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

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 risk that needs to be controlled to prevent the perturbation of gene expression. In yeast, the highly conserved helicase Sen1 restricts pervasive transcription by inducing termination of non-coding transcription. However, the mechanisms underlying the timely recruitment of Sen1 to ncRNAs are poorly understood. Here we employ combined biochemical, structural and genomic approaches to shed light on the protein interactions responsible for the specific function of Sen1 in non-coding transcription. We show that Sen1-dependent termination strictly depends on the recognition of a particular phosphorylated form of the carboxy terminal domain (CTD) of RNA polymerase II by the N-terminal domain of Sen1. In addition, we identify a short motif in an intrinsically disordered region of Sen1 that mimics the phosphorylated CTD and we show that this motif is bound by the CTD-interacting domain of Nrd1, an RNA-binding protein that recognizes specific sequences enriched in ncRNAs. This unique protein configuration in which both a reader and a mimic of the phosphorylated CTD coexist provides a novel paradigm for the study of protein-protein interactions controlling the action of transcription-related factors.