy Research And Technique 2024, 87: 1926-1932. PMID: 38558482, DOI: 10.1002/jemt.24561.Peer-Reviewed Original ResearchConceptsSecretory cellsSpatial distribution of transcriptsSecretory cells of salivary glandsDetected RNA moleculesDetection of transcriptsDistribution of transcriptsInvestigate gene expressionPigmented cuticleHigh-resolution analysisRNA moleculesCells of salivary glandsHybridization chain reactionAphid headsGene expressionPrincipal glandChain reactionTranscriptionAmplification approachInsect headAcyrthosiphon pisumHybridisation chain reactionCuticleMultiplex approachSmall organismsSHP
2022
The RIG-I receptor adopts two different conformations for distinguishing host from viral RNA ligands
Wang W, Pyle AM. The RIG-I receptor adopts two different conformations for distinguishing host from viral RNA ligands. Molecular Cell 2022, 82: 4131-4144.e6. PMID: 36272408, PMCID: PMC9707737, DOI: 10.1016/j.molcel.2022.09.029.Peer-Reviewed Original ResearchConceptsRNA moleculesRNA ligandsHigh-resolution cryo-EM structuresCryo-EM structureDouble-stranded RNARIG-I receptorInduction of autoimmunityViral RNA moleculesAutoinhibited conformationInnate immune receptorsHost RNARelated RNAProtein foldsMolecular basisUnique molecular featuresHigh-affinity conformationAntiviral sensingHost cellsRNA virusesRNA releaseImmune receptorsRNAViral RNAExquisite selectivityMolecular features
2021
Roles of microRNAs in inflammatory bowel disease
Jung H, Kim J, Lee K, Tizaoui K, Terrazzino S, Cargnin S, Smith L, Koyanagi A, Jacob L, Li H, Hong S, Yon D, Lee S, Kim M, Wasuwanich P, Karnsakul W, Shin J, Kronbichler A. Roles of microRNAs in inflammatory bowel disease. International Journal Of Biological Sciences 2021, 17: 2112-2123. PMID: 34131410, PMCID: PMC8193269, DOI: 10.7150/ijbs.59904.Peer-Reviewed Original ResearchConceptsInflammatory bowel diseaseRegulate gene expressionBowel diseaseSamples of IBD patientsTreatment of inflammatory bowel diseasePathogenesis of inflammatory bowel diseaseRNA moleculesSerum samples of IBD patientsChronic inflammatory diseaseTreat inflammatory bowel diseaseGene expressionHost immune responseIntestinal bacteriaQuality of life of patientsSignaling pathwayIntestinal barrierIntestinal epitheliumLife of patientsGastrointestinal symptomsIntracolonic administrationPathophysiological mechanismsIBD patientsInflammatory diseasesImmune responseColon tissues
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
2019
RIG-I Recognition of RNA Targets: The Influence of Terminal Base Pair Sequence and Overhangs on Affinity and Signaling
Ren X, Linehan MM, Iwasaki A, Pyle AM. RIG-I Recognition of RNA Targets: The Influence of Terminal Base Pair Sequence and Overhangs on Affinity and Signaling. Cell Reports 2019, 29: 3807-3815.e3. PMID: 31851914, DOI: 10.1016/j.celrep.2019.11.052.Peer-Reviewed Original ResearchConceptsRNA moleculesRIG-I activationBase pair sequenceHost RNA moleculesViral RNA moleculesRIG-I recognitionMolecular basisRNA variantsRNA targetsPair sequenceHuman cellsBase pairsImmune receptorsMechanisms of evasionTerminal base pairsLigand affinityWhole animalInterferon responseDeadly pathogenRNA therapeuticsMarburg virusCellsOverhangMoleculesSignaling
2018
Non-coding RNA regulation of endothelial and macrophage functions during atherosclerosis
Aryal B, Suárez Y. Non-coding RNA regulation of endothelial and macrophage functions during atherosclerosis. Vascular Pharmacology 2018, 114: 64-75. PMID: 29551552, PMCID: PMC6177333, DOI: 10.1016/j.vph.2018.03.001.Peer-Reviewed Original ResearchConceptsNon-coding RNAsNon-coding RNA regulationSmall non-coding RNAsMultiple cell functionsRNA regulationMacrophage functionRNA moleculesGene expressionPotential regulatorKey playersVascular biologyPathogenesis of atherosclerosisCell functionSpecific roleLncRNAsRegulationRNAMechanism of actionEndothelial cellsInitial eventVascular integrityRecruitment of monocytesMicroRNAsDevelopment of atherosclerosisBiology
2016
Airway Secretory microRNAome Changes during Rhinovirus Infection in Early Childhood
Gutierrez M, Gomez J, Perez G, Pancham K, Val S, Pillai D, Giri M, Ferrante S, Freishtat R, Rose M, Preciado D, Nino G. Airway Secretory microRNAome Changes during Rhinovirus Infection in Early Childhood. PLOS ONE 2016, 11: e0162244. PMID: 27643599, PMCID: PMC5028059, DOI: 10.1371/journal.pone.0162244.Peer-Reviewed Original ResearchConceptsRV infectionHuman bronchial epithelial cellsAirway secretionsExtracellular vesiclesCause of asthma exacerbationsAirways of young childrenHuman RV infectionsNasal airway secretionsHsa-miR-155Air-liquid interfaceRegulates antiviral immunityMonitor respiratory conditionsSecretion of extracellular vesiclesModify gene expressionAirways of individualsPotential biological relevanceBronchial epithelial cellsAge-matched controlsInnate immune responseDevelopment of asthmaBioinformatics toolsGene datasetsGenetic communicationNoncoding RNA moleculesRNA molecules
2014
RNA editing, epitranscriptomics, and processing in cancer progression
Witkin KL, Hanlon SE, Strasburger JA, Coffin JM, Jaffrey SR, Howcroft TK, Dedon PC, Steitz JA, Daschner PJ, Read-Connole E. RNA editing, epitranscriptomics, and processing in cancer progression. Cancer Biology & Therapy 2014, 16: 21-27. PMID: 25455629, PMCID: PMC4622672, DOI: 10.4161/15384047.2014.987555.Peer-Reviewed Original ResearchConceptsRNA modificationsRNA editingNetworks of RNAsTRNA base modificationsEpitranscriptomic RNA modificationsNuclear-cytoplasmic transportCancer progressionCellular stress pathwaysPrimary RNA sequenceRNA processingRNA splicingMRNA translationRNA interferenceRNA moleculesRegulated cleavageGene expressionCancer biologistsRNA sequencesBase modificationsCancer initiationCancer biologyStress pathwaysEnvironmental conditionsRNAEnzymatic pathwaysConstruction of Trypanosoma brucei Illumina RNA-Seq Libraries Enriched for Transcript Ends
Kolev NG, Ullu E, Tschudi C. Construction of Trypanosoma brucei Illumina RNA-Seq Libraries Enriched for Transcript Ends. Methods In Molecular Biology 2014, 1201: 165-175. PMID: 25388113, DOI: 10.1007/978-1-4939-1438-8_9.Peer-Reviewed Original ResearchConceptsHuman pathogen Trypanosoma bruceiHigh-throughput RNA sequencingLong polycistronic precursorsGenome-wide scaleIllumina RNA-seqPathogen Trypanosoma bruceiRNA polymerase IIRNA-seq librariesSingle-nucleotide resolutionTranscript endsTranscript boundariesTranscriptome annotationUnannotated genesPolymerase IICellular abundancePolycistronic precursorsTranscription initiationGene clusterRNA-seqPolyadenylation sitesRNA sequencingMRNA precursorsTrypanosoma bruceiRNA moleculesMRNA moleculesThe Properties of Long Noncoding RNAs that Regulate Chromatin
Rutenberg-Schoenberg M, Sexton A, Simon M. The Properties of Long Noncoding RNAs that Regulate Chromatin. Annual Review Of Genomics And Human Genetics 2014, 17: 1-26. DOI: 10.1146/annurev-genom-090314-024939.Peer-Reviewed Original ResearchChromatin-based processesLong noncoding RNAMechanisms of lncRNAsChromatin biologyChromatin structureLncRNA functionsNuclear roleHuman lncRNAsPosttranscriptional regulationNoncoding RNAsRNA moleculesGene expressionFinal online publication dateBiochemical mechanismsBroader roleRNAUpstream roleLncRNAsOnline publication dateHuman physiologyChromatinGenomicsTranscriptionBiologyMechanismIntergenic Transcriptional Interference Is Blocked by RNA Polymerase III Transcription Factor TFIIIB in Saccharomyces cerevisiae
Korde A, Rosselot J, Donze D. Intergenic Transcriptional Interference Is Blocked by RNA Polymerase III Transcription Factor TFIIIB in Saccharomyces cerevisiae. Genetics 2014, 196: 427-438. PMID: 24336746, PMCID: PMC3914616, DOI: 10.1534/genetics.113.160093.Peer-Reviewed Original ResearchConceptsRNA polymerase III complexTranscriptional interferenceRNA polymerase III transcription factor TFIIIBRNA polymerase II transcriptionAdditional nuclear functionsPolymerase II transcriptionEukaryotic RNA polymerase IIITranscription factor TFIIIBNitrogen starvation conditionsRNA polymerase IIIPervasive transcriptionTRNA genesChromatin boundariesNuclear functionsTFIIIB complexTranscription unitGene upstreamTransfer RNAReadthrough transcriptsRibosomal RNANucleosome phasingPolymerase IIIStarvation conditionsGene productsRNA molecules
2012
SIRNA-MEDIATED INHIBITION OF INTERLEUKINE-13 PRODUCTION IN VITRO
Shilovskiy I, Mazurov D, Shershakova N, Khaitov M. SIRNA-MEDIATED INHIBITION OF INTERLEUKINE-13 PRODUCTION IN VITRO. Russian Journal Of Allergy 2012, 9: 24-27. DOI: 10.36691/rja683.Peer-Reviewed Original ResearchExpression of IL-13Gene expressionIL-13Gene expression changesGene expression of miceSmall interfering RNA moleculesEfficiency of siRNAIL-13 in vitroExpression of IL-13 mRNARNA moleculesExpression of mouseConA-stimulated spleen cellsPathogenesis of allergic conditionsProtein productionCo-transfectionExpression changesGene expression of IL-13IL-13 mRNASiRNA moleculesGenesTwenty-Four HoursSiRNAQuantitative PCRGFP+ cellsSpleen cellsRNA–protein interactions in vivo: global gets specific
Änkö M, Neugebauer KM. RNA–protein interactions in vivo: global gets specific. Trends In Biochemical Sciences 2012, 37: 255-262. PMID: 22425269, DOI: 10.1016/j.tibs.2012.02.005.Peer-Reviewed Original ResearchConceptsNumerous protein domainsRNA-binding specificityRNA-protein interactionsEndogenous RNA moleculesShort RNA sequencesProperties of proteinsProtein domainsPolyadenylation factorsRNA moleculesRNA sequencesRNALimited repertoireProteinStructural determinationChaperonesCellsRecent advancesSplicingVivoSpecificitySequenceCrucial contributionDestabilizerRepertoireLocalization factor
2010
A potential role for intragenic miRNAs on their hosts' interactome
Hinske L, Galante P, Kuo W, Ohno-Machado L. A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics 2010, 11: 533. PMID: 20920310, PMCID: PMC3091682, DOI: 10.1186/1471-2164-11-533.Peer-Reviewed Original ResearchConceptsIntragenic miRNAsHost genesAdenylate/uridylate-rich elementsMiRNA targetsMRNA targetsHost interactomeGene cohortsMiRNA biogenesis pathwayNon-coding RNA moleculesHigh-confidence setMiRNA target genesProtein-coding regionsKEGG pathway analysisTight regulatory controlNegative feedback regulatorIntronic miRNAsMore intronsBiogenesis pathwayMiRNA genesNegative feedback loopUridylate-rich elementsCellular homeostasisTarget genesRNA moleculesInteractomeBacterial Riboswitch Discovery and Analysis
Ames T, Breaker R. Bacterial Riboswitch Discovery and Analysis. 2010, 433-454. DOI: 10.1002/9780470664001.ch20.Peer-Reviewed Original Research
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