Gene expression regulation by RNA-binding proteins during fly developmentntry Awaiting Update by Supervisor

Although the first steps in eukaryotic gene expression are nuclear, many post-transcriptional events determine the final fate of RNAs and impose additional complexity to gene expression. Current models suggest that mRNAs that encode functionally related proteins are co-ordinately regulated as post-transcriptional RNA operons (or regulons) through the formation of highly regulated RNA-protein complexes. Indeed, RNA-binding proteins can act as master regulators of gene expression by binding groups of functionally related mRNA. Importantly, defects in RNA-binding proteins cause a variety of pathologies ranging from cancer to muscular, neurological, metabolic, haematologic or immunological diseases.

Using Drosophila as a model system and a variety of techniques, our group seeks to identify and functionally characterize in vivo mRNAs sharing similar regulatory networks. Particularly, we are interested in understanding the cellular and developmental roles of the Polypyrimidine Tract Binding Protein, PTB. PTB belongs to the heterogeneous nuclear ribonucleoprotein family (hnRNP) of proteins, which associate with transcripts as they are synthesized and control multiple aspects of RNA processing, both in the nucleus and cytoplasm. However, it is still not clear how hnRNP proteins discriminate among multiple RNA targets and most importantly, the mechanisms they use to regulate specific RNA targets.

To understand the mechanisms of action of PTB, we have performed a yeast two-hybrid screen and identified potential new PTB-interacting partners. The results of our screen support a model in which PTB forms distinct complexes in: a) the cell cytoplasm, to regulate functionally-related mRNAs in association with other RNA-binding proteins; and b) in the nucleus, to regulate not only pre-mRNA splicing, but also likely chromatin structure and nuclear transcription.

This project is aimed at characterizing, both molecularly and functionally, these distinct PTB-containing complexes. To start defining their composition, the student will compare the in vivo sub-cellular distribution of PTB and its binding partners in different fly tissues. S/he will then use genome-wide approaches to identify: 1) RNA molecules associated with PTB and their binding partners, and 2) chromatin regions bound by PTB complexes. Finally, the student will use a variety of fly genetics tools to study the in vivo function of different PTB complexes.

We believe this is an exciting project as it has the potential to define new and exciting research questions, and will offer an excellent training opportunity to the student.