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Cell. 2016 Apr 7;165(2):372-81. doi: 10.1016/j.cell.2016.02.045. Epub 2016 Mar 24.

Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II.

Author information

1
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
2
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.
3
Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.
4
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. Electronic address: karla.neugebauer@yale.edu.

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.

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PMID:
27020755
PMCID:
PMC4826323
DOI:
10.1016/j.cell.2016.02.045
[Indexed for MEDLINE]
Free PMC Article
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