Comparative poly(A)+ RNA interactome capture reveals new proteins implicated in RNA regulation in fission yeast

ABSTRACT The nuclear RNA exosome plays a key role in mediating degradation, quality control and processing of multiple protein-coding and non-coding transcripts. Recognition of the specific RNA substrates by the exosome is mediated by the RNA-binding co-factors. Transient binding of co-factors either to substrate RNA or the exosome as well as rapid decay of the RNA substrates make identification of the co-factors challenging. Here we employ a comparative poly(A)+ RNA interactome capture approach in three different exosome mutant and unperturbed fission yeast cells to identify proteins that interact with poly(A)+ RNA in the exosome-dependent manner. Our analyses identified multiple proteins whose occupancy on RNA is altered in the exosome mutants. We demonstrate that zinc-finger protein Mub1 is required to maintain the levels of a subset of the exosome RNA substrates including mRNAs that encode for stress-responsive proteins. This finding highlight importance of exosome-dependent mRNA degradation in mediating cellular adaptation to stress.