2024
Emerging and re-emerging themes in co-transcriptional pre-mRNA splicing
Carrocci T, Neugebauer K. Emerging and re-emerging themes in co-transcriptional pre-mRNA splicing. Molecular Cell 2024, 84: 3656-3666. PMID: 39366353, PMCID: PMC11463726, DOI: 10.1016/j.molcel.2024.08.036.Peer-Reviewed Original ResearchConceptsPre-mRNA splicingCo-transcriptional pre-mRNA splicingCo-transcriptional RNA foldingCo-transcriptional processesRNA polymerase IIPre-messenger RNAFunctional messenger RNAsCapping enzymePolymerase IIDelayed splicingPolyadenylation machinerySplicing eventsPre-mRNAGene regulationMacromolecular machinesRNA foldingRNA synthesisMRNA isoformsProtein productionGene expressionSplicingRNARegulatory importanceCross-regulationMessenger RNAMultiple roles for AU-rich RNA binding proteins in the development of haematologic malignancies and their resistance to chemotherapy
Podszywalow-Bartnicka P, Neugebauer K. Multiple roles for AU-rich RNA binding proteins in the development of haematologic malignancies and their resistance to chemotherapy. RNA Biology 2024, 21: 1-17. PMID: 38798162, PMCID: PMC11135835, DOI: 10.1080/15476286.2024.2346688.Peer-Reviewed Original ResearchConceptsARE-binding proteinsRNA-binding proteinsAU-rich elementsStress granulesBinding proteinTranslational regulation of mRNAsImpact alternative splicingCytoplasmic stress granulesProtein-RNA bindingAdaptation to microenvironmentProtein-RNA networksBinding to AU-rich elementsCancer cell proteomePost-transcriptional regulationAU-rich RNA-binding proteinsRegulation of mRNAsChemotherapy resistanceGene expression levelsSequence motifsProtein-RNAMRNA structureMature mRNATranslational regulationAlternative splicingCell proteome
2021
DMA-tudor interaction modules control the specificity of in vivo condensates
Courchaine EM, Barentine AES, Straube K, Lee DR, Bewersdorf J, Neugebauer KM. DMA-tudor interaction modules control the specificity of in vivo condensates. Cell 2021, 184: 3612-3625.e17. PMID: 34115980, PMCID: PMC8402948, DOI: 10.1016/j.cell.2021.05.008.Peer-Reviewed Original Research
2020
Contribution of increasing plasma membrane to the energetic cost of early zebrafish embryogenesis
Rodenfels J, Sartori P, Golfier S, Nagendra K, Neugebauer K, Howard J. Contribution of increasing plasma membrane to the energetic cost of early zebrafish embryogenesis. Molecular Biology Of The Cell 2020, 31: 520-526. PMID: 32049586, PMCID: PMC7202076, DOI: 10.1091/mbc.e19-09-0529.Peer-Reviewed Original ResearchConceptsPlasma membraneEarly zebrafish embryogenesisEnergetic costSpecific developmental eventsTotal plasma membraneCell proliferationTwo-cell stageZebra fish embryosZebrafish embryogenesisTotal cell surface areaDNA replicationCell divisionEarly embryosDevelopmental eventsCleavage divisionsCell surface areaTotal cell numberCleavage stagesEmbryo volumeEmbryosCell numberMembraneTotal energy budgetProliferationEmbryogenesis
2018
RNA tales – how embryos read and discard messages from mom
Despic V, Neugebauer KM. RNA tales – how embryos read and discard messages from mom. Journal Of Cell Science 2018, 131: jcs201996. PMID: 29467249, DOI: 10.1242/jcs.201996.Peer-Reviewed Original ResearchConceptsZygotic genomePost-transcriptional regulatory pathwaysMaternal mRNA clearanceMaternal mRNA degradationEarly developmentContribution of microRNAsZygotic transitionMRNA clearanceRNA regulationMRNA decayCellular contextHigh-throughput methodZebrafish embryosFemale gametesMaternal mRNAsMolecular playersMRNA degradationRNA modificationsMolecular principlesRegulatory pathwaysGenomeLater stepsMZTSilent genomeEmbryos
2017
Analysis of RNA-protein interactions in vertebrate embryos using UV crosslinking approaches
Despic V, Dejung M, Butter F, Neugebauer KM. Analysis of RNA-protein interactions in vertebrate embryos using UV crosslinking approaches. Methods 2017, 126: 44-53. PMID: 28734934, DOI: 10.1016/j.ymeth.2017.07.013.Peer-Reviewed Original ResearchConceptsNumber of RBPsRNA-protein interactionsUnique biological contextZebrafish Danio rerioRegulated gene expressionInteractome captureVertebrate embryosDanio rerioRNA-seqCellular RNAGene expressionBiological contextRBPsRNAProteinGenomeRerioCrosslinking approachOrganismsEmbryosMRNAAnnotationExpressionVast frontierVivoCellular differentiation state modulates the mRNA export activity of SR proteins
Botti V, McNicoll F, Steiner MC, Richter FM, Solovyeva A, Wegener M, Schwich OD, Poser I, Zarnack K, Wittig I, Neugebauer KM, Müller-McNicoll M. Cellular differentiation state modulates the mRNA export activity of SR proteins. Journal Of Cell Biology 2017, 216: 1993-2009. PMID: 28592444, PMCID: PMC5496613, DOI: 10.1083/jcb.201610051.Peer-Reviewed Original ResearchMeSH KeywordsActive Transport, Cell NucleusAnimalsArginineCell DifferentiationCell NucleusDNA-Binding ProteinsHeLa CellsHumansImmunoprecipitationMethylationMiceNeurogenesisPhenotypePhosphorylationPluripotent Stem CellsProtein BindingProtein Processing, Post-TranslationalRepressor ProteinsRNA InterferenceRNA, MessengerRNA-Binding ProteinsSerine-Arginine Splicing FactorsTandem Mass SpectrometryTranscription FactorsTransfectionConceptsMRNA export activitySR proteinsP19 cellsMRNA exportSR protein family membersProtein-RNA interactionsMurine P19 cellsCellular differentiation stateProtein family membersLower phosphorylation levelsArginine methylationPluripotency factorsCytoplasmic mRNA levelsMRNA processingPosttranslational modificationsCellular dynamicsDifferentiated cellsNeural differentiationSRSF5Differentiation statePhosphorylation levelsHeLa cellsProteinExport activityMRNA levelsSpecial focus on the Cajal Body
Neugebauer KM. Special focus on the Cajal Body. RNA Biology 2017, 14: 669-670. PMID: 28486008, PMCID: PMC5519238, DOI: 10.1080/15476286.2017.1316928.Peer-Reviewed Original ResearchPurification of Zygotically Transcribed RNA through Metabolic Labeling of Early Zebrafish Embryos
Heyn P, Neugebauer KM. Purification of Zygotically Transcribed RNA through Metabolic Labeling of Early Zebrafish Embryos. Methods In Molecular Biology 2017, 1605: 121-131. PMID: 28456961, DOI: 10.1007/978-1-4939-6988-3_8.Peer-Reviewed Original ResearchDynamic 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 constellations
2016
Activation of transcription enforces the formation of distinct nuclear bodies in zebrafish embryos
Heyn P, Salmonowicz H, Rodenfels J, Neugebauer KM. Activation of transcription enforces the formation of distinct nuclear bodies in zebrafish embryos. RNA Biology 2016, 14: 752-760. PMID: 27858508, PMCID: PMC5519242, DOI: 10.1080/15476286.2016.1255397.Peer-Reviewed Original ResearchConceptsHistone locus bodyCajal bodiesNuclear bodiesSm ringHistone mRNA 3' end processingEnd processingMRNA 3' end processingDifferent nuclear bodiesDistinct nuclear bodiesNuclear body componentsDistinct regulatory functionsHLB formationHistone genesHistone transcriptsZygotic transcriptionTranscriptional silenceSplicing machineryRRNA processingEarly embryogenesisU7 snRNPNascent histoneZebrafish embryosDanio rerioCellular compartmentsTranscription inhibition
2015
Coilin: The first 25 years
Machyna M, Neugebauer KM, Staněk D. Coilin: The first 25 years. RNA Biology 2015, 12: 590-596. PMID: 25970135, PMCID: PMC4615369, DOI: 10.1080/15476286.2015.1034923.Peer-Reviewed Original ResearchQuantification 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 Research
2014
Introns and gene expression: Cellular constraints, transcriptional regulation, and evolutionary consequences
Heyn P, Kalinka AT, Tomancak P, Neugebauer KM. Introns and gene expression: Cellular constraints, transcriptional regulation, and evolutionary consequences. BioEssays 2014, 37: 148-154. PMID: 25400101, PMCID: PMC4654234, DOI: 10.1002/bies.201400138.Peer-Reviewed Original ResearchConceptsShort genesCellular constraintsImportant regulatory playersRNA polymerase IICell cycle constraintsLength of exonsNumber of transcriptsShorter cell cycleEvolutionary consequencesPolymerase IITranscriptional regulationAnimal ontogenyLong genesRegulatory playersTranscript productionDifferent genesGene expressionExpression profilesCell cycleEfficient expressionIntronsGenesCell typesTiming mechanismTranscriptsThe Coilin Interactome Identifies Hundreds of Small Noncoding RNAs that Traffic through Cajal Bodies
Machyna M, Kehr S, Straube K, Kappei D, Buchholz F, Butter F, Ule J, Hertel J, Stadler PF, Neugebauer KM. The Coilin Interactome Identifies Hundreds of Small Noncoding RNAs that Traffic through Cajal Bodies. Molecular Cell 2014, 56: 389-399. PMID: 25514182, DOI: 10.1016/j.molcel.2014.10.004.Peer-Reviewed Original ResearchConceptsCajal bodiesSmall nucleolar RNAsSmall nuclear RNASmall noncoding RNAsChIP-seq peaksCoilin proteinSnoRNA biogenesisRNP assemblySnRNP assemblyNcRNA metabolismSnRNA genesSubnuclear compartmentsCellular hubHuman snoRNAsMolecular functionsSnRNA transcriptsNucleolar RNAsNoncoding RNAsNuclear RNACoilinRNASignal trafficRole of CBAssemblySnRNAsThe Earliest Transcribed Zygotic Genes Are Short, Newly Evolved, and Different across Species
Heyn P, Kircher M, Dahl A, Kelso J, Tomancak P, Kalinka AT, Neugebauer KM. The Earliest Transcribed Zygotic Genes Are Short, Newly Evolved, and Different across Species. Cell Reports 2014, 6: 285-292. PMID: 24440719, DOI: 10.1016/j.celrep.2013.12.030.Peer-Reviewed Original ResearchConceptsZygotic genome activationZygotic genesEarly zygotic transcriptsOne-cell stageSignificant transcriptional activityRapid cell divisionComparison of fishGenome activationMitochondrial genomePurification of RNAZygotic controlEvolutionary plasticityMulticellular organismsNuclear genesZygotic transcriptsEarly embryogenesisShort genesDanio rerioAdaptive potentialCell divisionTranscriptional activityMetabolic labelingCell cycleEarly genesGenes
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 layerTranscriptionThe RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes
Änkö ML, Müller-McNicoll M, Brandl H, Curk T, Gorup C, Henry I, Ule J, Neugebauer KM. The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes. Genome Biology 2012, 13: r17. PMID: 22436691, PMCID: PMC3439968, DOI: 10.1186/gb-2012-13-3-r17.Peer-Reviewed Original ResearchConceptsSR proteinsSR protein family membersHistone mRNA metabolismConsensus binding motifsProtein family membersIntron-containing mRNAsCellular regulatory mechanismsNonsense-mediated decayNon-coding RNAsNumerous RNAsHistone transcriptsMRNA metabolismUnique RNASplicing eventsAlternative splicingRNA classesRNA recognitionRelated RNATarget genesSRSF4Binding motifRegulatory mechanismsRNA targetsSRSF3Murine 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
2011
Pause locally, splice globally
Oesterreich F, Bieberstein N, Neugebauer KM. Pause locally, splice globally. Trends In Cell Biology 2011, 21: 328-335. PMID: 21530266, DOI: 10.1016/j.tcb.2011.03.002.Peer-Reviewed Original ResearchConceptsRNA polymerase II elongation rateContext of chromatinProtein-coding transcriptsRNA polymerase IIPre-mRNA splicingTranscript bodyTranscriptional pausingHistone modificationsPolymerase IIIntron removalSplicingTranscriptionElongation rateGenesTranscriptsRecent evidenceChromatinIntronsPausingElongationRegulatorLocal regulationRegulationRecruitment