2025
Alternative Splicing Alterations in Patients With Amyotrophic Lateral Sclerosis: Link to the Disruption of TAR DNA‐Binding Protein 43 kDa Functions
Miwa T, Takeuchi E, Ogawa K, Abdelhamid R, Morita J, Hiraki Y, Yasumizu Y, Nakamura Y, Ohkura N, Saito Y, Murayama S, Nagai Y, Mochizuki H, Nagano S. Alternative Splicing Alterations in Patients With Amyotrophic Lateral Sclerosis: Link to the Disruption of TAR DNA‐Binding Protein 43 kDa Functions. Neurology And Clinical Neuroscience 2025, 13: 187-194. DOI: 10.1111/ncn3.12880.Peer-Reviewed Original ResearchAlternative splicing alterationsAlternative splicingTDP-43Splicing changesSplicing alterationsAmyotrophic lateral sclerosis pathologyAmyotrophic lateral sclerosisDNA-binding proteinsDysregulation of alternative splicingTAR DNA-binding proteinAberrant alternative splicingTAR DNA-binding protein 43 kDaSH-SY5Y cellsRNA metabolismDNA-binding protein 43 kDaNovel genesSplicing patternsNeurons of patientsRNA sequencingSplicingLateral sclerosisMotor neuronsTreatment of amyotrophic lateral sclerosisPolymerase chain reaction analysisMotor neurons of patients
2024
Ataxin-2 polyglutamine expansions aberrantly sequester TDP-43 ribonucleoprotein condensates disrupting mRNA transport and local translation in neurons
Wijegunawardana D, Nayak A, Vishal S, Venkatesh N, Gopal P. Ataxin-2 polyglutamine expansions aberrantly sequester TDP-43 ribonucleoprotein condensates disrupting mRNA transport and local translation in neurons. Developmental Cell 2024, 60: 253-269.e5. PMID: 39419034, PMCID: PMC12063900, DOI: 10.1016/j.devcel.2024.09.023.Peer-Reviewed Original ResearchRNA-binding proteinsAtaxin-2PolyQ expansionTDP-43Like-SmLocal translationAmyotrophic lateral sclerosisDNA-binding proteinsTransactive response DNA-binding proteinLocalization of mRNAAssociated with increased riskRNA metabolismCytoskeletal mRNAsMRNA transportPolyglutamine expansionRNP condensatesMotor neuron axonsRegulatory functionsRibonucleoproteinMotor neuron integrityNeuronal integrityCortical neuronsLiquid-like propertiesNeuronal axonsMotilityRNA modifications in the progression of liver diseases: from fatty liver to cancer
Li S, Mehal W, Ouyang X. RNA modifications in the progression of liver diseases: from fatty liver to cancer. Science China Life Sciences 2024, 67: 2105-2119. PMID: 38809498, PMCID: PMC11545962, DOI: 10.1007/s11427-023-2494-x.Peer-Reviewed Original ResearchRNA modificationsRNA metabolismRNA speciesNon-alcoholic fatty liver diseaseN1-methyladenosineCellular functionsN6-methyladenosineGene expressionRNANon-alcoholic steatohepatitisFatty liver to non-alcoholic steatohepatitisM6AHepatocellular carcinomaGlobal health concernFatty liver diseaseLiver diseaseM5CHigher risk of metabolic syndromePseudouridineAssociated with higher risk of metabolic syndromePathological conditionsRisk of metabolic syndromeGenes-methyladenosineProgression of liver diseaseHighly Reactive Group I Introns Ubiquitous in Pathogenic Fungi
Liu T, Pyle A. Highly Reactive Group I Introns Ubiquitous in Pathogenic Fungi. Journal Of Molecular Biology 2024, 436: 168513. PMID: 38447889, DOI: 10.1016/j.jmb.2024.168513.Peer-Reviewed Original ResearchGroup I intronsAntifungal drug targetsRNA metabolismPathogenic fungiPhylogeny of fungiSelf-splicing intronsDrug targetsSystemic fungal infectionsGenetic hotspotsRiboregulatory elementsMitochondrial intronsMitochondrial genesBioinformatics pipelineC. aurisCandida aurisRelevant fungiRNA elementsAspergillus fumigatusC. albicansHousekeeping genesCandida albicansNoncoding transcriptomeCryptococcus neoformansFungal infectionsFungi
2023
FUS Alters circRNA Metabolism in Human Motor Neurons Carrying the ALS-Linked P525L Mutation
Colantoni A, Capauto D, Alfano V, D’Ambra E, D’Uva S, Tartaglia G, Morlando M. FUS Alters circRNA Metabolism in Human Motor Neurons Carrying the ALS-Linked P525L Mutation. International Journal Of Molecular Sciences 2023, 24: 3181. PMID: 36834591, PMCID: PMC9968238, DOI: 10.3390/ijms24043181.Peer-Reviewed Original ResearchConceptsRNA metabolismHuman motor neuronsNuclear/cytoplasmic partitioningNon-canonical splicing eventsAspects of RNASubset of circRNAsCytoplasmic partitioningCytoplasmic circRNAsSplicing eventsMutant proteinsCircular RNAsMotor neuronsAlu repeatsExon compositionCircRNAsProteinRNAMutationsFUS mutationsKey eventsFUSPreferential bindingP525L mutationMetabolismPivotal role
2022
An RNAi screen of RNA helicases identifies eIF4A3 as a regulator of embryonic stem cell identity
Li D, Yang J, Malik V, Huang Y, Huang X, Zhou H, Wang J. An RNAi screen of RNA helicases identifies eIF4A3 as a regulator of embryonic stem cell identity. Nucleic Acids Research 2022, 50: 12462-12479. PMID: 36416264, PMCID: PMC9757061, DOI: 10.1093/nar/gkac1084.Peer-Reviewed Original ResearchConceptsExon junction complexRNA helicaseRNA interferenceEmbryonic stem cellsPost-transcriptionallyEmbryonic stem cell identityEfficient nuclear exportRNA interference screenCell cycle progression of ESCsPost-transcriptional controlCell cycle regulationStem cell identityCell cycle progressionMaintenance of embryonic stem cellsStem cell pluripotencyLoss of pluripotencyRNA metabolismDEAD-boxCell cycle dysregulationCell identityCycle regulationCell pluripotencyCell cyclePluripotency controlCyclin B1piRNA/PIWI Protein Complex as a Potential Biomarker in Sporadic Amyotrophic Lateral Sclerosis
Abdelhamid R, Ogawa K, Beck G, Ikenaka K, Takeuchi E, Yasumizu Y, Jinno J, Kimura Y, Baba K, Nagai Y, Okada Y, Saito Y, Murayama S, Mochizuki H, Nagano S. piRNA/PIWI Protein Complex as a Potential Biomarker in Sporadic Amyotrophic Lateral Sclerosis. Molecular Neurobiology 2022, 59: 1693-1705. PMID: 35015250, PMCID: PMC8882100, DOI: 10.1007/s12035-021-02686-2.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsNon-coding RNAsBind to PIWI-interacting RNAsDysregulation of piRNAsControl postmortem brain samplesAmyotrophic lateral sclerosisTDP-43Biogenesis of RNAsAggregation of TAR DNA-binding protein 43RNA-binding proteinsTAR DNA-binding protein 43DNA-binding protein 43Abnormal RNA metabolismNcRNA biogenesisPIWI proteinsPiwi homologsSilencing 1Sporadic ALSRNA metabolismRNA-seqTDP-43 pathologyProtein complexesPIWIL1Sporadic amyotrophic lateral sclerosisPathological hallmark
2021
UHRF1 regulates alternative splicing by interacting with splicing factors and U snRNAs in a H3R2me involved manner
Xu P, Zhang L, Xiao Y, Li W, Hu Z, Zhang R, Li J, Wu F, Xi Y, Zou Q, Wang Z, Guo R, Ma H, Dong S, Xiao M, Yang Z, Ren X, Wei C, Yu W. UHRF1 regulates alternative splicing by interacting with splicing factors and U snRNAs in a H3R2me involved manner. Human Molecular Genetics 2021, 30: 2110-2122. PMID: 34196368, DOI: 10.1093/hmg/ddab178.Peer-Reviewed Original ResearchConceptsU snRNAsSplicing factorsDNA methylation maintenanceAlternative splicing eventsFunctions of UHRF1RNA splicing regulationAlternative RNA splicingDNA damage repairU2 snRNAMethylation maintenanceProtein interactomeRNA metabolismSplicing regulationRNA splicingSplicing eventsSpliceosome componentsAlternative splicingRNA interactomeUHRF1Chromatin configurationBinding preferencesCell cycleMolecular basisBiological processesMethylation status
2020
Regulation and Function of RNA Pseudouridylation in Human Cells
Borchardt EK, Martinez NM, Gilbert WV. Regulation and Function of RNA Pseudouridylation in Human Cells. Annual Review Of Genetics 2020, 54: 1-28. PMID: 32870730, PMCID: PMC8007080, DOI: 10.1146/annurev-genet-112618-043830.Peer-Reviewed Original ResearchConceptsRNA pseudouridylationHuman cellsRNA-binding proteinDistinct RNA sequencesMRNA pseudouridylationPseudouridine synthasesMolecular functionsRNA metabolismPseudouridylationGene expressionRNA conformationRNA targetsProtein productionRNA sequencesMessenger RNADiverse classRNATherapeutic mRNAWidespread effectsDestabilizing interactionsCellsRecent advancesSplicingSynthasesPotential effectsRNA-binding proteins in neurological development and disease
Prashad S, Gopal PP. RNA-binding proteins in neurological development and disease. RNA Biology 2020, 18: 972-987. PMID: 32865115, PMCID: PMC8216196, DOI: 10.1080/15476286.2020.1809186.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsRNA-binding proteinGene expressionDisease-linked RNA-binding proteinsHigh-throughput transcriptomic analysisRNA processing stepsAberrant RNA metabolismAberrant RNA processingRecent exciting studiesRNA processingRNA metabolismMRNA traffickingAlternative splicingMultifunctional proteinTranscriptomic analysisSplicing misregulationMRNA stabilityMolecular mechanismsProtein resultsNeuronal homeostasisNeurodevelopmental defectsNeuronal proteinsFunctional consequencesPleiotropic effectsSpatiotemporal controlProteinSequencing 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
Uncoupling of nucleo-cytoplasmic RNA export and localization during stress
Hochberg-Laufer H, Schwed-Gross A, Neugebauer KM, Shav-Tal Y. Uncoupling of nucleo-cytoplasmic RNA export and localization during stress. Nucleic Acids Research 2019, 47: 4778-4797. PMID: 30864659, PMCID: PMC6511838, DOI: 10.1093/nar/gkz168.Peer-Reviewed Original ResearchConceptsRNA-binding proteinStress granulesNuclear specklesMRNA exportFormation of SGsCytoplasmic stress granulesSub-cellular compartmentsGene expression pathwaysMRNA export adaptorsComplex recruitmentEukaryotic cellsRNA exportRNA metabolismExport adaptorGranule assemblyNuclear proteinsExpression pathwaysRNAStress inductionMRNACytoplasmProteinPotent inhibitorCellsNucleoporins
2018
The role of 3′ end uridylation in RNA metabolism and cellular physiology
Zigáčková D, Vaňáčová Š. The role of 3′ end uridylation in RNA metabolism and cellular physiology. Philosophical Transactions Of The Royal Society B Biological Sciences 2018, 373: 20180171. PMID: 30397107, PMCID: PMC6232591, DOI: 10.1098/rstb.2018.0171.Peer-Reviewed Original ResearchConceptsRNA metabolismRegulation of stabilityCell cycle regulationNumber of pathwaysRNA maturationEukaryotic RNAOrganismal levelCellular physiologyCycle regulationRNA degradationCellular RNADiverse rolesWidespread modificationCell deathUridylationRNAMajority of modificationsCurrent knowledgeLife cycleCritical roleTheme issueRegulationPathwayMetabolismEukaryotesGaining insight into transcriptome‐wide RNA population dynamics through the chemistry of 4‐thiouridine
Duffy EE, Schofield JA, Simon MD. Gaining insight into transcriptome‐wide RNA population dynamics through the chemistry of 4‐thiouridine. Wiley Interdisciplinary Reviews - RNA 2018, 10: e1513. PMID: 30370679, PMCID: PMC6768404, DOI: 10.1002/wrna.1513.Peer-Reviewed Original ResearchConceptsDifferent RNA populationsRNA populationsNumerous experimental strategiesCellular RNA levelsMetabolic labeling experimentsRNA levelsRNA metabolismRNA turnoverRNA stabilityRNA transcriptionRNA sequencingMetabolic labelingPopulation dynamicsMetabolic labelTargeted incorporationRNA analysisRNA methodWhole cellsC mutationLabeling experimentsExperimental strategiesSequencingAvailable poolGenomeCellsRNA m6A modification and its function in diseases
Tong J, Flavell RA, Li HB. RNA m6A modification and its function in diseases. Frontiers Of Medicine 2018, 12: 481-489. PMID: 30097961, DOI: 10.1007/s11684-018-0654-8.Peer-Reviewed Original ResearchConceptsM6A modificationPost-transcriptional RNA modificationsRegulation of m6ACore catalytic componentFunction of m6ARNA m6A modificationRNA metabolismRegulatory networksRNA modificationsPhysiological contextHuman diseasesPhysiological roleM6ACatalytic componentFunctional relevanceCell linesM6A modulatorsDifferent cellsDisease conditionsTranscriptomeRecent advancesErasersRegulatorBindsModificationNup159 Weakens Gle1 Binding to Dbp5 But Does Not Accelerate ADP Release
Wong EV, Gray S, Cao W, Montpetit R, Montpetit B, De La Cruz EM. Nup159 Weakens Gle1 Binding to Dbp5 But Does Not Accelerate ADP Release. Journal Of Molecular Biology 2018, 430: 2080-2095. PMID: 29782832, PMCID: PMC6003625, DOI: 10.1016/j.jmb.2018.05.025.Peer-Reviewed Original ResearchConceptsEssential DEAD-box proteinADP releaseDbp5's ATPase activityDEAD-box proteinsNucleotide exchange factorsDbp5 activityMRNA exportRNA metabolismExchange factorDbp5Cellular processesATPase cyclingNup159Gle1ATP affinityMechanochemical cycleATPase activityADPATP releaseDDX19NTPasesNucleoporinsDetailed characterizationRNARegulatorCharacterization of the lncRNA transcriptome in mESC-derived motor neurons: Implications for FUS-ALS
Biscarini S, Capauto D, Peruzzi G, Lu L, Colantoni A, Santini T, Shneider NA, Caffarelli E, Laneve P, Bozzoni I. Characterization of the lncRNA transcriptome in mESC-derived motor neurons: Implications for FUS-ALS. Stem Cell Research 2018, 27: 172-179. PMID: 29449089, DOI: 10.1016/j.scr.2018.01.037.Peer-Reviewed Original ResearchConceptsLong non-coding transcriptomeMouse motor neuronsAmyotrophic lateral sclerosisNon-coding transcriptomeMotor neuronsSevere amyotrophic lateral sclerosisAberrant RNA metabolismLong non-coding RNAsStem cellsEmbryonic stem cellsNon-coding RNAsInduced pluripotent stem cellsNervous system developmentPluripotent stem cellsRNA metabolismLncRNA transcriptomeDifferentiation systemLateral sclerosisTDP-43TranscriptomeFUS-ALSCandidate lncRNAsCrucial playersCausative mutationsEssential role
2017
Dynamic RNA–protein interactions underlie the zebrafish maternal-to-zygotic transition
Despic V, Dejung M, Gu M, Krishnan J, Zhang J, Herzel L, Straube K, Gerstein MB, Butter F, Neugebauer KM. Dynamic RNA–protein interactions underlie the zebrafish maternal-to-zygotic transition. Genome Research 2017, 27: 1184-1194. PMID: 28381614, PMCID: PMC5495070, DOI: 10.1101/gr.215954.116.Peer-Reviewed Original ResearchConceptsZygotic genome activationRNA-protein interactionsMaternal mRNAsZygotic transitionSplicing factorsDynamic RNA-protein interactionsMRNA interactome capturePost-transcriptional regulationMRNA splicing factorsRNA processing eventsTranscription-dependent mannerNumerous splicing factorsInteractome captureGenome activationSequence-specific associationHnRNP proteinsRNA metabolismDramatic translocationZebrafish embryosProcessing eventsICLIP dataDevelopmental transitionsRNA targetsReporter assaysProtein constellationsDrosophila CG3303 is an essential endoribonuclease linked to TDP-43-mediated neurodegeneration
Laneve P, Piacentini L, Casale AM, Capauto D, Gioia U, Cappucci U, Di Carlo V, Bozzoni I, Di Micco P, Morea V, Di Franco CA, Caffarelli E. Drosophila CG3303 is an essential endoribonuclease linked to TDP-43-mediated neurodegeneration. Scientific Reports 2017, 7: 41559. PMID: 28139767, PMCID: PMC5282483, DOI: 10.1038/srep41559.Peer-Reviewed Original ResearchConceptsEukaryotic RNA metabolismDrosophila nervous systemTDP-43-mediated neurodegenerationImportant biological processesNovel family memberUnique biochemical featuresEssential endoribonucleaseRibosome biogenesisDrosophila viabilityRNA metabolismPositive regulatorFunctional characterisationBiosynthetic enzymesRibonuclease familyGene productsBiological processesMolecular levelNervous system activityBiochemical featuresCholinergic circuitsPhenotypeViral replicationNervous systemImmature phenotypeFamily members
2014
p53-directed translational control can shape and expand the universe of p53 target genes
Zaccara S, Tebaldi T, Pederiva C, Ciribilli Y, Bisio A, Inga A. p53-directed translational control can shape and expand the universe of p53 target genes. Cell Death & Differentiation 2014, 21: 1522-1534. PMID: 24926617, PMCID: PMC4158691, DOI: 10.1038/cdd.2014.79.Peer-Reviewed Original ResearchMeSH KeywordsApoptosisCell CycleCell Line, TumorDEAD-box RNA HelicasesDNADNA-Binding ProteinsDoxorubicinGene Expression ProfilingGene Expression RegulationGene Regulatory NetworksHeterogeneous Nuclear Ribonucleoprotein D0Heterogeneous-Nuclear Ribonucleoprotein DHumansImidazolesMCF-7 CellsNuclear ProteinsPeptide Chain Elongation, TranslationalPiperazinesRNARNA InterferenceRNA-Binding ProteinsRNA, MessengerRNA, Small InterferingSerine-Arginine Splicing FactorsTumor Suppressor Protein p53Y-Box-Binding Protein 1ConceptsPost-transcriptional controlTranslational controlP53-dependent cellular responseTranslational levelGenome-wide transcriptome analysisCellular responsesRNA-binding proteinCell cycle functionP53-regulated genesGene expression responsesP53 target genesP53 transcriptional targetsDirect p53 transcriptional targetP53-dependent mannerTranscription variationTranscriptional networksPolysomal profilingRNA metabolismTranslatome analysisTranscriptome analysisCellular contextTranscriptional targetsExpression responsesMaster regulatorTarget genes
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