title: Global analysis of nascent RNA reveals transcriptional pausing in terminal exons.
abstract: Pre-mRNA splicing is catalyzed by the spliceosome, which can assemble on pre-mRNA cotranscriptionally. However, whether splicing generally occurs during transcription has not been addressed. Indeed, splicing catalysis is expected to occur posttranscriptionally in yeast, where the shortness of terminal exons should leave insufficient time for splicing. Here, we isolate endogenous S. cerevisiae nascent RNA and determine gene-specific splicing efficiencies and transcription profiles, using high-density tiling microarrays. Surprisingly, we find that splicing occurs cotranscriptionally for the majority of intron-containing genes. Analysis of transcription profiles reveals Pol II pausing within the terminal exons of these genes. Intronless and inefficiently spliced genes lack this pause. In silico simulations of transcription and splicing kinetics confirm that this pausing event provides sufficient time for splicing before termination. The discovery of terminal exon pausing demonstrates functional coupling of transcription and splicing near gene ends.
authors.affiliation: Max Planck Institute of Molecular Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.
authors.forename: Fernando
authors.initials: F
authors.lastname: Carrillo Oesterreich
authors.forename: Stephan
authors.initials: S
authors.lastname: Preibisch
authors.forename: Karla M
authors.initials: KM
authors.lastname: Neugebauer
mesh_terms: D002843:Chromatin / Q000378:metabolism; D005091:Exons / Q000235:genetics*; D005800:Genes, Fungal / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D040901:Proteomics; D012319:RNA Polymerase II / Q000378:metabolism; D012322:RNA Precursors / Q000235:genetics* / Q000378:metabolism; D012326:RNA Splicing / Q000235:genetics; D012331:RNA, Fungal / Q000235:genetics* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D013347:Subcellular Fractions / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D012322:RNA Precursors; D012331:RNA, Fungal; D029701:Saccharomyces cerevisiae Proteins; D012319:RNA Polymerase II