The RNA Polymerase II C-terminal Domain-interacting Domain of Yeast Nrd1 Contributes to the Choice of Termination Pathway and Couples to RNA Processing by the Nuclear Exosome

Heo

Journal of Biological Chemistry

et al. 2016

Self Cite

The yeast Nrd1 interacts with the C-terminal domain (CTD) of RNA polymerase II (RNApII) through its CTD-interacting domain (CID) and also associates with the nuclear exosome, thereby acting as both a transcription termination and RNA processing factor. Previously, we found that the Nrd1 CID is required to recruit the nuclear exosome to the Nrd1 complex, but it was not clear which exosome subunits were contacted. Here, we show that two nuclear exosome cofactors, Mpp6 and Trf4, directly and competitively interact with the Nrd1 CID and differentially regulate the association of Nrd1 with two catalytic subunits of the exosome. Importantly, Mpp6 promotes the processing of Nrd1-terminated transcripts preferentially by Dis3, whereas Trf4 leads to Rrp6-dependent processing. This suggests that Mpp6 and Trf4 may play a role in choosing a particular RNA processing route for Nrd1-terminated transcripts within the exosome by guiding the transcripts to the appropriate exonuclease.The Nrd1-Nab3-Sen1 complex terminates transcription of small non-coding RNAs by RNApII 2 (1-4). Nrd1 and Nab3 are sequence-specific RNA binding proteins, and Sen1 helicase (senataxin in humans) has an ATPase activity that directly dissociates RNApII from the templates (5). Nrd1 also recognizes the serine 5-phosphorylated (Ser(P)-5) CTD of RNApII using its CID (6). Because the Ser(P)-5 CTD is prevalent in the early stage of transcription, the Nrd1 CID-RNApII CTD interaction has been suggested to dictate a regional specificity of Nrd1-Nab3-Sen1-dependent transcription termination (7). Indeed, Nrd1havingtheCIDofRtt103thatrecognizestheSerine2-phosphorylated CTD becomes capable of triggering RNApII termination at regions where Nrd1-Nab3 binding sites and serine 2-phosphorylated CTD are co-localized, satisfyingly confirming this model (8).The RNAs generated via Nrd1-Nab3-Sen1-dependent termination are trimmed or degraded by the exosome, mediated by Nrd1 complex interactions with this 3Ј-5Ј exonuclease (9). Intriguingly, swapping or deletion of the Nrd1 CID reduced the interaction between Nrd1 and the exosome (8), indicating that the Nrd1 CID also plays an important role in coupling termination and RNA processing by recruiting the exosome.The nuclear exosome consists of the core exosome and a nuclear-specific subunit Rrp6 (PM/Scl100 in humans) that functions in RNA 3Ј-end processing using 3Ј-5Ј exoribonuclease activity (10 -13). The core exosome is a catalytically inactive barrel-shaped complex composed of nine subunits (Exo-9: RNase pleckstrin homology-like proteins (Rrp41/42/43/45/46 and Mtr3) and S1/KH domain proteins (Rrp4/40 and Csl4)) as well as Dis3 (also known as Rrp44), which is a 3Ј-5Ј exo/endonuclease. Located at the bottom of Exo-9, Dis3 trims or degrades the RNA substrates passed through the central pore of . In contrast, Rrp6 sits on top of the Exo-9 S1/KH ring above the central channel, and the RNAs traverse the S1/KH ring and enter into the active site of Rrp6 for degradation (15,16).The TRAMP (Trf4/5-Air1/2-Mtr4 polyadenylation) complex is ...

supporting

confidence: 68%

Section: Discussionmentioning

confidence: 99%

Section: Identification Of Proteins Interacting With the Nrd1 Cid-mentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

Exosome Cofactors Connect Transcription Termination to RNA Processing by Guiding Terminated Transcripts to the Appropriate Exonuclease within the Nuclear Exosome

Heo

Journal of Biological Chemistry

et al. 2016

Self Cite

“…The Nrd1 CID is known to affect RNA degradation, as it interacts directly with Trf4 and so couples the nuclear exosome with nascent RNA Kubicek et al 2012;Heo et al 2013;Tudek et al 2014). We therefore investigated the possibility that the observed aberrant Nrd1 recruitment in pcf11-13 may affect RNA turnover.…”

Section: Associated Recruitment Of Nrd1 and Pcf11 On Nrd-dependent Genesmentioning

confidence: 99%

Pcf11 orchestrates transcription termination pathways in yeast

2015

In Saccharomyces cerevisiae, short noncoding RNA (ncRNA) generated by RNA polymerase II (Pol II) are terminated by the NRD complex consisting of Nrd1, Nab3, and Sen1. We now show that Pcf11, a component of the cleavage and polyadenylation complex (CPAC), is also generally required for NRD-dependent transcription termination through the action of its C-terminal domain (CTD)-interacting domain (CID). Pcf11 localizes downstream from Nrd1 on NRD terminators, and its recruitment depends on Nrd1. Furthermore, mutation of the Pcf11 CID results in Nrd1 retention on chromatin, delayed degradation of ncRNA, and restricted Pol II CTD Ser2 phosphorylation and Sen1-Pol II interaction. Finally, the pcf11-13 and sen1-1 mutant phenotypes are very similar, as both accumulate RNA:DNA hybrids and display Pol II pausing downstream from NRD terminators. We predict a mechanism by which the exchange of Nrd1 and Pcf11 on chromatin facilitates Pol II pausing and CTD Ser2-P phosphorylation. This in turn promotes Sen1 activity that is required for NRD-dependent transcription termination in vivo.

Rrp6: Integrated roles in nuclear RNA metabolism and transcription termination

Fox

Mosley

2015

WIREs RNA

The yeast RNA exosome is a eukaryotic ribonuclease complex essential for RNA processing, surveillance and turnover. It is comprised of a barrel-shaped core and cap as well as a 3’–5’ ribonuclease known as Dis3 which contains both endo- and exonuclease domains. A second exonuclease, Rrp6, is added in the nucleus. Dis3 and Rrp6 have both shared and distinct roles in RNA metabolism, and this review will focus primarily on Rrp6 and the roles of the RNA exosome in the nucleus. The functions of the nuclear exosome are modulated by cofactors and interacting partners specific to each type of substrate. Generally, the cofactor TRAMP (Trf4/5-Air2/1-Mtr4 polyadenylation) complex helps unwind unstable RNAs, RNAs requiring processing such as rRNAs, tRNAs, or snRNAs or improperly processed RNAs and direct it toward the exosome. In yeast, Rrp6 interacts with Nrd1, the cap binding complex (CBC), and RNA Polymerase II to aid in nascent RNA processing, termination, and polyA tail length regulation. Recent studies have shown that proper termination and processing of short, non-coding RNAs by Rrp6 is particularly important for transcription regulation across the genome and has important implications for regulation of diverse processes at the cellular level. Loss of proper Rrp6 and exosome activity may contribute to various pathologies such as autoimmune disease, neurological disorders, and cancer.