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 RNACo-transcriptional gene regulation in eukaryotes and prokaryotes
Shine M, Gordon J, Schärfen L, Zigackova D, Herzel L, Neugebauer K. Co-transcriptional gene regulation in eukaryotes and prokaryotes. Nature Reviews Molecular Cell Biology 2024, 25: 534-554. PMID: 38509203, PMCID: PMC11199108, DOI: 10.1038/s41580-024-00706-2.Peer-Reviewed Original ResearchRNA polymeraseRNA biogenesisRNA processingGene regulationDevelopment of RNA sequencingTranscription to translationRNA processing intermediatesGene expression stepsCo-transcriptional activityCellular stress responseNascent RNATranscriptional readthroughNascent transcriptsTranscriptional coordinationIntron retentionRNA foldingEukaryotesProkaryotesExpression stepsRNA sequencingTransient transcriptionGene expressionTranscriptionStress responseRNA
2023
Splicing under stress: A matter of time and place
Podszywalow-Bartnicka P, Neugebauer K. Splicing under stress: A matter of time and place. Journal Of Cell Biology 2023, 222: e202311014. PMID: 37988026, PMCID: PMC10660129, DOI: 10.1083/jcb.202311014.Peer-Reviewed Original Research
2022
Identification 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
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
2016
Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II
Oesterreich F, Herzel L, Straube K, Hujer K, Howard J, Neugebauer KM. Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II. Cell 2016, 165: 372-381. PMID: 27020755, PMCID: PMC4826323, DOI: 10.1016/j.cell.2016.02.045.Peer-Reviewed Original ResearchConceptsRNA polymerase IIPolymerase IIPol IIProtein-coding genesPol II progressionRNA sequencing methodsGene expression pathwaysRate of transcriptionEndogenous genesSplicing catalysisSplicing profilesSpliceosome assemblyExpression pathwaysSpliced productsGene expressionIntronsSplicingSequencing methodsMechanistic insightsGenesRegulationKinetic competitionEukaryotesSpliceosomeTranscription
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 mechanismTranscripts
2012
Transcription and Pre‐mRNA processing in space and time
Neugebauer K. Transcription and Pre‐mRNA processing in space and time. The FASEB Journal 2012, 26: 228.2-228.2. DOI: 10.1096/fasebj.26.1_supplement.228.2.Peer-Reviewed Original ResearchRNA processingGene expression pathwaysPre-mRNA processingGene lengthRNA transportSubcellular organizationZebrafish embryosMammalian cellsMassive transcriptionRNA polymeraseCellular compartmentsExpression pathwaysGene transcriptionGene expressionBiological contextMolecular mechanismsTranscriptionProcessing machineryElongation rateGenesCellsYeastPolymeraseRNAMachinery
2010
Dynamic control of Cajal body number during zebrafish embryogenesis
Strzelecka M, Oates AC, Neugebauer KM. Dynamic control of Cajal body number during zebrafish embryogenesis. Nucleus 2010, 1: 96-108. PMID: 21327108, PMCID: PMC3035118, DOI: 10.4161/nucl.1.1.10680.Peer-Reviewed Original ResearchConceptsCajal bodiesEnd processing factorsGene expressionZygotic genome activationZygotic gene expressionRNA processing machineryDistinct nuclear bodiesMRNA splicing machineryCajal body numberLive-cell imagingCB numberHours of developmentGenome activationZebrafish embryogenesisNuclear subcompartmentsSnRNP biogenesisSplicing machineryZebrafish embryosCell divisionNuclear bodiesCB assemblyEmbryonic cellsMaternal contributionProcessing machineryEmbryos
1993
Distinct 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