2025
Biallelic variants in the conserved ribosomal protein chaperone gene PDCD2 are associated with hydrops fetalis and early pregnancy loss
Landry-Voyer A, Holling T, Mis E, Hassani Z, Alawi M, Ji W, Jeffries L, Kutsche K, Bachand F, Lakhani S. Biallelic variants in the conserved ribosomal protein chaperone gene PDCD2 are associated with hydrops fetalis and early pregnancy loss. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2426078122. PMID: 40208938, PMCID: PMC12012559, DOI: 10.1073/pnas.2426078122.Peer-Reviewed Original ResearchConceptsRibosomal RNA processingRNA processingNonimmune hydrops fetalisRibosomal biogenesis disordersNext generation sequencingRibosome biogenesisPregnancy lossPatient variantsMolecular chaperonesExome sequencingGeneration sequencingPDCD2Biallelic variantsGenetic variantsHydrops fetalisIndependent familiesIn vivo approachesAffected fetusMolecular causesPrimary fibroblastsDevelopmental defectsMonogenic disordersAssociated with hydrops fetalisUS5Early pregnancy loss
2024
Identification of coilin interactors reveals coordinated control of Cajal body number and structure
Escayola D, Zhang C, Nischwitz E, Schärfen L, Dörner K, Straube K, Kutay U, Butter F, Neugebauer K. Identification of coilin interactors reveals coordinated control of Cajal body number and structure. Journal Of Cell Biology 2024, 224: e202305081. PMID: 39602297, PMCID: PMC11602656, DOI: 10.1083/jcb.202305081.Peer-Reviewed Original ResearchConceptsCajal bodiesSurvival motor neuron proteinCB assemblyModulating posttranslational modificationsRegulate RNA processingProtein interactorsProximity biotinylationRNA processingGenetic lociPosttranslational modificationsGene activationTranscription factorsFunctional screeningBiomolecular condensatesCoilinNeuronal proteinsCell nucleiProteinNuclear levelsNuclear positivityCB componentsCB numberBody numberAssemblyRibosomeA Unified Post-Transcriptional Mechanism Regulates Intron Retention in Splicing Factor-Mutant MDS
Boddu P, Roy R, Baumgartner F, Hutter S, Haferlach T, Pillai M. A Unified Post-Transcriptional Mechanism Regulates Intron Retention in Splicing Factor-Mutant MDS. Blood 2024, 144: 2732-2732. DOI: 10.1182/blood-2024-211458.Peer-Reviewed Original ResearchRNA-binding proteinsIntron retentionAlternative splicing patternsPost-transcriptional mechanismsIR eventsSF mutationsSR proteinsSF3B1 mutantsAnalyzed RNA-seq datasetsMyelodysplastic syndromeCo-transcriptional splicingCo-transcriptional mechanismsRNA-seq datasetsPost-transcriptional splicingWild-typeSub-compartmentsNuclear sub-compartmentsHEK293T cellsGene expression analysisWild-type K562 cellsRNA processingMutant cellsPhospho-proteomicsExon featuresAS eventsProteomic basis for pancreatic acinar cell carcinoma and pancreatoblastoma as similar yet distinct entities
Tanaka A, Ogawa M, Zhou Y, Hendrickson R, Miele M, Li Z, Klimstra D, Wang J, Roehrl M. Proteomic basis for pancreatic acinar cell carcinoma and pancreatoblastoma as similar yet distinct entities. Npj Precision Oncology 2024, 8: 221. PMID: 39363045, PMCID: PMC11449907, DOI: 10.1038/s41698-024-00708-5.Peer-Reviewed Original ResearchAcinar cell carcinomaPancreatic ductal adenocarcinomaActin-based processesPathway activity differencesCell carcinomaChromosome organizationChromosomal proteinsProteomic basisRNA processingIGF2 pathwayProtein expression patternsEpithelial-to-mesenchymal transitionProteogenomic profilingPancreatic acinar cell carcinomaProteomic landscapeDNA repairCell cycleRare pancreatic malignancyExpression patternsMitochondrial dysfunctionStem cell phenotypeMetabolic adaptationProteinExtracellular matrixPancreatic malignancySpatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues
Bai Z, Zhang D, Gao Y, Tao B, Zhang D, Bao S, Enninful A, Wang Y, Li H, Su G, Tian X, Zhang N, Xiao Y, Liu Y, Gerstein M, Li M, Xing Y, Lu J, Xu M, Fan R. Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues. Cell 2024, 187: 6760-6779.e24. PMID: 39353436, PMCID: PMC11568911, DOI: 10.1016/j.cell.2024.09.001.Peer-Reviewed Original ResearchRNA biologyWhole-transcriptome sequencingMicroRNA regulatory networkSplicing dynamicsDeterministic barcodingRNA speciesRNA processingRNA variantsFFPE tissuesRegulatory networksTranscriptome sequencingSpliced isoformsNon-malignant cellsTumor clonal architecturesClonal architectureGene expressionCellular dynamicsRNAArchival formalin-fixed paraffin-embedded tissueMalignant subclonesFormalin-fixed paraffin-embedded (FFPEFFPE samplesParaffin-embedded (FFPEBiologyHuman lymphomasCo-transcriptional gene regulation in eukaryotes and prokaryotes
Shine M, Gordon J, Schärfen L, Zigackova D, Herzel L, Neugebauer K. Co-transcriptional gene regulation in eukaryotes and prokaryotes. Nature Reviews Molecular Cell Biology 2024, 25: 534-554. PMID: 38509203, PMCID: PMC11199108, DOI: 10.1038/s41580-024-00706-2.Peer-Reviewed Original ResearchRNA polymeraseRNA biogenesisRNA processingGene regulationDevelopment of RNA sequencingTranscription to translationRNA processing intermediatesGene expression stepsCo-transcriptional activityCellular stress responseNascent RNATranscriptional readthroughNascent transcriptsTranscriptional coordinationIntron retentionRNA foldingEukaryotesProkaryotesExpression stepsRNA sequencingTransient transcriptionGene expressionTranscriptionStress responseRNANon-mutational neoantigens in disease
Stern L, Clement C, Galluzzi L, Santambrogio L. Non-mutational neoantigens in disease. Nature Immunology 2024, 25: 29-40. PMID: 38168954, PMCID: PMC11075006, DOI: 10.1038/s41590-023-01664-1.Peer-Reviewed Original ResearchConceptsNon-canonical initiation codonsPost-translational protein modificationMature T cellsRibosomal RNA processingAlternative RNA splicingProtein-coding regionsNon-mutational mechanismsAbility of mammalsRNA processingRNA splicingInitiation codonProtein modificationHuman diseasesMature T cell repertoireAntigenic peptidesImmune recognitionAdaptive immune responsesT cellsAntigenic determinantsMHC class ICellsSplicingNovel antigenic determinantsMammalsCodon
2023
NOC1 is a direct MYC target, and its protein interactome dissects its activity in controlling nucleolar function
Manara V, Radoani M, Belli R, Peroni D, Destefanis F, Angheben L, Tome G, Tebaldi T, Bellosta P. NOC1 is a direct MYC target, and its protein interactome dissects its activity in controlling nucleolar function. Frontiers In Cell And Developmental Biology 2023, 11: 1293420. PMID: 38213308, PMCID: PMC10782387, DOI: 10.3389/fcell.2023.1293420.Peer-Reviewed Original ResearchNucleolar homeostasisRRNA processingNucleolar structureDirect Myc targetsNuclear mRNA exportMYC transcription factorsProtein interactome analysisE-box sequenceCellular stress responseDirect functional linkN6-methyladenosine (m6A) methylationPotential involvementRibosome biogenesisMRNA exportSubnuclear compartmentsProtein interactomeRibosomal maturationFunctional MycRNA processingRibosomal biogenesisNucleolar proteinsRNA splicingNucleolar localizationInteractome analysisNucleolar functionInduced alternative splicing an opportunity to study PCSK9 protein isoforms at physiologically relevant concentrations
Cale J, Ham K, Li D, McIntosh C, Watts G, Wilton S, Aung-Htut M. Induced alternative splicing an opportunity to study PCSK9 protein isoforms at physiologically relevant concentrations. Scientific Reports 2023, 13: 19725. PMID: 37957262, PMCID: PMC10643364, DOI: 10.1038/s41598-023-47005-y.Peer-Reviewed Original ResearchConceptsProtein isoformsAntisense oligomersModulate RNA processingLDL receptorInduce alternative splicingLevels of LDL receptorPhysiologically relevant concentrationsHuh-7 cellsLow-density lipoprotein (LDL) receptorProtein domainsRNA processingAlternative splicingExon 2Exon 8Target exonsHinge regionExonHuh-7LDL receptor activityIsoformsPhysiologically relevant levelsLDL uptakeSplicingIsoform expressionProtein overexpressionPhase separation and pathologic transitions of RNP condensates in neurons: implications for amyotrophic lateral sclerosis, frontotemporal dementia and other neurodegenerative disorders
Naskar A, Nayak A, Salaikumaran M, Vishal S, Gopal P. Phase separation and pathologic transitions of RNP condensates in neurons: implications for amyotrophic lateral sclerosis, frontotemporal dementia and other neurodegenerative disorders. Frontiers In Molecular Neuroscience 2023, 16: 1242925. PMID: 37720552, PMCID: PMC10502346, DOI: 10.3389/fnmol.2023.1242925.Peer-Reviewed Original ResearchAberrant phase transitionsMRNA transportFormation of ribonucleoproteinMembrane-less organellesPathogenic protein aggregationStress granule assemblyALS/frontotemporal dementiaSynaptic functionNeurodegenerative diseasesProcessing bodiesCajal bodiesRNA processingHigher-order structureSpatiotemporal regulationStress granulesTransport granulesAmyotrophic lateral sclerosisGranule assemblyProtein aggregationBiomolecular condensatesMRNA stabilityGene expressionLocal translationPhysiological functionsRBPs
2022
Deconvolution of in vivo protein-RNA contacts using fractionated eCLIP-seq
Biancon G, Busarello E, Joshi P, Lesch B, Halene S, Tebaldi T. Deconvolution of in vivo protein-RNA contacts using fractionated eCLIP-seq. STAR Protocols 2022, 3: 101823. PMID: 36595959, PMCID: PMC9676202, DOI: 10.1016/j.xpro.2022.101823.Peer-Reviewed Original ResearchConceptsProtein-RNA interactionsIndividual RNA-binding proteinsTranscriptome-wide analysisThousands of RNAsProtein-RNA contactsRNA-binding proteinSingle nucleotide levelComputational analysis pipelineRNA processingMulticomponent complexesRNA immunoprecipitationRead countsComplete detailsAnalysis pipelineAdditional levelProteinImmunoprecipitationRNAInteractionComplexesA review of DICER1: structure, function and contribution to disease
Meiklejohn K, Darbinyan A, Barbieri A. A review of DICER1: structure, function and contribution to disease. Diagnostic Histopathology 2022, 28: 329-336. DOI: 10.1016/j.mpdhp.2022.05.004.Peer-Reviewed Original Research
2021
Modulation of RNA Splicing Enhances Response to BCL2 Inhibition in Acute Myeloid Leukemia
Wang E, Pineda J, Bourcier J, Stahl M, Penson A, Wakiro I, Singer M, Cui D, Erickson C, Knorr K, Stanley R, Chen X, McMillan E, Bossard C, Aifantis I, Bradley R, Abdel-Wahab O. Modulation of RNA Splicing Enhances Response to BCL2 Inhibition in Acute Myeloid Leukemia. Blood 2021, 138: 507. DOI: 10.1182/blood-2021-146373.Peer-Reviewed Original ResearchCdc2-like kinasePre-mRNA splicingRNA splicing factorsSplicing factorsRNA processingAcute myeloid leukemiaRNA splicingBCL2 inhibitionGenetic screeningPhosphorylation of splicing factorsRegulate pre-mRNA splicingModulates RNA splicingSR protein functionResistance to therapyAntiapoptotic protein Bcl-2Overcome venetoclax resistanceRNA processing factorsDrug responseAML drugsGenome-wide CRISPR/Cas9 screenEntity's Board of DirectorsDrug-gene interactionsProtein Bcl-2Treated AML cellsAnti-apoptotic factors
2020
RNA-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 controlProtein
2019
Purification of Endogenous Tagged TRAMP4/5 and Exosome Complexes from Yeast and In Vitro Polyadenylation-Exosome Activation Assays
Zigáčková D, Rájecká V, Vaňáčová Š. Purification of Endogenous Tagged TRAMP4/5 and Exosome Complexes from Yeast and In Vitro Polyadenylation-Exosome Activation Assays. Methods In Molecular Biology 2019, 2062: 237-253. PMID: 31768980, DOI: 10.1007/978-1-4939-9822-7_12.Peer-Reviewed Original ResearchConceptsActivity of exosomesTRAMP complexExosome complexPolyadenylation complexRNA maturationRNA processingProtein complexesProtein domainsAuxiliary proteinsRNA substratesIndividual subunitsHigh processivityYeastParticular mutationAberrant formsActivation assaysRNAExosomesComplexesTRAMPWeak activityProcessivityPurificationSubunitsComplete degradation
2018
SRSF2 mutations drive oncogenesis by activating a global program of aberrant alternative splicing in hematopoietic cells
Liang Y, Tebaldi T, Rejeski K, Joshi P, Stefani G, Taylor A, Song Y, Vasic R, Maziarz J, Balasubramanian K, Ardasheva A, Ding A, Quattrone A, Halene S. SRSF2 mutations drive oncogenesis by activating a global program of aberrant alternative splicing in hematopoietic cells. Leukemia 2018, 32: 2659-2671. PMID: 29858584, PMCID: PMC6274620, DOI: 10.1038/s41375-018-0152-7.Peer-Reviewed Original ResearchConceptsSplicing factorsRNA processingAlternative splicingGene productsSplicing factor SRSF2Gene regulatory eventsAberrant alternative splicingSplice alterationsRecurrent mutationsSplicing proteinsHITS-CLIPSR familyMRNA splicingSplicing genesHematopoietic differentiationRegulatory eventsImpairs hematopoietic differentiationMolecular explanationWidespread modificationSplicingHematopoietic cellsMutationsBinding eventsOncogenesisProteinDynamics and Function of Nuclear Bodies during Embryogenesis
Escayola D, Neugebauer K. Dynamics and Function of Nuclear Bodies during Embryogenesis. Biochemistry 2018, 57: 2462-2469. PMID: 29473743, DOI: 10.1021/acs.biochem.7b01262.Peer-Reviewed Original ResearchConceptsNuclear bodiesCajal bodiesRNA processingZygotic gene productsRNA-protein complexesEfficient RNA processingFunction of nucleoliNuclear body formationGene elementsVariety of organismsZygotic genomeZygotic transitionGenomic lociNascent RNAModel organismsNuclear stepsTranscriptional activationEarly embryosNuclear proteinsGene productsGene locusMembraneless organellesBody formationExcellent modelCell nuclei
2016
α-Amanitin Restrains Cancer Relapse from Drug-Tolerant Cell Subpopulations via TAF15
Kume K, Ikeda M, Miura S, Ito K, Sato KA, Ohmori Y, Endo F, Katagiri H, Ishida K, Ito C, Iwaya T, Nishizuka SS. α-Amanitin Restrains Cancer Relapse from Drug-Tolerant Cell Subpopulations via TAF15. Scientific Reports 2016, 6: 25895. PMID: 27181033, PMCID: PMC4867652, DOI: 10.1038/srep25895.Peer-Reviewed Original ResearchMeSH KeywordsAlpha-AmanitinAnimalsCell Line, TumorCisplatinDown-RegulationDrug ResistanceEnzyme InhibitorsGene Expression Regulation, NeoplasticHCT116 CellsHeLa CellsHT29 CellsHumansMCF-7 CellsMicePeritoneal NeoplasmsProteomicsSecondary PreventionTATA-Binding Protein Associated FactorsTranscription, GeneticXenograft Model Antitumor AssaysConceptsΑ-amanitinRNA polymerase II inhibitorProtein expression patternsTranscriptional machineryRNA processingProteomic characterizationFunctional screeningTranscriptional levelExpression patternsTAF15II inhibitorsCancer cellsSubstantial frequencyDTC formationCancer relapseCell subpopulationsSubpopulationsTranscriptionMouse modelMachineryRNAPresence of drugsStemnessColoniesExpression
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 pathwaysNuclear bodies: RNA‐rich powerhouses of the cell (471.3)
Neugebauer K, Machyna M, Straube K, Heyn P. Nuclear bodies: RNA‐rich powerhouses of the cell (471.3). The FASEB Journal 2014, 28 DOI: 10.1096/fasebj.28.1_supplement.471.3.Peer-Reviewed Original ResearchHistone locus bodyCajal bodiesNuclear bodiesZygotic genome activationTrafficking of RNAsEarly zebrafish embryogenesisSites of transcriptionSite of assemblyGenome activationSpliceosomal snRNPsZebrafish embryogenesisRNA processingHistone mRNAMRNA splicingEnd formationMacromolecular complexesLow-affinity interactionsNuclear morphologyCell nucleiCommon organizational featuresLipid bilayersRNAEfficient assemblyDifferent functionsMolecular composition
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