Genome-Wide Distribution of Yeast RNA Polymerase II and Its Control by Sen1 Helicase

Abstract

Functional engagement of RNA polymerase II (Pol II) with eukaryotic chromosomes is a fundamental and highly regulated biological process. Here we present a high-resolution map of Pol II occupancy across the entire yeast genome. We compared a wild-type strain with a strain bearing a substitution in the Sen1 helicase, which is a Pol II termination factor for noncoding RNA genes. The wild-type pattern of Pol II distribution provides unexpected insights into the mechanisms by which genes are repressed or silenced. Remarkably, a single amino acid substitution that compromises Sen1 function causes profound changes in Pol II distribution over both noncoding and protein-coding genes, establishing an important function of Sen1 in the regulation of transcription. Given the strong similarity of the yeast and human Sen1 proteins, our results suggest that progressive neurological disorders caused by substitutions in the human Sen1 homolog Senataxin may be due to misregulation of transcription.

Transcription termination by nuclear RNA polymerases

“…Genome-wide analysis of RNAPII distribution in a SEN1 mutant strain confirmed the involvement of Sen1 in transcription termination of snoRNAs (Ursic et al 1997;Rasmussen and Culbertson 1998) and other short transcripts (Steinmetz et al 2006b). ChIP analysis showed RNAPII read-through at most snoRNAs genes in a SEN1 mutant strain or a strain defective for its helicase activity (Kim et al 2006;Steinmetz et al 2006b).…”

“…Another possibility is that it could function at the site of termination to help disrupt the ternary complex. Furthermore, even though Sen1 was previously detected at snoRNAs genes (Kim et al 2006), readthrough at noncoding and some coding genes in a SEN1 mutant strain supports Sen1 involvement in termination of both class of RNAs (Steinmetz et al 2006b). Sen1 is a large, low-abundance nuclear protein that interacts with the CTD (Ursic et al 2004) and is implicated in processing of a variety of noncoding RNAs (Winey and Culbertson 1988;Ursic et al 1995).…”

“…ChIP analysis showed RNAPII read-through at most snoRNAs genes in a SEN1 mutant strain or a strain defective for its helicase activity (Kim et al 2006;Steinmetz et al 2006b). Sen1 associates with the CTD and also coprecipitates with several snoRNAs and some snRNAs (Yuryev et al 1996;Ursic et al 1997Ursic et al , 2004.…”

“…An important feature of termination appears to be the distance traveled by RNAPII when it reaches the terminator. The Nrd1 complex is implicated in transcription of short transcripts (Steinmetz et al 2006b). As explained below, this regulation reflects the different stages of CTD phosphorylation.…”

Sen1 has unique structural features grafted on the architecture of the Upf1‐like helicase family

“…While Nrd1‐Nab3 couples the NNS complex to RNA degradation, Sen1 is the key enzyme in the transcription termination reaction (Porrua & Libri, 2013). Sen1 has also been shown to be involved in termination of short protein‐coding genes (Steinmetz et al , 2006), and inactivation of Sen1 leads to the accumulation of R‐loops (RNA:DNA hybrids that form during transcription when the nascent RNA invades the DNA template) (Mischo et al , 2011). …”