2024
Co-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
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
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 differencesSpliceosomeInsectsCellsYeastHow 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
Cajal bodies: where form meets function
Machyna M, Heyn P, Neugebauer KM. Cajal bodies: where form meets function. Wiley Interdisciplinary Reviews - RNA 2012, 4: 17-34. PMID: 23042601, DOI: 10.1002/wrna.1139.Peer-Reviewed Original ResearchConceptsCajal bodiesCB assemblyHistone locus bodyHistone gene clusterRibosome biogenesisGene clusterHistone mRNATelomere maintenanceCellular functionsRNA speciesWidespread mechanismCell nucleiSurprising complexityBiochemical processesAltered affinityBody assemblyAssembly propertiesRibonucleoproteinDistinct structuresAssemblyPre-existing substructuresBiogenesisSplicingAdditional layerTranscriptionTranscription 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
2011
Pause locally, splice globally
Oesterreich F, Bieberstein N, Neugebauer KM. Pause locally, splice globally. Trends In Cell Biology 2011, 21: 328-335. PMID: 21530266, DOI: 10.1016/j.tcb.2011.03.002.Peer-Reviewed Original ResearchConceptsRNA polymerase II elongation rateContext of chromatinProtein-coding transcriptsRNA polymerase IIPre-mRNA splicingTranscript bodyTranscriptional pausingHistone modificationsPolymerase IIIntron removalSplicingTranscriptionElongation rateGenesTranscriptsRecent evidenceChromatinIntronsPausingElongationRegulatorLocal regulationRegulationRecruitment
2010
Global Analysis of Nascent RNA Reveals Transcriptional Pausing in Terminal Exons
Oesterreich F, Preibisch S, Neugebauer KM. Global Analysis of Nascent RNA Reveals Transcriptional Pausing in Terminal Exons. Molecular Cell 2010, 40: 571-581. PMID: 21095587, DOI: 10.1016/j.molcel.2010.11.004.Peer-Reviewed Original ResearchConceptsTerminal exonNascent RNATranscription profilesIntron-containing genesHigh-density tiling microarraysPre-mRNA splicingSplicing kineticsTranscriptional pausingTiling microarraysPol IISplicing catalysisSplicing efficiencyGenes lackSplicingExonsTranscriptionGenesRNAGlobal analysisFunctional couplingSilico simulationsIntronlessSpliceosomePausingYeast
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