RNA decay and processing activities of the RNA exosome

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Abstract The RNA exosome plays important roles in 3' end processing of a variety of ncRNAs and is also responsible for 3' to 5' degradation of both mRNAs and nc RNAs. By preferentially degrading aberrant mRNAs and ncRNAs it also maintains the overall fidelity of gene expression. Given the central role of the RNA exosome in a wide variety of RNA processing and degradation reactions, it is not surprising that it is required for cell viability. The long tern goal of our research is to achieve a greater understanding of how the RNA exosome carries out its diverse functions. The RNA exosome is a 10-subunit complex that adopts an overall donut-shaped structure. Nine of the subunits are catalytically inactive, and form the majority of the donut. The 10th subunit is associated with one opening of the donut and confers both 3' to 5' exoribonuclease and endoribonuclease activity on the RNA exosome complex. In the past 10 years much progress has been made in understanding the structure and biochemistry of the RNA exosome. Although isolated Rrp44 or the RNA exosome has nuclease activity in vitro, activity in vivo strictly requires over a dozen other proteins. Although it is clear that these RNA exosome cofactors control the activity and specificity of the RNA exosome, how these cofactors achieve this is essentially completely unknown. The overall goal of the proposed research is to resolve how the RNA exosome cofactors mediate its in vivo activities. We will focus on Ski7 and Rrp6, two of the three RNA exosome cofactors that are known to directly interact with the RNA exosome. Both genetic and biochemical data suggest that they are important in part because they mediate interaction with additional RNA exosome cofactors.