Biogenesis, Function and Turnover of Noncoding RNAs

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The long-term goals of our laboratory are to understand how noncoding RNAs function, how cells recognize and degrade defective and unneeded RNAs, and how failure to degrade these RNAs affects cell function and contributes to human disease. One focus of our work is an abundant class of ribonucleoproteins (RNPs), known as Ro60 RNPs, which are widespread in animal cells and present in many bacteria. The major protein component, the ring-shaped Ro 60 kDa autoantigen, was discovered because it is a clinically important target of autoantibodies in patients with systemic lupus erythematosus and Sjogren's syndrome. In all organisms examined, Ro60 binds noncoding RNAs called Y RNAs. By studying Ro60 RNPs in bacteria, we uncovered a novel role for ncRNA, that of tethering a protein cofactor to an effector protein to alter its function. Specifically, we discovered that a bacterial Ro60 ortholog was tethered by Y RNA to a ring-shaped ribonuclease, forming a new double-ringed RNA degradation machine. We are currently working to define the functions of Ro60 RNPs in mammalian cells. As part of this effort, we used CRISPR to generate mouse embryonic stem cell lines lacking Ro60 and Y RNAs. Our studies revealed that, as in bacteria, one role of Y RNAs is to tether Ro60 to diverse proteins to create specialized RNPs. In a second focus, we are characterizing the roles of RNA surveillance pathways in mammalian and bacterial cell physiology. A recent accomplishment was our discovery that a long mysterious bacterial RNA repair operon is regulated by binding of damaged tRNAs to a transcriptional activator protein. These studies identified a new signaling pathway involving defective tRNAs and implicate the operon in tRNA repair.