Non-coding RNAs and their mechanisms and functions

My research is focused on two different areas of biology. The area to which most of our effort is devoted concerns the molecular mechanisms and functions of small non-coding RNAs. Two classes of small RNAs interest us: microRNAs (miRNAs) and short interfering RNAs (siRNAs). Both are generated by Dicer processing of RNA precursors and both associate with Argonaute proteins to repress post-transcriptional gene expression. Both classes of RNAs have enormous implications for human disease, both in causing it and potentially treating it. Therefore, it is important to obtain a basic understanding of how these RNAs work, how they are regulated, and what broad biological functions they have. We focus on studying these questions in the model organism Drosophila because the mechanisms and regulation thus far discovered in flies are highly similar to humans. The rich genetics of Drosophila enable functional experiments that would not be possible in mammals. This award will support our efforts to discover new principles of small RNA regulation and flush out necessary detailed information about previous discoveries. For example, we found extracellular signals to regulate the biogenesis steps and effector steps of the miRNA pathway. Free fatty acid signaling attenuates miRNA-mediated repression whereas TGFβ signaling activates nuclear processing of miRNA precursor molecules. We found that some miRNAs function not simply to repress protein expression levels but also expression noise. Gene expression can be variable because of chance, environmental stress, and genomic stress. Variability is especially harmful in situations where many cells in a tissue must behave uniformly, and variability is a hallmark of cancer cells. We found two conserved miRNAs suppress the impact of all three sources of variability on gene expression. Future work will uncover the mechanisms of regulation and functionality, and explore how generally they are used in this and other species. A recent discovery by us suggests that merely reducing the protein translation capacity of cells by 50% can bypass their need for miRNAs altogether. Why this is so is another future aim. A second area of our interest seeks a biophysical understanding of tissue morphology: how do we explain the characteristic shapes and levels of organization of cellular tissues? The link between molecular forces on the subcellular (nm) scale and morphology on the tissue scale (mm) has not been made. We combine mathematical modeling and genetic experiments in Drosophila to define these links. A future direction is to adapt our proven approaches to explore how mechanical forces experienced by cells within tissues cause changes in their gene expression programs. Understanding the biophysical nature of tissues will have great benefit for tissue engineering