Understanding double-stranded RNA recognition in human cells

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PROJECT SUMMARY Specific recognition of double-stranded RNA (dsRNA) structures underlies key biological processes from development to antiviral immune responses, and involves a host of dsRNA- binding proteins. Biochemical and structural studies have delineated how these proteins interact with model ligands, yet dsRNAs that they encounter in cells are far more complex. Moreover, little is known about how cells regulate dsRNA recognition. The goal of my lab is to understand how dsRNA-binding proteins interact with natural dsRNAs in cells, connecting biochemical models of dsRNA recognition to cellular dsRNA recognition and regulation. In the next five years, we will focus on dsRNA recognition in microRNA (miRNA) biogenesis and innate immune sensing. During miRNA biogenesis, Microprocessor recognizes and cleaves hairpin-like structures from long transcripts called primary miRNAs (pri-miRNAs). My previous research built a unifying model of human pri-miRNA and discovered that an optimal miRNA hairpin enhances the cleavage of a suboptimal miRNA hairpin on the same transcript—known as cluster assistance. Because nearly 40% of human miRNAs reside in clusters, with many implicated in diseases and influenced by cluster assistance, we propose to dissect this fundamental regulatory mechanism in miRNA biogenesis using biochemical, single-molecule, and structural approaches. Recognition of dsRNA by innate immune sensors such as RIG-I and MDA5 initiates antiviral responses. Recent studies show that endogenous dsRNAs can also activate these sensors, sometimes resulting in autoinflammatory and autoimmune diseases. The recognition of self dsRNAs therefore needs to be restricted by proteins that modify, degrade or shield endogenous dsRNAs. Building on our expertise in dsRNA recognition and processing, we will 1) develop new biochemical methods to identify dsRNA ligands of innate immune sensors, and 2) develop new genetic screen methods to identify factors that restrict self dsRNA sensing in innate immunity. Together these studies will provide crucial insights into how cellular dsRNAs are sensed and regulated, with therapeutic implications for cancer, autoimmune and infectious diseases.