Transcriptional Activation by Small RNA: Mechanism and Design Rules

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DESCRIPTION (provided by applicant): The goal of this application is to establish a new paradigm of gene regulation mediated by small RNA. Until recently, small RNAs have been thought to function mainly as the mediators of an evolutionally conserved gene silencing mechanism known as RNAi. We and others discovered that small double stranded RNA (dsRNA) targeting gene promoter sequence can induce potent and prolonged gene activation at the transcriptional level and in a sequence-specific manner, a phenomenon we termed RNAa. Despite the enormous potential for reprogramming gene expression in living cells, the molecular mechanism of RNAa is largely unknown and the rules for target selection are still quite obscure. We propose to use a combination of genomic, bioinformatic, and molecular biology approaches to address the following questions: How is transcriptional activation by promoter-targeted dsRNA achieved? What are the molecular machines involved? Is RNAa naturally exploited by cells for physiological function? What are the general rules governing the sensitivity and specificity of dsRNA-promoter targeting? Understanding the molecular mechanism of RNAa and establishing it as a new paradigm are likely to transform the way gene function is studied and diseases such as cancer are treated.