Phosphorylation of the RNA polymerase II C-terminal domain dictates transcription termination choice

Abstract

Cryptic unstable transcripts (CUTs) are short, 300-600-nucleotide (nt) RNA polymerase II transcripts that are rapidly degraded by the nuclear RNA exosome in yeast. CUTs are widespread and probably represent the largest share of hidden transcription in the yeast genome. Similarly to small nucleolar and small nuclear RNAs, transcription of CUT-encoding genes is terminated by the Nrd1 complex pathway. We show here that this termination mode and ensuing CUTs degradation crucially depend on the position of RNA polymerase II relative to the transcription start site. Notably, position sensing correlates with the phosphorylation status of the polymerase C-terminal domain (CTD). The Nrd1 complex is recruited to chromatin via interactions with both the nascent RNA and the CTD, but a permissive phosphorylation status of the latter is absolutely required for efficient transcription termination. We discuss the mechanism underlying the regulation of coexisting cryptic and mRNA-productive transcription.

Divergent transcription: A new feature of active promoters

“…Nrd1 directly interacts with the transcription complex by binding Ser-5p and the nascent RNA through its CID and RRM domains, respectively, 62 whereas Ser-2 phosphorylation is antagonistic to Nrd1 binding and Nrd1 function in early termination. 63 Ser-2 phosphorylation is important for proper termination and pre-mRNA processing of gene transcripts. 64 The lack of Ser-2p dependent activities upstream of promoters leads us to believe that promoters contain information that leads to asymmetric delivery of the P-TEFb/ctk1 kinase (Fig.…”

Transcription termination by nuclear RNA polymerases

“…After Nrd1-dependent termination by RNAPII, CUTs are rapidly polyadenylated by the TRAMP complex, and then degraded by the nuclear exosome (Wyers et al 2005;Arigo et al 2006b;Houalla et al 2006;Thiebaut et al 2006). Recently, Gudipati et al (2008) showed that Nrd1-dependent termination of CUTs is inhibited by CTD phosphorylation on Ser2 and promoted by Ser5 phosphorylation. They also showed that binding of Nrd1 to the nascent transcript, even if not sufficient, is necessary for efficient termination.…”

“…The studies of Gudipati et al (2008) and Vasiljeva et al (2008a) provide an explanation of why termination depends on the distance traveled by RNAPII, and how RNAPII chooses between the 39 cleavage and polyadenylation pathway for mRNA termination and the Nrd1 complex for noncoding RNAs, short ORFs and CUT termination. Short transcripts are mostly associated with Ser5 phosphorylation, which recruits the Nrd1 complex.…”

“…Nrd1 (nuclear pre-mRNA down-regulation) is an essential nuclear RNA-binding protein that directs termination of snoRNA and some mRNA transcripts, in association with an interacting protein, the helicase Sen1 (Steinmetz and Brow 1996;Steinmetz et al 2001;Ursic et al 2004;Vasiljeva and Buratowski 2006). Nrd1 contains a CID (Meinhart and Cramer 2004;Meinhart et al 2005) that interacts with CTD phosphorylated at Ser5 (Conrad et al 2000;Gudipati et al 2008;Vasiljeva et al 2008a). Nrd1 also interacts with another essential RNA-binding protein, Nab3 (Yuryev et al 1996).…”

An end in sight? Xrn2 and transcriptional termination by RNA polymerase II

“…For example, the choice of termination pathway in budding yeast is influenced at least in part by the relative densities of Serine 5 and 2 phosphorylation (Ser5p and Ser2p) on the CTD [24]. Ser5p is higher at the beginning of the transcription cycle favouring termination by Nrd1.…”