Résumé
A large share of the non-coding transcriptome in yeast is controlled by the Nrd1-Nab3-Sen1 (NNS) complex, which promotes transcription termination of non-coding RNA (ncRNA) genes, and by the nuclear exosome, which limits the steady-state levels of the transcripts produced. How unconstrained ncRNA levels affect RNA metabolism and gene expression are long-standing and important questions. 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, inducing termination defects at NNS targets. ncRNA-dependent, genome-wide termination defects can be recapitulated by the expression of a degradation-resistant, 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 abundance, and the importance of nuclear ncRNA degradation.
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•Degradation of ncRNAs by the exosome frees bound termination factors Nab3 and Nrd1•Exosome inhibition triggers accumulation of ncRNAs complexed with Nab3 and Nrd1•Out-titration of Nab3 and Nrd1 by ncRNAs decreases NNS co-transcriptional binding•A circular RNA decoy recapitulates the global impairment of NNS-dependent termination
Coupling between NNS-dependent termination and exosome degradation rids cells of excess pervasive ncRNAs. Villa et al. show that nuclear accumulation of ncRNAs because of exosome inhibition or expression of a decoy RNA sequesters ncRNA termination factors, thus preventing efficient recycling back to elongating RNAPII and transcription termination.