SummarySen1 of S. cerevisiae is a known component of the NRD complex implicated in transcription termination of nonpolyadenylated as well as some polyadenylated RNA polymerase II transcripts. We now show that Sen1 helicase possesses a wider function by restricting the occurrence of RNA:DNA hybrids that may naturally form during transcription, when nascent RNA hybridizes to DNA prior to its packaging into RNA protein complexes. These hybrids displace the nontranscribed strand and create R loop structures. Loss of Sen1 results in transient R loop accumulation and so elicits transcription-associated recombination. SEN1 genetically interacts with DNA repair genes, suggesting that R loop resolution requires proteins involved in homologous recombination. Based on these findings, we propose that R loop formation is a frequent event during transcription and a key function of Sen1 is to prevent their accumulation and associated genome instability.

Eukaryotic genomes are extensively transcribed, forming both messenger (m) and noncoding (nc) RNAs. ncRNAs made by RNA polymerase II (Pol II) often initiate from bidirectional promoters (nucleosome-depleted chromatin) that synthesise mRNA and ncRNA in opposite directions. We demonstrate that actively transcribed mRNA encoding genes by adopting a gene loop conformation, restrict divergent transcription of ncRNAs. Since gene loop formation depends on a protein factor (Ssu72) that co-associates with both promoter and terminator, its inactivation leads to increased synthesis of promoter-associated divergent ncRNAs, referred to as Ssu72 restricted transcripts (SRT). Similarly, inactivation of individual gene loops by gene mutation enhances SRT synthesis. We demonstrate that gene loop conformation enforces transcriptional directionality on otherwise bidirectional promoters.

Both RNA polymerase I and II (Pol I and Pol II) in budding yeast employ a functionally homologous "torpedo-like" mechanism to promote transcriptional termination. For two well-defined Pol II-transcribed genes, CYC1 and PMA1, we demonstrate that both Rat1p exonuclease and Sen1p helicase are required for efficient termination by promoting degradation of the nascent transcript associated with Pol II, following mRNA 3 end processing. Similarly, Pol I termination relies on prior Rnt1p cleavage at the 3 end of the pre-rRNA 35S transcript. This is followed by the combined actions of Rat1p and Sen1p to degrade the Pol I-associated nascent transcript that consequently promote termination in the downstream rDNA spacer sequence. Our data suggest that the previously defined in vitro Pol I termination mechanism involving the action of the Reb1p DNA-binding factor to "road-block" Pol I transcription close to the termination region may have overlooked more complex in vivo molecular processes.[Keywords: 5Ј-3Ј exonuclease; RNA polymerase I; S. cerevisiae; transcription termination] Supplemental material is available at http://www.genesdev.org. Nuclear transcription in eukaryotes is performed by three different DNA-dependent RNA polymerases (Pol I, Pol II, and Pol III) resulting in the synthesis of ribosomal RNA (rRNA), messenger RNA (mRNA), and small noncoding RNAs (5S rRNA and tRNA). Other small RNAs (e.g., snRNAs) are synthesized by either Pol II or Pol III (Archambault and Friesen 1993). Knowledge of the molecular details that result in transcriptional initiation (e.g., through enhancer and promoter recognition) is now quite well advanced, especially for Pol II. However, the subsequent stages of the transcription cycle, elongation and termination, are less well described. In particular, the molecular process that switches each class of polymerase from processive elongation into termination is poorly understood but may differ significantly for each polymerase class. For Pol III, which copies relatively short genes, the mechanism of termination appears to be an intrinsic feature of the polymerase itself and especially the small subunit Rpc11p. Here simple sensestrand oligo(dT) sequences appear to define Pol III termination sites (Braglia et al. 2005). In marked contrast, the mechanism of Pol II termination is far more complex, being intimately connected to processing of the premRNA. Thus capping, splicing, and cleavage/polyadenylation of the pre-mRNA all occur cotranscriptionally, mediated by mRNA processing factors that are known to interact directly or indirectly with the Pol II large subunit, the C-terminal domain (CTD) region, depending on its phosphorylation state (Orphanides and Reinberg 2002). Significantly, Pol II termination is dependent on pre-mRNA 3Ј end processing and requires a specific set of termination factors and complex genetic signals (Proudfoot 2004;Buratowski 2005). Additionally, Pol II termination requires at least some of the cleavage/polyadenylation factors that, as well as processing the premRNA, may el...

Termination of transcription by RNA polymerase II requires two distinct processes: The formation of a defined 3′ end of the transcribed RNA, as well as the disengagement of RNA polymerase from its DNA template. Both processes are intimately connected and equally pivotal in the process of functional messenger RNA production. However, research in recent years has elaborated how both processes can additionally be employed to control gene expression in qualitative and quantitative ways. This review embraces these new findings and attempts to paint a broader picture of how this final step in the transcription cycle is of critical importance to many aspects of gene regulation. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.

SummaryTranscription termination of RNA polymerase II (Pol II) on protein-coding genes in S. cerevisiae relies on pA site recognition by 3′ end processing factors. Here we demonstrate the existence of two alternative termination mechanisms that rescue polymerases failing to disengage from the template at pA sites. One of these fail-safe mechanisms is mediated by the NRD complex, similar to termination of short noncoding genes. The other termination mechanism is mediated by Rnt1 cleavage of the nascent transcript. Both fail-safe termination mechanisms trigger degradation of readthrough transcripts by the exosome. However, Rnt1-mediated termination can also enhance the usage of weak pA signals and thereby generate functional mRNA. We propose that these alternative Pol II termination pathways serve the dual function of avoiding transcription interference and promoting rapid removal of aberrant transcripts.