Pcf11 orchestrates transcription termination pathways in yeast

Grzechnik, Pawel; Gdula, Michal R.; Proudfoot, Nick J.

doi:10.1101/gad.251470.114

Cited by 70 publications

(77 citation statements)

References 64 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Interestingly, NMR studies had previously shown that Rtt103 interacts with pSer2 marks and cooperatively engages Pcf11 at protein-coding genes (20). However, a strain harboring pcf11-13, an allele that disrupts interaction with the CTD, displays defective termination at a set of snoRNA genes (38). These pcf11-13-sensitive snoRNAs coincide with snoRNAs that display termination defects in our T4A strain (P = 0.011) ( Fig.…”

Section: Discussionmentioning

confidence: 62%

See 1 more Smart Citation

Different phosphoisoforms of RNA polymerase II engage the Rtt103 termination factor in a structurally analogous manner

Nemec

Yang

Gilmore

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

The carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) orchestrates dynamic recruitment of specific cellular machines during different stages of transcription. Signature phosphorylation patterns of Y 1 S 2 P 3 T 4 S 5 P 6 S 7 heptapeptide repeats of the CTD engage specific "readers." Whereas phospho-Ser5 and phospho-Ser2 marks are ubiquitous, phospho-Thr4 is reported to only impact specific genes. Here, we identify a role for phospho-Thr4 in transcription termination at noncoding small nucleolar RNA (snoRNA) genes. Quantitative proteomics reveals an interactome of known readers as well as protein complexes that were not known to rely on Thr4 for association with Pol II. The data indicate a key role for Thr4 in engaging the machinery used for transcription elongation and termination. We focus on Rtt103, a protein that binds phosphoSer2 and phospho-Thr4 marks and facilitates transcription termination at protein-coding genes. To elucidate how Rtt103 engages two distinct CTD modifications that are differentially enriched at noncoding genes, we relied on NMR analysis of Rtt103 in complex with phospho-Thr4-or phospho-Ser2-bearing CTD peptides. The structural data reveal that Rtt103 interacts with phospho-Thr4 in a manner analogous to its interaction with phospho-Ser2-modified CTD. The same set of hydrogen bonds involving either the oxygen on phospho-Thr4 and the hydroxyl on Ser2, or the phosphate on Ser2 and the Thr4 hydroxyl, can be formed by rotation of an arginine side chain, leaving the intermolecular interface otherwise unperturbed. This economy of design enables Rtt103 to engage Pol II at distinct sets of genes with differentially enriched CTD marks.ach stage of transcription relies on ordered recruitment and exchange of specific protein complexes that act on RNA polymerase II, its nascent transcripts, and the underlying chromatin. This dynamic process is orchestrated via patterned posttranslational modifications of the carboxyl-terminal domain (CTD). This unusual and essential domain of Rpb1, the largest component of the 12-subunit polymerase, consists of repeating Y 1 S 2 P 3 T 4 S 5 P 6 S 7 heptapeptides (26 repeats in budding yeast and 52 in humans) (1). The mechanistic consequences of phosphorylating Ser5 and Ser2 have been well documented (2-11). However, the role of Thr4 phosphorylation (pThr4), and even the necessity of Thr4 for cellular survival, appears to differ among closely related species and between growth conditions within a given species (12-15). Recent mass spectrometric analysis of an extensively engineered CTD revealed a paucity of pThr4, raising questions about the importance of this mark (16). In contrast, similar studies found pThr4 marks at levels comparable to or greater than the ubiquitously placed pSer2 mark in both yeast and human cells (17). Thus, much remains to be understood about the natural abundance and functional role of pThr4 marks on the endogenous, unmodified CTD.Previous studies suggest that pThr4 has roles in transcriptional elongation, 3ʹ-...

show abstract

Section: Discussionmentioning

confidence: 62%

“…Previous work suggests a role for pSer2 in snoRNA termination (37)(38)(39). Therefore, we examined the levels of pSer2 as well as pThr4, normalized to Rpb3 levels, across snoRNA genes in a WT strain.…”

Section: Resultsmentioning

confidence: 99%

Different phosphoisoforms of RNA polymerase II engage the Rtt103 termination factor in a structurally analogous manner

Nemec

Yang

Gilmore

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…Given the lack of a direct homolog for the NNS complex in higher eukaryotes, we speculate that in vertebrates PCF11 might be a functional counterpart of yeast Nrd1. Interestingly, yeast PCF11 gene is also controlled by NNS-dependent premature termination (Creamer et al, 2011), and cooperates with the NNS complex (Grzechnik et al, 2015). Overall we predict that transcription attenuation is a fundamental gene regulatory mechanism conserved in all eukaryotes.…”

Section: Premature Termination As a Regulatory Paradigm In Vertebratesmentioning

confidence: 64%

Selective roles of vertebrate PCF11 in premature and full-length transcript termination

Kamieniarz-Gdula

Gdula

Panser

et al. 2018

Preprint

View full text Add to dashboard Cite

The pervasive nature of RNA polymerase II (Pol II) transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation (CPA) factor PCF11, which directly binds to the Pol II C-terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11-mediated termination is essential for vertebrate development. A range of genomic analyses, including: mNET-seq, 3' mRNA-seq, chromatin RNA-seq and ChIP-seq, reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome-wide. PCF11 binds preferentially between closely spaced genes, where it prevents transcriptional interference and downstream gene silencing. Notably, PCF11 is sub-stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto-regulatory mechanism involving premature termination of its own transcript, and are important for normal development. Both in human cell culture and during zebrafish development, PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination.

show abstract

“…Interestingly, the apparent role of Seb1 in fission yeast 3 ′ end processing mirrors functions of Pcf11 in S. cerevisiae, a protein that also interacts with the CTD of RNAPII (Barilla et al 2001). Similarly to Seb1, Pcf11 is involved in transcription termination of both coding RNAs and ncRNAs as well as in poly(A) site selection (Grzechnik et al 2015). Despite these similarities, we found that the expression of S. pombe Seb1 did not rescue a Pcf11 deficiency in S. cerevisiae (Supplemental Fig.…”

Section: Seb1 Controls Poly(a) Site Selectionmentioning

confidence: 98%

The Nrd1-like protein Seb1 coordinates cotranscriptional 3′ end processing and polyadenylation site selection

et al. 2016

View full text Add to dashboard Cite

Termination of RNA polymerase II (RNAPII) transcription is associated with RNA 3 ′ end formation. For coding genes, termination is initiated by the cleavage/polyadenylation machinery. In contrast, a majority of noncoding transcription events in Saccharomyces cerevisiae does not rely on RNA cleavage for termination but instead terminates via a pathway that requires the Nrd1-Nab3-Sen1 (NNS) complex. Here we show that the Schizosaccharomyces pombe ortholog of Nrd1, Seb1, does not function in NNS-like termination but promotes polyadenylation site selection of coding and noncoding genes. We found that Seb1 associates with 3 ′ end processing factors, is enriched at the 3 ′ end of genes, and binds RNA motifs downstream from cleavage sites. Importantly, a deficiency in Seb1 resulted in widespread changes in 3 ′ untranslated region (UTR) length as a consequence of increased alternative polyadenylation. Given that Seb1 levels affected the recruitment of conserved 3 ′ end processing factors, our findings indicate that the conserved RNA-binding protein Seb1 cotranscriptionally controls alternative polyadenylation.

show abstract

Pcf11 orchestrates transcription termination pathways in yeast

Cited by 70 publications

References 64 publications

Different phosphoisoforms of RNA polymerase II engage the Rtt103 termination factor in a structurally analogous manner

Different phosphoisoforms of RNA polymerase II engage the Rtt103 termination factor in a structurally analogous manner

Selective roles of vertebrate PCF11 in premature and full-length transcript termination

The Nrd1-like protein Seb1 coordinates cotranscriptional 3′ end processing and polyadenylation site selection

Contact Info

Product

Resources

About