Non-Coding RNAs in Gene Regulation, Genome Defense, and Epigenetic Inheritance

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PROJECT SUMMARY / ABSTRACT Epigenetic systems regulate gene expression during reproduction and development and the misregulation of these pathways leads to disease. Non-coding RNAs are major regulators and orchestrators of epigenetic processes in all eukaryotes. For instance, non-coding RNA directs paramutation in plants, heterochromatin formation in yeast, genome rearrangement in paramecium, and X-chromosome inactivation and imprinting in mammals. Additionally, while most epigenetic information is erased each and every generation to ensure totipotency of the germline, in some cases, epigenetic information escapes reprogramming and passes across generations (termed transgenerational epigenetic inheritance or TEI). Current evidence suggests that non- coding RNAs are major informational vectors for TEI in plants, worms, insects, and, possibly, mammals. The long-term goal of my research program is to understand how non-coding RNA regulates and sculpts gene expression programs and how this regulation is, in some cases, passed across generations. We are using the metazoan model organism C. elegans to address these questions. To date our work has identified a nuclear branch of the RNA interference (RNAi) pathway, which uses small interfering (si)RNAs to regulate chromatin states and inhibit RNAP II elongation. We have also identified pathways and systems required for transmission of epigenetic information across generations. Our recent studies have identified a new type of membraneless organelle that houses proteins needed for TEI, identified two pathways that act as natural breaks on TEI, and defined an underlying mechanism for TEI mediated by a new form of RNA modification that we helped discover. And because we find that transposable elements are a major target of the C. elegans epigenetic inheritance pathways, we theorize that one function of non-coding RNAs and TEI systems is to help inoculate progeny against the expression of nucleic acid parasites. Deregulation of epigenetic pathways contributes to the etiology of a number of human diseases. The extensive links existing between non-coding RNA and epigenetic processes in all eukaryotes suggests that the work we are doing in C. elegans will lead to insights that will be applicable to all animals and, therefore may help us understand and treat disease in people.