title: Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II.
abstract: Protein-coding genes in eukaryotes are transcribed by RNA polymerase II (Pol II) and introns are removed from pre-mRNA by the spliceosome. Understanding the time lag between Pol II progression and splicing could provide mechanistic insights into the regulation of gene expression. Here, we present two single-molecule nascent RNA sequencing methods that directly determine the progress of splicing catalysis as a function of Pol II position. Endogenous genes were analyzed on a global scale in budding yeast. We show that splicing is 50% complete when Pol II is only 45 nt downstream of introns, with the first spliced products observed as introns emerge from Pol II. Perturbations that slow the rate of spliceosome assembly or speed up the rate of transcription caused splicing delays, showing that regulation of both processes determines in vivo splicing profiles. We propose that matched rates streamline the gene expression pathway, while allowing regulation through kinetic competition.
authors.affiliation: Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA.
authors.forename: Fernando Carrillo
authors.initials: FC
authors.lastname: Oesterreich
authors.affiliation: Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA.|Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany.
authors.forename: Lydia
authors.initials: L
authors.lastname: Herzel
authors.affiliation: Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA.
authors.forename: Korinna
authors.initials: K
authors.lastname: Straube
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany.
authors.forename: Katja
authors.initials: K
authors.lastname: Hujer
authors.affiliation: Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA.
authors.forename: Jonathon
authors.initials: J
authors.lastname: Howard
authors.affiliation: Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA.
authors.forename: Karla M
authors.initials: KM
authors.lastname: Neugebauer
mesh_terms: D007438:Introns; D007700:Kinetics; D012319:RNA Polymerase II / Q000378:metabolism*; D012326:RNA Splicing; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D012568:Schizosaccharomyces / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods; D017381:Spliceosomes / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D012319:RNA Polymerase II