Small Silencing RNAs: Mechanism and Biology

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We are passionately committed to understanding how small RNAs-small interfering RNAs (siRNAs), microRNAs (miRNAs),and PIWI-interacting RNAs (piRNAs)-regulate gene expression in plants, fungi, and animals.

The model organism, Drosophila melanogaster is the center of our studies, but what we learn in flies, we test in mammalian cell extracts, in cultured human and mouse cell lines, and in vivo in mice to identify where these processes are conserved and where they diverge between flies and mammals.

The mechanism of RNA interference (RNAi).  A decade of study of the RNAi pathway in our and other laboratories has established a mechanistic framework for RNAi in flies, but many challenges remain. New technologies are under development in our laboratory to meet these challenges, including single-molecule fluorescence techniques to study the cycle of RISC maturation and function, and deep sequencing methods that allow us to compare millions of different sequences in a single experiment to test the contribution of each siRNA nucleotide to binding and catalysis. Many of the proteins required for RNAi in Drosophila have subsequently been identified as components of the human pathway, but we do not yet know how they function. Building a better understanding of the human RNAi pathway is a key challenge for our laboratory.

miRNA biogenesis and function.  miRNAs are small RNAs that regulate mRNA expression. miRNAs nearly always pair partially with their target mRNAs, unlike siRNAs which typically pair fully. In flies, siRNAs are made by Dicer-2, but miRNAs are produced by Dicer-1, acting together with its partner protein, Loquacious (Loqs). Loqs is required for germ line stem cells to retain their identity, and a major effort in our laboratory is to identify how Loqs helps specify stem cell fate. The structure of a small RNA duplex-not the identity of the Dicer paralog that produces them - determines its sorting between two different Argonaute proteins, Ago1 and Ago2, that regulate mRNA expression by distinct mechanisms. While we have learned much about the molecular basis for partitioning highly paired small RNA duplexes into the Ago2 pathway, we know little about the parallel mechanism that sends most, but not all, miRNAs to Ago1. We are actively seeking to identify the Ago1-loading machinery and to learn if such small RNA sorting occur in mammals.

piRNAs and endo-siRNAs: defending the genome.  piRNAs form the third major class of small RNAs in flies and mammals. The dominant class of piRNAs in flies silence selfish genetic elements such as transposons. piRNAs are produced by a mechanism distinct from both the RNAi and miRNA pathways. Understanding how piRNAs are made and how they function is a major focus in the laboratory. We also seek to understand the endo-siRNA pathway, which defends the soma against selfish genetic elements, much as the piRNA protects the germ line.

Huntington's Disease and RNAi Therapy.  Together with Neil Aronin, we seek to develop siRNA-based drugs to treat Huntington's disease (HD), a devastating, invariably fatal, neurodegenerative genetic disease. Our goal is to create siRNAs that destroy the mutant, disease-causing huntingtin mRNA, while leaving the wild-type version intact. We are currently working to improve the durability and delivery of anti-HD siRNAs in mouse models of the disease.