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 changesLandscapeOrganismsDihydrouridineSequencingIdentification of Alternative Polyadenylation in Cyanidioschyzon merolae Through Long-Read Sequencing of mRNA
Schärfen L, Zigackova D, Reimer KA, Stark MR, Slat VA, Francoeur NJ, Wells ML, Zhou L, Blackshear PJ, Neugebauer KM, Rader SD. Identification of Alternative Polyadenylation in Cyanidioschyzon merolae Through Long-Read Sequencing of mRNA. Frontiers In Genetics 2022, 12: 818697. PMID: 35154260, PMCID: PMC8831791, DOI: 10.3389/fgene.2021.818697.Peer-Reviewed Original ResearchAlternative polyadenylationNon-model organismsRNA processing pathwaysLong-Read SequencingCyanidioschyzon merolaeSplicing statusSplicing machineryMammalian cellsRegulatory stepMRNA stabilityRed algaVolcanic hot springsGene expressionRich mediumPolyadenylationBiological importanceOrganismsSite usageProtein expressionHot springsYeastAlgaProcessing pathwaysSequencingMRNA
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 frontierVivo
2013
Counting on co-transcriptional splicing
Brugiolo M, Herzel L, Neugebauer KM. Counting on co-transcriptional splicing. Faculty Reviews 2013, 5: 9. PMID: 23638305, PMCID: PMC3619158, DOI: 10.12703/p5-9.Peer-Reviewed Original ResearchCo-transcriptional splicingMultiple model organismsProcess of transcriptionModel organismsSplicing machineryTranscription terminationSplicing eventsIntron removalMammalian cellsIntron sequencesBioinformatics analysisPlace coSplicingExperimental accessibilityMost cellsGlobal datasetTranscriptionOrganismsMRNAExperimental approachBroad differencesSpliceosomeInsectsCellsYeast
2010
The differential interaction of snRNPs with pre-mRNA reveals splicing kinetics in living cells
Huranová M, Ivani I, Benda A, Poser I, Brody Y, Hof M, Shav-Tal Y, Neugebauer KM, Staněk D. The differential interaction of snRNPs with pre-mRNA reveals splicing kinetics in living cells. Journal Of Cell Biology 2010, 191: 75-86. PMID: 20921136, PMCID: PMC2953428, DOI: 10.1083/jcb.201004030.Peer-Reviewed Original ResearchConceptsSmall nuclear RNP particlesPrecursor messenger RNA splicingMessenger RNA splicingBinding of U1Live-cell imagingRate of splicingNuclear RNP particlesLarge ribonucleoproteinSnRNP componentsRNA splicingSpliceosome assemblyAdditional proteinsRNP particlesHuman cellsSplicingLiving cellsCell nucleiDifferential interactionsEndogenous levelsSpliceosomeMRNARibonucleoproteinCell imagingCore componentCells
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