2024
Multiple 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
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 ResearchMeSH KeywordsAnimalsProtein BindingRNA-Binding ProteinsUltraviolet RaysVertebratesZebrafishZebrafish ProteinsConceptsNumber 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 levels
2014
The 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 CBAssemblySnRNAs
2013
How cells get the message: dynamic assembly and function of mRNA–protein complexes
Müller-McNicoll M, Neugebauer KM. How cells get the message: dynamic assembly and function of mRNA–protein complexes. Nature Reviews Genetics 2013, 14: 275-287. PMID: 23478349, DOI: 10.1038/nrg3434.Peer-Reviewed Original Research
2012
First Exon Length Controls Active Chromatin Signatures and Transcription
Bieberstein NI, Oesterreich F, Straube K, Neugebauer KM. First Exon Length Controls Active Chromatin Signatures and Transcription. Cell Reports 2012, 2: 62-68. PMID: 22840397, DOI: 10.1016/j.celrep.2012.05.019.Peer-Reviewed Original ResearchConceptsGeneral transcription factorsTranscription start siteFirst exonShort first exonExon-intron organizationGenome-wide analysisHistone modifications H3K4me3Active chromatin signatureRNA polymerase IIRole of splicingTransgenic cell linesChIP-seq dataLong first exonChromatin signaturesGene architectureExon-intron boundariesHigh expression levelsAntisense transcriptionTranscriptional outputPolymerase IIH3K4me3 levelsGene activityTSS usageTranscription factorsExon lengthRNA–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
Cotranscriptional spliceosome assembly and splicing are independent of the Prp40p WW domain
Görnemann J, Barrandon C, Hujer K, Rutz B, Rigaut G, Kotovic KM, Faux C, Neugebauer KM, Séraphin B. Cotranscriptional spliceosome assembly and splicing are independent of the Prp40p WW domain. RNA 2011, 17: 2119-2129. PMID: 22020974, PMCID: PMC3222125, DOI: 10.1261/rna.02646811.Peer-Reviewed Original ResearchConceptsC-terminal domainWW domainsSpliceosome assemblyU1 snRNPPol II C-terminal domainCotranscriptional spliceosome assemblyComplex cellular functionsRNA polymerase IIProtein-protein interactionsPre-mRNA splicingU2 snRNP recruitmentSplice site recognitionCotranscriptional recruitmentTranscriptional machineryPolymerase IIPol IIU5 snRNPLarge subunitSplicing factorsCellular functionsStable heterodimerComplex assemblyPrp40Spliceosome formationAffinity purification
2010
Binding properties and dynamic localization of an alternative isoform of the cap-binding complex subunit CBP20
Pabis M, Neufeld N, Shav-Tal Y, Neugebauer KM. Binding properties and dynamic localization of an alternative isoform of the cap-binding complex subunit CBP20. Nucleus 2010, 1: 412-421. PMID: 21326824, PMCID: PMC3037537, DOI: 10.4161/nucl.1.5.12839.Peer-Reviewed Original ResearchConceptsCap-binding complexRNA recognition motifSmall nuclear RNAMessenger RNAsRNA polymerase II transcriptsNuclear cap-binding complexActive transcription sitesPolymerase II transcriptsM7G capAlternative splice variantsGuanosine capRNA processingCBP80 subunitHuman cell linesCBP20Transcription sitesG capAlternative isoformsNuclear RNATranscription inhibitionRecognition motifMammalian speciesCBP80High-affinity bindingFrame deletionGlobal analysis reveals SRp20- and SRp75-specific mRNPs in cycling and neural cells
Änkö M, Morales L, Henry I, Beyer A, Neugebauer KM. Global analysis reveals SRp20- and SRp75-specific mRNPs in cycling and neural cells. Nature Structural & Molecular Biology 2010, 17: 962-970. PMID: 20639886, DOI: 10.1038/nsmb.1862.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell CycleCell DifferentiationCell Line, TumorChromosomes, Artificial, BacterialGene Expression Regulation, NeoplasticGene Knockdown TechniquesGreen Fluorescent ProteinsImmunoprecipitationMiceNeuronsOrgan SpecificityProtein BindingRibonucleoproteinsRNA, MessengerRNA-Binding ProteinsSerine-Arginine Splicing Factors
1995
A Subset of SR Proteins Activates Splicing of the Cardiac Troponin T Alternative Exon by Direct Interactions with an Exonic Enhancer
Ramchatesingh J, Zahler A, Neugebauer K, Roth M, Cooper T. A Subset of SR Proteins Activates Splicing of the Cardiac Troponin T Alternative Exon by Direct Interactions with an Exonic Enhancer. Molecular And Cellular Biology 1995, 15: 4898-4907. PMID: 7651409, PMCID: PMC230736, DOI: 10.1128/mcb.15.9.4898.Peer-Reviewed Original Research