Mechanisms of substrate selectivity of the nuclear RNA exosome complex.

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Cell growth, development and successful adaptation to a fluid environment require the orchestrated expression of thousands of genes. Coordinated changes in RNA stability play an important role during transitions between different cellular states, and are an integral component of many stress response pathways. The 3’ to 5’ exonucleolytic RNA exosome complex is a major regulator of RNA stability in the cell and degrades many types of RNA substrates. It is involved in numerous RNA-processing events while specifically targeting spurious and aberrant RNAs for destruction, and also acts in post-transcriptional gene regulation. The ability of the exosome to faithfully identify its substrates is the basis of its regulatory functions in the cell and is of utter importance for cellular well-being. Dysregulation of the nuclear RNA exosome leads to cancer and disease.The overall goal of my research is to define the mechanisms involved in the regulation of exosome selectivity. While the molecular function and the structure of the complex are very well understood, the factors that determine substrate selectivity and allow regulation of its activity remain largely obscure. This project will address key outstanding questions in the field: How can the nuclear RNA surveillance machinery distinguish spurious transcripts from functional ones? What factors are involved in exosome targeting and how is substrate selection regulated in response to external cues? In particular, using a comparative proteomics approach based on the RNA interactome capture technique, I want to identify RNA-binding proteins that direct RNA substrates towards the exosome, and aim to understand how these factors determine the specificity of the exosome complex. How do these proteins recognise their substrates, and how do they promote RNA decay? A particular focus of my research will be the effect of cellular stress conditions on the substrate specificity of the exosome complex to identify dynamic exosome targeting mechanisms that help to drive cellular adaptation, specifically in response to DNA damage. DNA damage triggers a complex gene regulatory programme that can be taken as a paradigm for the role of transcriptional and post-transcriptional mechanisms in cellular stress resistance. The essential RNA helicase Dbp2 plays a vital role in this process, and I want to understand its function in detail. Together, these studies will be fundamental for our understanding of how post-transcriptional mechanisms shape gene expression programs that promote survival and determine cell fate.