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
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
Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies
Biancon G, Joshi P, Zimmer JT, Hunck T, Gao Y, Lessard MD, Courchaine E, Barentine AES, Machyna M, Botti V, Qin A, Gbyli R, Patel A, Song Y, Kiefer L, Viero G, Neuenkirchen N, Lin H, Bewersdorf J, Simon MD, Neugebauer KM, Tebaldi T, Halene S. Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies. Molecular Cell 2022, 82: 1107-1122.e7. PMID: 35303483, PMCID: PMC8988922, DOI: 10.1016/j.molcel.2022.02.025.Peer-Reviewed Original Research
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
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
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 ResearchMeSH KeywordsCell NucleusCytoplasmModels, GeneticProtein BindingProtein BiosynthesisRibonucleoproteinsRNA-Binding ProteinsTranscription, Genetic
2012
The 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
2010
Global 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
2009
SR Protein Family Members Display Diverse Activities in the Formation of Nascent and Mature mRNPs In Vivo
Sapra AK, Änkö M, Grishina I, Lorenz M, Pabis M, Poser I, Rollins J, Weiland EM, Neugebauer KM. SR Protein Family Members Display Diverse Activities in the Formation of Nascent and Mature mRNPs In Vivo. Molecular Cell 2009, 34: 179-190. PMID: 19394295, DOI: 10.1016/j.molcel.2009.02.031.Peer-Reviewed Original ResearchMeSH KeywordsChromatin ImmunoprecipitationChromosomes, Artificial, BacterialFluorescence Resonance Energy TransferGenes, fosGreen Fluorescent ProteinsHeLa CellsHumansNuclear ProteinsPromoter Regions, GeneticRecombinant Fusion ProteinsRibonucleoproteinsRNA SplicingRNA-Binding ProteinsTranscription, GeneticConceptsRNA recognition motifSR proteinsCytoplasmic mRNAPol IIProtein interactionsSR protein family membersFRET/FLIMMRNA splicing factorsProtein family membersStable cell linesMRNP remodelingMRNA lifetimeGene regulationFormation of nascentSplicing factorsRecognition motifPromoter controlFamily membersAdditional roleProteinRNACell linesIndividual family membersMRNADiverse activities
2000
SR proteins are autoantigens in patients with systemic lupus erythematosus: Importance of phosphoepitopes
Neugebauer K, Merrill J, Wener M, Lahita R, Roth M. SR proteins are autoantigens in patients with systemic lupus erythematosus: Importance of phosphoepitopes. Arthritis & Rheumatism 2000, 43: 1768-1778. PMID: 10943867, DOI: 10.1002/1529-0131(200008)43:8<1768::aid-anr13>3.0.co;2-9.Peer-Reviewed Original ResearchConceptsSystemic lupus erythematosusEnzyme-linked immunosorbent assaySLE patientsLupus erythematosusDiagnosis of SLEPrimary antiphospholipid syndromeGroup of patientsSera of patientsAntiphospholipid syndromeProtein reactivityRheumatoid arthritisPatient seraPatientsAutoantigensImmunosorbent assayAntigen recognitionSerumErythematosusFurther studiesSeparate groupsDisordersBind dsDNAArthritisAutoantibodiesAutoimmunity
1998
Regulation of Alternative Polyadenylation by U1 snRNPs and SRp20
Lou H, Neugebauer K, Gagel R, Berget S. Regulation of Alternative Polyadenylation by U1 snRNPs and SRp20. Molecular And Cellular Biology 1998, 18: 4977-4985. PMID: 9710581, PMCID: PMC109082, DOI: 10.1128/mcb.18.9.4977.Peer-Reviewed Original ResearchAnimalsBase SequenceCalcitoninCalcitonin Gene-Related PeptideConsensus SequenceEnhancer Elements, GeneticExonsHumansMetallothioneinMiceMolecular Sequence DataPoly ARatsRibonucleoprotein, U1 Small NuclearRNA PrecursorsRNA Processing, Post-TranscriptionalRNA-Binding ProteinsSequence AlignmentSequence Homology, Nucleic AcidSerine-Arginine Splicing FactorsThyroid GlandVertebrates
1997
Distribution of pre-mRNA splicing factors at sites of RNA polymerase II transcription.
Neugebauer K, Roth M. Distribution of pre-mRNA splicing factors at sites of RNA polymerase II transcription. Genes & Development 1997, 11: 1148-1159. PMID: 9159396, DOI: 10.1101/gad.11.9.1148.Peer-Reviewed Original ResearchMeSH KeywordsAntibodies, MonoclonalBinding SitesCell NucleusFluorescent Antibody Technique, IndirectHeLa CellsHumansNuclear ProteinsPhosphoproteinsRibonucleoproteins, Small NuclearRNA Polymerase IIRNA PrecursorsRNA SplicingRNA-Binding ProteinsSerine-Arginine Splicing FactorsTranscription, GeneticUridine TriphosphateConceptsRNA polymerase II transcriptionPolymerase II transcriptionMRNA splicing factorsSplicing factorsSR familyPre-mRNA splicingVisualization of hundredsHeLa cell nucleiSplicing regulatorsActive genesTranscription unitMRNA splicingGene regulatorsGene transcriptionPre-mRNADistinct functionsRNA synthesisTranscriptionCell nucleiSplicingSingle memberRegulatorActive site
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 ResearchA conserved epitope on a subset of SR proteins defines a larger family of Pre-mRNA splicing factors.
Neugebauer K, Stolk J, Roth M. A conserved epitope on a subset of SR proteins defines a larger family of Pre-mRNA splicing factors. Journal Of Cell Biology 1995, 129: 899-908. PMID: 7538140, PMCID: PMC2120486, DOI: 10.1083/jcb.129.4.899.Peer-Reviewed Original Research
1993
Human SR proteins and isolation of a cDNA encoding SRp75.
Zahler A, Neugebauer K, Stolk J, Roth M. Human SR proteins and isolation of a cDNA encoding SRp75. Molecular And Cellular Biology 1993, 13: 4023-4028. PMID: 8321209, PMCID: PMC359951, DOI: 10.1128/mcb.13.7.4023.Peer-Reviewed Original ResearchConceptsRNA recognition motifSR proteinsN-terminal RNA recognition motifLong C-terminal domainPolymerase II transcriptionHuman SR proteinsSR family membersC-terminal domainFamily of proteinsGlycine-rich regionApparent molecular massCDNA clonesRecognition motifSRp75Mobility shiftArginine residuesMolecular massSR domainProteinInternal regionSerineCommon epitopesActive siteFamily membersSRp55Distinct Functions of SR Proteins in Alternative pre-mRNA Splicing
Zahler A, Neugebauer K, Lane W, Roth M. Distinct Functions of SR Proteins in Alternative pre-mRNA Splicing. Science 1993, 260: 219-222. PMID: 8385799, DOI: 10.1126/science.8385799.Peer-Reviewed Original ResearchConceptsSR proteinsAlternative splicingDistinct functionsAlternative pre-mRNA splicingPrecursor messenger RNAMRNA splicing factorsPre-mRNA splicingSR familySplicing factorsMRNA splicingVariety of tissuesGene expressionSplicingMessenger RNAProteinCommon mechanismFundamental roleFamilyRNARegulationExpressionEntire familyFunctionMembers