General Regulatory Factors Control the Fidelity of Transcription by Restricting Non-coding and Ectopic Initiation

Challal, Drice; Barucco, Mara; Kubik, Slawomir; Feuerbach, Frank; Candelli, Tito; Geoffroy, H; Benaksas, Chaima; Shore, David; Libri, Domenico

doi:10.1016/j.molcel.2018.11.037

Cited by 58 publications

(84 citation statements)

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“…For mRNAs, we used the annotations in Challal et al (2018). For the 5 0 and the 3 0 end of mature snoRNAs, we used the annotations in Xu et al (2009).…”

Section: Annotationsmentioning

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

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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.

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“…For mRNAs, we used the annotations in Challal et al (2018). For the 5 0 and the 3 0 end of mature snoRNAs, we used the annotations in Xu et al (2009).…”

Section: Annotationsmentioning

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

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“…To detect the binding of Nab3 and Nrd1 in vivo, we employed an improved version of the crosslinking and cDNA analysis protocol (CRAC) (Granneman et al, 2009;Candelli et al, 2018;Challal et al, 2018). The proteins of interest are purified after a step of in vivo UV crosslinking and the covalently associated transcripts are sequenced, which provides a read-out of the extent and position of RNA binding.…”

Section: Rna Degradation Is Required For Releasing Nrd1 and Nab3 Frommentioning

confidence: 99%

“…CRAC signals can have two components: one, post-transcriptional, deriving from the binding of proteins to RNAs that have been released from the site of transcription; a second, co-transcriptional, due to proteins binding to the nascent RNA. Because the CRAC signal depends on the levels of transcription, which might differ in wild type (wt) and exosome-defective rrp6∆ cells, we also measured transcription by RNAPII CRAC (Milligan et al, 2016;Candelli et al, 2018;Challal et al, 2018) in the two genetic backgrounds.…”

Section: Rna Degradation Is Required For Releasing Nrd1 and Nab3 Frommentioning

confidence: 99%

“…To extend these findings to a genomewide perspective, we focused on a manually curated representative subset of 329 CUTs. We chose to generate a reannotated model set of CUTs (see STAR Methods; Table S1) because early annotations, mainly based on the automated detection of microarray signals , do not generally take into account novel and more accurate datasets defining the TSS, the termination region and the RNAPII occupancy (Malabat et al, 2015;Roy et al, 2016;Challal et al, 2018) Also, we took into account the NNS dependency (Roy et al, 2016;Candelli et al, 2018), for a better distinction of CUTs that are NNS targets from other non-coding RNAs.…”

Section: Rna Degradation Is Required For Releasing Nrd1 and Nab3 Frommentioning

confidence: 99%

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Degradation of non-coding RNAs promotes recycling of termination factors at sites of transcription

Villa

Barucco

Martin-Niclos

et al. 2019

Preprint

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A large share of the non-coding transcriptome in yeast is controlled by the Nrd1-Nab3-Sen1 (NNS) complex, which promotes transcription termination of noncoding RNA (ncRNA) genes, and by the nuclear exosome, which limits the steady state levels of the transcripts produced. How global ncRNA levels impinge on cellular functions is a longstanding and important question. Here we show that degradation of ncRNAs by the exosome is required for freeing Nrd1 and Nab3 from the released transcript after termination. In exosome mutants, these factors are sequestered by ncRNAs and cannot be efficiently recycled to sites of transcription, which induces termination defects genome-wide. ncRNA-dependent, genome-wide termination defects can be recapitulated by the expression of a degradationresistant, circular RNA containing a natural NNS target in exosome proficient cells.Our results have important implications for the mechanism of termination, the general impact of ncRNAs on cellular physiology and the importance of nuclear ncRNA degradation.Government through its "Investments for the Future" program.This work has benefited from the facilities and expertise of the high throughput sequencing core facility of I2BC (Centre de Recherche de Gif -http://www.i2bc-saclay.fr/). AUTHORS CONTRIBUTION Conceptualization, D.L., T.V., and A.J.; Methodology, T.V., M.B., and M-J.M.N.; Software, M.B.; Formal Analysis, M.B., T.V., and D.L.; Investigation, T.V., M-J.M.N., and D.L.; Writing -Original Draft, T.V. and D.L.; Writing -Review and Editing, T.V. and D.L.; Funding Acquisition, D.L.; Supervision, D.L.

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“…Annotations 4 For mRNAs we used the annotations in Challal et al, 2018. For the 5' and 5 the 3' end of mature snoRNAs snoRNAs we used the annotations in Xu et al, 2008(Xu et al, 6 2009).…”

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confidence: 99%

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

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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...

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General Regulatory Factors Control the Fidelity of Transcription by Restricting Non-coding and Ectopic Initiation

Cited by 58 publications

References 54 publications

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

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

Degradation of non-coding RNAs promotes recycling of termination factors at sites of transcription

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

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