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
2021
Generation of scalable cancer models by combining AAV-intron-trap, CRISPR/Cas9, and inducible Cre-recombinase
Boddu PC, Gupta AK, Kim JS, Neugebauer KM, Waldman T, Pillai MM. Generation of scalable cancer models by combining AAV-intron-trap, CRISPR/Cas9, and inducible Cre-recombinase. Communications Biology 2021, 4: 1184. PMID: 34645977, PMCID: PMC8514589, DOI: 10.1038/s42003-021-02690-1.Peer-Reviewed Original Research
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
The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes
Änkö ML, Müller-McNicoll M, Brandl H, Curk T, Gorup C, Henry I, Ule J, Neugebauer KM. The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes. Genome Biology 2012, 13: r17. PMID: 22436691, PMCID: PMC3439968, DOI: 10.1186/gb-2012-13-3-r17.Peer-Reviewed Original ResearchConceptsSR proteinsSR protein family membersHistone mRNA metabolismConsensus binding motifsProtein family membersIntron-containing mRNAsCellular regulatory mechanismsNonsense-mediated decayNon-coding RNAsNumerous RNAsHistone transcriptsMRNA metabolismUnique RNASplicing eventsAlternative splicingRNA classesRNA recognitionRelated RNATarget genesSRSF4Binding motifRegulatory mechanismsRNA targetsSRSF3Murine cells
2011
The In Vivo Kinetics of RNA Polymerase II Elongation during Co-Transcriptional Splicing
Brody Y, Neufeld N, Bieberstein N, Causse SZ, Böhnlein EM, Neugebauer KM, Darzacq X, Shav-Tal Y. The In Vivo Kinetics of RNA Polymerase II Elongation during Co-Transcriptional Splicing. PLOS Biology 2011, 9: e1000573. PMID: 21264352, PMCID: PMC3019111, DOI: 10.1371/journal.pbio.1000573.Peer-Reviewed Original ResearchMeSH KeywordsBeta-GlobinsFluorescence Recovery After PhotobleachingGreen Fluorescent ProteinsHumansIntronsInverted Repeat SequencesLac RepressorsRecombinant Fusion ProteinsRibonucleoproteins, Small NuclearRNA Polymerase IIRNA PrecursorsRNA SplicingRNA, MessengerSpliceosomesTranscription, GeneticTumor Cells, CulturedConceptsNumber of intronsU1 snRNPPol II elongation ratesRNA polymerase II elongationRNA polymerase II enzymeSplicing-independent roleTranscription elongation kineticsIntron-containing genesCo-transcriptional splicingPolymerase II elongationCompletion of splicingTranscribed pre-mRNARNA processing eventsInducible gene constructsPol II elongationElongation ratePolymerase elongation ratesNascent RNATranscriptional elongationIntronless genesSpliceosome componentsTranscription terminationSplicing machineryTranscription sitesGene end