The conserved protein Seb1 drives transcription termination by binding RNA polymerase II and nascent RNA

Wittmann, Sina; Renner, Max; Watts, Beth Rosina; Adams, Oliver; Huseyin, Miles K.; Baejen, Carlo; Omari, Kamel El; Kilchert, Cornelia; Heo, Dong-Hyuk; Kecman, Tea; Cramer, Patrick; Grimes, Jonathan M.; Vasiljeva, Lidia

doi:10.1038/ncomms14861

Cited by 56 publications

(81 citation statements)

References 72 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The NIM is one of the very few sequence regions of the C-terminal domain of Sen1 that are 3 conserved in the closest S. cerevisiae relatives, suggesting that this mode of interaction 4 between Sen1 and Nrd1 is conserved in these yeast species (figure EV1). Conversely, in 5 agreement with previous data showing that Nrd1 and Sen1 orthologues do not interact with 6 each other in S. pombe (Lemay et al, 2016;Wittmann et al, 2017) and with the fact that no 7 Nrd1 homologue could be identified in association with human Sen1(Yüce and West, 2013), 8 we did not detect any putative NIM in Sen1 orthologues from these organisms. 9 10 Structural analyses of the Nrd1 CID-Sen1 NIM interaction 11 To compare the interaction of the newly identified Sen1 NIM (fragment harboring amino acids 12 2052-2063) and the previously identified Trf4 NIM with Nrd1 CID, we performed a quantitative 13 solution-binding assay using fluorescence anisotropy (FA) with purified recombinant Nrd1 CID 14 and synthetic NIM peptides.…”

supporting

confidence: 90%

Termination of non-coding transcription in yeast relies on both a CTD-interaction domain and a CTD-mimic in Sen1

Han

Jasnovidova

Haidara

et al. 2018

Preprint

View full text Add to dashboard Cite

1Pervasive transcription is a widespread phenomenon leading to the production of a plethora 2 of non-coding RNAs (ncRNAs) without apparent function. Pervasive transcription poses a risk 3 that needs to be controlled to prevent the perturbation of gene expression. In yeast, the highly 4 conserved helicase Sen1 restricts pervasive transcription by inducing termination of non-5 coding transcription. However, the mechanisms underlying the specific function of Sen1 at 6 ncRNAs are poorly understood. Here we identify a motif in an intrinsically disordered region of 7 Sen1 that mimics the phosphorylated carboxy terminal domain (CTD) of RNA polymerase II 8 and characterize structurally its recognition by the CTD-interacting domain of Nrd1, an RNA-9 binding protein that binds specific sequences in ncRNAs. In addition, we show that Sen1-10 dependent termination strictly requires the recognition of the Ser5-phosphorylated form of the 11 CTD by the N-terminal domain of Sen1. Furthermore, we find that the N-terminal and the C-12 terminal domains of Sen1 can mediate intra-molecular interactions. Our results shed light onto 13 the network of protein-protein interactions that control termination of non-coding transcription 14 by Sen1. 16The concept of pervasive transcription emerged over a decade ago upon the discovery that a 2 large fraction of both the prokaryotic and the eukaryotic transcriptomes is composed of non-3 coding RNAs (ncRNAs) without any obvious function. Pervasive transcription is potentially 4 harmful for cell homeostasis since it can interfere with normal transcription of canonical genes 5 and provoke the accumulation of toxic RNAs. Therefore, all organisms studied to date have 6 evolved different mechanisms to circumvent the negative consequences of pervasive 7 transcription. These mechanisms often rely on transcription termination and RNA degradation 8 (for review, see Jensen et al., 2013). 9In S. cerevisiae there are two major pathways for termination of RNA polymerase II (RNAPII) 10 transcription. A pathway that depends on a macromolecular complex including the cleavage 11 and polyadenylation factor (CPF) is essentially responsible for transcription termination at 12 protein-coding genes, whereas the Nrd1-Nab3-Sen1 (NNS) complex targets a large fraction of 13 the non-coding RNAs (ncRNAs) produced in the cell. Specifically, the NNS complex terminates 14 transcription of most snoRNAs and a class of ncRNAs dubbed CUTs, for cryptic unstable 15 transcripts, that constitutes the major product of pervasive transcription (for review, see Porrua 16and Libri, 2015). While snoRNAs are important for the correct modification of rRNA, CUTs are 17 generally considered as non-functional molecules (Arigo et al., 2006;Schulz et al., 2013; 18 Thiebaut et al., 2006;Wyers et al., 2005). 19Each pathway is associated with distinct nuclease and polyA-polymerase activities that 20 determine the stability and functionality of the RNAs they take care of. Precursors of mRNAs 21 are cleaved at their 3' ends at the so-called polyA si...

show abstract

supporting

confidence: 90%

Termination of non-coding transcription in yeast relies on both a CTD-interaction domain and a CTD-mimic in Sen1

Han

Jasnovidova

Haidara

et al. 2018

Preprint

View full text Add to dashboard Cite

show abstract

“…Our inspection of the structure of S. pombe Seb1 (43) suggests that it may have a counterpart of the lysine-rich surface motif responsible for inositol polyphosphate binding in the ENTH domain (40). Seb1 interacts physically with the fission yeast CPF complex (43). It is conceivable that IPP interaction with Seb1 (or one of the other fission yeast CID proteins) enhances 3'-processing/termination.…”

Section: Discussionmentioning

confidence: 99%

Inositol pyrophosphates impact phosphate homeostasis via modulation of RNA 3’ processing and transcription termination

Sánchez

Garg

Schwer

et al. 2019

Preprint

View full text Add to dashboard Cite

Fission yeast phosphate acquisition genes pho1, pho84, and tgp1 are repressed in phosphate-rich medium by transcription of upstream lncRNAs. Here we show that phosphate homeostasis is subject to metabolite control by inositol pyrophosphates (IPPs), exerted through the 3'-processing/termination machinery and the Pol2 CTD code. Increasing IP8 (via Asp1 IPP pyrophosphatase mutation) de-represses the PHO regulon and leads to precocious termination of prt lncRNA synthesis. pho1 de-repression by IP8 depends on cleavage-polyadenylation factor (CPF) subunits, termination factor Rhn1, and the Thr4 letter of the CTD code. pho1 de-repression by mutation of the Ser7 CTD letter depends on IP8. Simultaneous inactivation of the Asp1 and Aps1 IPP pyrophosphatases is lethal, but this lethality is suppressed by mutations of CPF subunits Ppn1, Swd22, Ssu72, and Ctf1 and CTD mutation T4A. Failure to synthesize IP8 (via Asp1 IPP kinase mutation) results in pho1 hyper-repression. Synthetic lethality of asp1∆ with Ppn1, Swd22, and Ssu72 mutations argues that IP8 plays an important role in essential 3'processing/termination events, albeit in a manner genetically redundant to CPF. Transcriptional profiling delineates an IPP-responsive regulon composed of genes overexpressed when IP8 levels are increased. Our results establish a novel role for IPPs in cell physiology.

show abstract

“…The NIM is one of the very few sequence regions of the C-terminal domain of Sen1 that are conserved in the closest S. cerevisiae relatives, suggesting that this mode of interaction between Sen1 and Nrd1 is conserved in these yeast species ( Fig EV1) pombe (Lemay et al, 2016;Wittmann et al, 2017) and with the fact that no Nrd1 homologue could be identified in association with human Sen1(Yü ce & West, 2013), we did not detect any putative NIM in Sen1 orthologues from these organisms.…”

Section: Sen1 Possesses a Ctd Mimic That Is Recognized By The Cid Dommentioning

confidence: 99%

Termination of non‐coding transcription in yeast relies on both an RNA Pol II CTD interaction domain and a CTD‐mimicking region in Sen1

et al. 2020

View full text Add to dashboard Cite

Pervasive transcription is a widespread phenomenon leading to the production of a plethora of non‐coding RNAs (ncRNAs) without apparent function. Pervasive transcription poses a threat to proper gene expression that needs to be controlled. In yeast, the highly conserved helicase Sen1 restricts pervasive transcription by inducing termination of non‐coding transcription. However, the mechanisms underlying the specific function of Sen1 at ncRNAs are poorly understood. Here, we identify a motif in an intrinsically disordered region of Sen1 that mimics the phosphorylated carboxy‐terminal domain (CTD) of RNA polymerase II, and structurally characterize its recognition by the CTD‐interacting domain of Nrd1, an RNA‐binding protein that binds specific sequences in ncRNAs. In addition, we show that Sen1‐dependent termination strictly requires CTD recognition by the N‐terminal domain of Sen1. We provide evidence that the Sen1‐CTD interaction does not promote initial Sen1 recruitment, but rather enhances Sen1 capacity to induce the release of paused RNAPII from the DNA. Our results shed light on the network of protein–protein interactions that control termination of non‐coding transcription by Sen1.

show abstract

The conserved protein Seb1 drives transcription termination by binding RNA polymerase II and nascent RNA

Cited by 56 publications

References 72 publications

Termination of non-coding transcription in yeast relies on both a CTD-interaction domain and a CTD-mimic in Sen1

Termination of non-coding transcription in yeast relies on both a CTD-interaction domain and a CTD-mimic in Sen1

Inositol pyrophosphates impact phosphate homeostasis via modulation of RNA 3’ processing and transcription termination

Termination of non‐coding transcription in yeast relies on both an RNA Pol II CTD interaction domain and a CTD‐mimicking region in Sen1

Contact Info

Product

Resources

About