2023
Tudor–dimethylarginine interactions: the condensed version
Šimčíková D, Gelles-Watnick S, Neugebauer K. Tudor–dimethylarginine interactions: the condensed version. Trends In Biochemical Sciences 2023, 48: 689-698. PMID: 37156649, PMCID: PMC10524826, DOI: 10.1016/j.tibs.2023.04.003.Peer-Reviewed Original ResearchConceptsSurvival motor neuron (SMN) proteinTudor domainDiverse cellular functionsRNA-RNA interactionsSMN Tudor domainMotor neuron proteinCellular functionsProtein localizationProtein-RNASpinal muscular atrophyProtein ligandsNeuron proteinIntramolecular interactionsMuscular atrophyProteinInteractionFunctionLigandsModificationBiomolecularCellsLocalizationOpen questionDomainFormation
2022
Transcriptome-wide mapping reveals a diverse dihydrouridine landscape including mRNA
Draycott AS, Schaening-Burgos C, Rojas-Duran MF, Wilson L, Schärfen L, Neugebauer KM, Nachtergaele S, Gilbert WV. Transcriptome-wide mapping reveals a diverse dihydrouridine landscape including mRNA. PLOS Biology 2022, 20: e3001622. PMID: 35609439, PMCID: PMC9129914, DOI: 10.1371/journal.pbio.3001622.Peer-Reviewed Original ResearchConceptsTranscriptome-wide mappingSmall nucleolar RNAsFunctional RNA structuresSingle-nucleotide resolutionStem-loop regionEukaryotic ribosomesNucleolar RNAsPre-mRNARNA structureRNA targetsDihydrouridine synthaseHuman diseasesMRNARNANovel classFunctional componentsSplicingTRNARibosomesYeastDependent changesLandscapeOrganismsDihydrouridineSequencing
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
Dynamics 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
2015
Quantification of co-transcriptional splicing from RNA-Seq data
Herzel L, Neugebauer KM. Quantification of co-transcriptional splicing from RNA-Seq data. Methods 2015, 85: 36-43. PMID: 25929182, DOI: 10.1016/j.ymeth.2015.04.024.Peer-Reviewed Original ResearchRNA: master or servant?
Neugebauer KM. RNA: master or servant? RNA 2015, 21: 701-702. PMID: 25780198, PMCID: PMC4371340, DOI: 10.1261/rna.051250.115.Peer-Reviewed Original ResearchRNA
2012
Cajal bodies: where form meets function
Machyna M, Heyn P, Neugebauer KM. Cajal bodies: where form meets function. Wiley Interdisciplinary Reviews - RNA 2012, 4: 17-34. PMID: 23042601, DOI: 10.1002/wrna.1139.Peer-Reviewed Original ResearchConceptsCajal bodiesCB assemblyHistone locus bodyHistone gene clusterRibosome biogenesisGene clusterHistone mRNATelomere maintenanceCellular functionsRNA speciesWidespread mechanismCell nucleiSurprising complexityBiochemical processesAltered affinityBody assemblyAssembly propertiesRibonucleoproteinDistinct structuresAssemblyPre-existing substructuresBiogenesisSplicingAdditional layerTranscriptionRNA–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