Illuminating cellular dark matter through the development of novel chemical tools

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PROJECT SUMMARY There is a vast repertoire of species within cells for which we have a poor understanding of their function and biomolecular interactions. These species can be referred to as the “dark matter” of biology, as their mechanism of action is hidden from conventional observation. Our laboratory seeks to illuminate the function of cellular “dark matter” through the development of new chemical technology. The proposed research program will pursue two major research thrusts. First, we plan to develop tools for site-specific RNA modification, and apply these tools for the manipulation, imaging, and isolation of disease relevant RNA protein complexes. We will create tools for use in live cells and develop the ability to covalently recruit proteins to RNA, forming RNA-protein macromolecular conjugates. The technology will be applied to study RNAs implicated in disease. Specifically, we are interested in characterizing the pathways of pathogenicity for the C9orf72 nucleotide repeat expansion RNA, which is thought to play a major role in genetic amyotrophic lateral sclerosis (ALS). In the second thrust, we will carry out the in situ synthesis of lipid species within living cells, with the goal of uncovering the molecular mechanism by which enigmatic lipid species affect cell behavior. We plan to develop approaches enabling the selective and bioorthogonal delivery of sphingolipids to living cells. Building upon technology previously developed in our lab, we will deliver cell permeable lipid precursors which will spontaneously assemble into functional lipids within the cell. Leveraging this approach, we will create photoaffinity probes for the pulldown of sphingolipid-interacting proteins, with the goal of elucidating the protein partners of the non-canonical deoxysphingolipid 1-deoxydihydroceramide, which is cytotoxic and implicated in several diseases. Realization of our research program goals would improve our knowledge of cell biology and lead to the development of new tools for interrogating RNA and lipid species. Our long-term vision is to create and apply technology that enables improved mechanistic understanding of biomolecular interactions, leading to an increased understanding of human disease, and accelerating the development of possible therapeutic interventions.