The RNA Exosome Promotes Transcription Termination of backtracked RNA Polymerase II. The RNA Exosome Promotes Transcription Termination of backtracked RNA Polymerase II

Large fractions of genomes are expressed in most eukaryotic cells, generating a diverse repertoire of protein-coding and non-coding transcripts. With such complexity, and as the number of mRNA molecules per cell are often low, it is clear that errors anywhere in the gene expression process could have profound consequences on cellular functions. The exosome is a conserved RNA degradation machine that plays a fundamental role in monitoring the quality of gene expression in the nucleus. The current view is that the nuclear exosome constantly scrutinizes transcription and contributes to post-transcriptional turnover of faulty mRNAs. Yet, how nuclear RNA surveillance by the exosome is coordinated with transcription is still unknown. Here we show that the exosome can directly target the transcription machinery by terminating transcription events associated with paused and backtracked RNA polymerase II (RNAPII), contrary to the notion that the exosome acts exclusively on RNAs that have been released by RNAPII. Our data support a mechanism by which RNAPII backtracking provides a free RNA 3' end for the core exosome, resulting in transcription termination with the concomitant degradation of the associated transcript. These findings uncover a mechanism of co-transcriptional RNA surveillance whereby termination of transcription by the exosome prevents aberrant read-through RNAs and transcriptional interference at neighboring genes.