RNA degradation plays multiple essential functions in the control of gene expression. It not only regulates global transcript abundance, but also provides quality control mechanisms to eliminate improperly processed or mis-localized transcripts, or those containing premature translation termination codons (PTCs). Work in our laboratory focuses on two major RNA degradation pathways in eukaryotic cells: Nonsense- Mediated Decay (NMD), which degrades PTC-containing transcripts, and the Exosome, which processes a variety of non-coding RNAs and also degrades transcripts during quality-control processes. A combination of genomic approaches and classical genetic and biochemical analyses has allowed us to identify new roles for these pathways in gene regulation, including proofreading of splice site selection, regulation of specific mRNAs and the mechanisms underlying distinct modes of Pol.II termination. We have also identified the molecular consequences of clinical mutations in exosome subunits implicated in pontocerebellar hypoplasia (PCH). The work proposed in this application will broadly expand our understanding of the role of the subunits of the exosome and of its associated factors on RNA processing and degradation genome-wide. In addition, we will determine how the activity of the exosome is controlled during stress, and how it cooperates with other RNA quality control pathways such as those coupled to translation. Finally we will characterize the mechanisms that promote 3-end formation for a novel class of mRNAs, which use a mechanism completely independent from the classical cleavage and polyadenylation pathway. Overall, the proposed studies will provide major advances in our understanding of the mechanisms involved in eukaryotic post-transcriptional regulations and RNA processing.
Mutations resulting in many genetic diseases affect the structure and function of proteins involved in RNA processing and degradation. For instance, mutations of RNA exosome subunits result in Pontocerebellar Hypoplasia and mutations of NMD factors affect a variety of diseases and therapeutic treatment. Our studies of the control of gene expression by ribonucleases and our characterization of the roles of RNA exosome subunits will shed light on the molecular mechanisms that are perturbed in diseases affecting RNA metabolism.