Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes.
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.
Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
Carlo
C
Baejen
Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
Jessica
J
Andreani
Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
Phillipp
P
Torkler
Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
Sofia
S
Battaglia
Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
Bjoern
B
Schwalb
Karolinska Institutet, Department of Biosciences and Nutrition, Center for Innovative Medicine and Science for Life Laboratory, Novum, Hälsovägen 7, 141 83 Huddinge, Sweden.
Michael
M
Lidschreiber
Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
Kerstin C
KC
Maier
Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
Andrea
A
Boltendahl
Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
Petra
P
Rus
Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.
Stephanie
S
Esslinger
Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany. Electronic address: johannes.soeding@mpibpc.mpg.de.
Johannes
J
Söding
Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany. Electronic address: patrick.cramer@mpibpc.mpg.de.
Patrick
P
Cramer
D001665:Binding Sites; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics / Q000378:metabolism; D004271:DNA, Fungal / Q000235:genetics / Q000378:metabolism*; D005095:Exoribonucleases / Q000235:genetics / Q000378:metabolism; D008957:Models, Genetic; D011485:Protein Binding; D026721:RNA 3' End Processing; D012319:RNA Polymerase II / Q000235:genetics / Q000378:metabolism*; D012322:RNA Precursors / Q000096:biosynthesis* / Q000235:genetics; D012331:RNA, Fungal / Q000096:biosynthesis* / Q000235:genetics; D012333:RNA, Messenger / Q000096:biosynthesis* / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000201:enzymology* / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D035602:Transcriptional Elongation Factors / Q000235:genetics / Q000378:metabolism; D039221:mRNA Cleavage and Polyadenylation Factors / Q000235:genetics / Q000378:metabolism
D002868:Chromosomal Proteins, Non-Histone; D004271:DNA, Fungal; C512637:PCF11 protein, S cerevisiae; D012322:RNA Precursors; D012331:RNA, Fungal; D012333:RNA, Messenger; D029701:Saccharomyces cerevisiae Proteins; D035602:Transcriptional Elongation Factors; C450401:YSH1 protein, S cerevisiae; D039221:mRNA Cleavage and Polyadenylation Factors; C069940:SPT5 transcriptional elongation factor; C075577:RAT1 protein, S cerevisiae; D012319:RNA Polymerase II; D005095:Exoribonucleases
RNA polymerase II; Torpedo nuclease; poly-adenylation; pre-mRNA 3′-processing; transcription termination