Project description:Nuclear 3’ to 5’ nuclease RNA exosome plays a key role in quality control and processing of multiple protein-coding and non-coding transcripts made by RNA polymerase II. A mechanistic understanding of exosome function remains a challenge given the large number of RNA species and intervening RNA processing factors. Here we analysed changes in the poly(A)+ RNA proteins interactome provoked by mutations in three distinct subunits of the nuclear RNA exosome. Our data demonstrate a functional connection between Rrp6 and Mtl1 in controlling processing and levels of multiple protein-coding and non-coding transcripts. Furthermore, we show that exosome mutants accumulate components of U1 and U2 snRNPs and show depletion of NTC components from RNA suggesting that the stage prior to the activation of the spliceosome represents a critical quality control step. We have also identified potential new RNA binding factors involved in exosome regulation, including a zinc-finger protein called Mub1 that controls levels of selected transcripts encoding for proteins implicated in stress response. Collectively, our data have provided a global view of RNA metabolism alterations in exosome deficient cells and revealed RNA binding proteins that may act as novel exosome cofactors.
Project description:Cryptic unstable transcripts (CUTs) are rapidly degraded by the nuclear exosome, however, the way they are recognized and targeted to the exosome is not fully understood. The recently identified Schizosaccharomyces pombe MTREC complex has been shown to promote degradation of meiotic mRNAs and regulatory ncRNAs. Here, we report that the MTREC complex is also the major nuclear exosome targeting complex for CUTs and unspliced mRNAs. MTREC complex specifically binds to CUTs, meiotic mRNAs and unspliced mRNA transcripts and targets these RNAs for degradation by the nuclear exosome, while the TRAMP complex has only a minor role in this process. The MTREC complex physically interacts with the nuclear exosome and with various RNA-binding and -processing complexes, coupling RNA processing to the RNA degradation machinery. Our study reveals the central role of the evolutionarily conserved MTREC complex in RNA quality control, and in the recognition and elimination of aberrant, cryptic transcripts. RNA sequencing of WT and mutant S.pombe strains, processed data is normalized to median non-intron containing gene-expression, no replicates