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

Abstract

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...

Identification of three sequence motifs in the transcription termination factor Sen1 that mediate direct interactions with Nrd1

“…In conclusion, we have identified three NIMs in the CTS of budding yeast Sen1 and elucidated the molecular basis for their recognition by Nrd1 CID. The identification of one of these NIMs (NIM2) in ScSen1 was independently reported recently (25). Although neither the Sen1…”

Identification of Three Sequence Motifs in the Transcription Termination Factor Sen1 that Mediate Direct Interactions with Nrd1

“…In conclusion, we have identified three NIMs in the CTS of budding yeast Sen1 and elucidated the molecular basis for their recognition by Nrd1 CID. The identification of one of these NIMs (NIM2) in ScSen1 was independently reported recently (Han et al, 2018). Although neither the Sen1 NIMs nor Nrd1 CID is essential for supporting viability, deletions do show termination defects in a reporter assay.…”