ncRNA: Structure, Interactions and Inhibition

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Project Summary/Abstract This project studies the structural principles underlying the biological function of non- coding RNAs and investigates new approaches to inhibiting their function in disease. It studies how these transcripts fold; how they recognize other RNAs, RNA-binding proteins and epigenetic enzymes; how functional SNPs correlated with cancer progression or patient prognosis affect RNA structure and protein binding. It aims to develop engineered proteins and peptide mimetics to inhibit ncRNA misfunction in human cancers. Its premise is that providing molecular mechanistic insight on ncRNA through structure analysis and the establishment of structure-function relationships is one of the most important current outstanding questions in molecular structural biology, because of the enormous gap in knowledge created by the discovery that hundreds of thousands of transcripts are actively transcribed. Furthermore, the widespread occurrence of functional genetic variation in ncRNAs, and the association of mutation or mis-expression of ncRNAs with disease outcome in patients underscore the biomedical importance of these transcripts and reveal their potential therapeutic value. Molecular insight is necessary to fully understand their biological function, frame hypotheses on how misregulation, mutation or post-transcriptional modification causally lead to human disease, identify and validate molecular targets and discover new chemistry for pharmacological intervention. These broad goals will be pursued through a multi-scale approach to establishing the structure of ncRNAs, including the high resolution investigation of domains where specific functions reside, and of their interaction with proteins and microRNAs. The project will also pursue the further development of engineered proteins and peptide mimetics that target functional domains of ncRNAs involved in malignant transformation. In collaboration with cancer and developmental biologists, we will conduct experiments in primary cell lines and model organisms to parallel our biochemical, biophysical and structural investigations, and obtain cellular and organismal validation of the activity and mechanism of action of new inhibitors.