Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes

Carlo Baejen; Jessica Andreani; Phillipp Torkler; Sofia Battaglia; Bjoern Schwalb; Michael Lidschreiber; Kerstin C Maier; Andrea Boltendahl; Petra Rus; Stephanie Esslinger; Johannes Söding; Patrick Cramer

doi:10.1016/j.molcel.2017.02.009

Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes

Mol Cell. 2017 Apr 6;66(1):38-49.e6. doi: 10.1016/j.molcel.2017.02.009. Epub 2017 Mar 16.

Affiliations

¹ Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
² Karolinska Institutet, Department of Biosciences and Nutrition, Center for Innovative Medicine and Science for Life Laboratory, Novum, Hälsovägen 7, 141 83 Huddinge, Sweden.
³ Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.
⁴ Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany. Electronic address: [email protected].
⁵ Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany. Electronic address: [email protected].

PMID: 28318822
DOI: 10.1016/j.molcel.2017.02.009

Abstract

At the end of protein-coding genes, RNA polymerase (Pol) II undergoes a concerted transition that involves 3'-processing of the pre-mRNA and transcription termination. Here, we present a genome-wide analysis of the 3'-transition in budding yeast. We find that the 3'-transition globally requires the Pol II elongation factor Spt5 and factors involved in the recognition of the polyadenylation (pA) site and in endonucleolytic RNA cleavage. Pol II release from DNA occurs in a narrow termination window downstream of the pA site and requires the "torpedo" exonuclease Rat1 (XRN2 in human). The Rat1-interacting factor Rai1 contributes to RNA degradation downstream of the pA site. Defects in the 3'-transition can result in increased transcription at downstream genes.

Keywords: RNA polymerase II; Torpedo nuclease; poly-adenylation; pre-mRNA 3′-processing; transcription termination.

MeSH terms

Binding Sites
Chromosomal Proteins, Non-Histone / genetics
Chromosomal Proteins, Non-Histone / metabolism
DNA, Fungal / genetics
DNA, Fungal / metabolism*
Exoribonucleases / genetics
Exoribonucleases / metabolism
Models, Genetic
Protein Binding
RNA 3' End Processing*
RNA Polymerase II / genetics
RNA Polymerase II / metabolism*
RNA Precursors / biosynthesis*
RNA Precursors / genetics
RNA, Fungal / biosynthesis*
RNA, Fungal / genetics
RNA, Messenger / biosynthesis*
RNA, Messenger / genetics
Saccharomyces cerevisiae / enzymology*
Saccharomyces cerevisiae / genetics
Saccharomyces cerevisiae Proteins / genetics
Saccharomyces cerevisiae Proteins / metabolism*
Transcriptional Elongation Factors / genetics
Transcriptional Elongation Factors / metabolism
mRNA Cleavage and Polyadenylation Factors / genetics
mRNA Cleavage and Polyadenylation Factors / metabolism

Substances

Chromosomal Proteins, Non-Histone
DNA, Fungal
PCF11 protein, S cerevisiae
RNA Precursors
RNA, Fungal
RNA, Messenger
Saccharomyces cerevisiae Proteins
Transcriptional Elongation Factors
YSH1 protein, S cerevisiae
mRNA Cleavage and Polyadenylation Factors
SPT5 transcriptional elongation factor
RAT1 protein, S cerevisiae
RNA Polymerase II
Exoribonucleases