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
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
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 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 levelsPurification 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 Research
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 Research
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
RNA–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
Structural basis for dimethylarginine recognition by the Tudor domains of human SMN and SPF30 proteins
Tripsianes K, Madl T, Machyna M, Fessas D, Englbrecht C, Fischer U, Neugebauer KM, Sattler M. Structural basis for dimethylarginine recognition by the Tudor domains of human SMN and SPF30 proteins. Nature Structural & Molecular Biology 2011, 18: 1414-1420. PMID: 22101937, DOI: 10.1038/nsmb.2185.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceArginineBinding SitesHumansModels, MolecularMolecular Sequence DataNuclear Magnetic Resonance, BiomolecularProtein Structure, TertiaryRibonucleoproteins, Small NuclearRNA Splicing FactorsSequence AlignmentSMN Complex ProteinsSurvival of Motor Neuron 1 ProteinThermodynamics
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
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. DOI: 10.1128/mcb.13.7.4023-4028.1993.Peer-Reviewed Original ResearchRNA 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 membersSRp55Human 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
1987
Embryonic neural retinal cell response to extracellular matrix proteins: developmental changes and effects of the cell substratum attachment antibody (CSAT).
Hall D, Neugebauer K, Reichardt L. Embryonic neural retinal cell response to extracellular matrix proteins: developmental changes and effects of the cell substratum attachment antibody (CSAT). Journal Of Cell Biology 1987, 104: 623-634. PMID: 3493247, PMCID: PMC2114555, DOI: 10.1083/jcb.104.3.623.Peer-Reviewed Original ResearchConceptsCSAT antibodySubstrate preferenceNeurite outgrowthNeural retinal cellsExtracellular matrix substratesProfile of proteinsExtracellular matrix proteinsCollagen IVExtracellular matrix constituentsCell surface glycoproteinExtracellular matrix glycoproteinCell attachmentCell surface moleculesRetinal cellsCellular responsesMatrix proteinsNeuronal differentiationMatrix substratesEmbryonic day 6Matrix glycoproteinNeurite extensionProteinSurface glycoproteinCell interactionsSurface molecules