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 mechanismTranscriptsThe Earliest Transcribed Zygotic Genes Are Short, Newly Evolved, and Different across Species
Heyn P, Kircher M, Dahl A, Kelso J, Tomancak P, Kalinka AT, Neugebauer KM. The Earliest Transcribed Zygotic Genes Are Short, Newly Evolved, and Different across Species. Cell Reports 2014, 6: 285-292. PMID: 24440719, DOI: 10.1016/j.celrep.2013.12.030.Peer-Reviewed Original ResearchConceptsZygotic genome activationZygotic genesEarly zygotic transcriptsOne-cell stageSignificant transcriptional activityRapid cell divisionComparison of fishGenome activationMitochondrial genomePurification of RNAZygotic controlEvolutionary plasticityMulticellular organismsNuclear genesZygotic transcriptsEarly embryogenesisShort genesDanio rerioAdaptive potentialCell divisionTranscriptional activityMetabolic labelingCell cycleEarly genesGenes
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
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