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 cells lacking one or both of the two mouse Y RNAs. Despite reports that Y RNAs are essential for DNA replication in animal cells, mouse embryonic stem cells lacking both Y RNAs divided normally. However, cells lacking Y RNAs had reduced levels of Ro60, a defect that we could complement by expressing Y RNA in these cells. We also demonstrated that Ro60 regulates the subcellular location of Ro60 and that Y RNAs tether Ro60 to diverse proteins to create specialized RNPs. Together, these data reveal that the functions of Y RNAs are closely connected to those of their Ro60 partner. In a second focus, we are characterizing the roles of RNA surveillance pathways in mammalian cell physiology. Here, a recent accomplishment was our discovery that the multinuclease complex known as the RNA exosome represses differentiation of human embryonic stem cells. We showed that the exosome restrains differentiation in part by degrading pre-mRNAs encoding FOXH1, a transcription factor crucial for formation of mesendoderm, the precursor to both mesoderm and endoderm. These studies revealed the importance of RNA degradation in maintaining human embryonic stem cell pluripotency.