PROJECT SUMMARY / ABSTRACT Invasive foreign nucleic acids such as transposons and viruses pose a threat to all organisms, potentially causing genome instability and diseases including cancer and infertility. In animals, germline-expressed small RNAs known as piRNAs interact with PIWI-clade Argonaute proteins and act as a guardian of the genome by silencing transposable elements. The long-term goal of my laboratory is to address two critical functions of small RNA-mediated genome defense: (1) How do cells distinguish “self” from “non-self” nucleic acids? (2) How do cells epigenetically silence foreign nucleic acids for generations. One astonishing feature of piRNAs is their sequence diversity. Despite their critical role in transposon silencing, tens of thousands of piRNAs exhibit remarkable sequence diversity and do not map to transposons. Using C. elegans as a model organism, our recent research suggests diverse piRNAs provide sequence complexity needed for germ cells to recognize various foreign nucleic acids. Remarkably, endogenous genes carry licensing signals that confer resistance to piRNA silencing. Therefore, our research suggests gene-licensing as a key mechanism that prevents endogenous genes from silencing. However, the nature of the gene-licensing signals and how they counter gene silencing remain poorly understood. piRNAs can trigger epigenetically stable silencing of foreign nucleic acids for generations. The inheritance of gene silencing requires germline secondary small RNAs (22G-RNAs) and chromatin modifications. However, only some foreign nucleic acids are stably silenced by piRNAs. It is unknown what determines the stability of piRNA silencing. We will test the hypothesis that the competition between silencing and licensing signals act on mRNAs determines their expression states, and only genes of strongly silenced states are stably silenced for generations. Taken together, this proposal will investigate the mechanisms that protect self genes from gene silencing. In addition, we will examine how the inheritance of piRNA silencing is determined. In Aim-1, we will adapt genetic and biochemical approaches to investigate the mechanism of gene licensing. In Aim-2, We will investigate how the licensing and silencing pathways compete to determine the expression or silencing of germline transcripts over generations. In Aim-3 we will use our piRNA reporter to identify novel factors that promote and inhibit piRNA silencing. These studies will provide fundamental insights into the small RNA-mediated genome defense system, as well as into the molecular basis of epigenetic inheritance. As PIWI mutants exhibit fertility defects in various animals, our research will uncover the molecular mechanism underlying some fertility defects in humans.

PIWI interacting RNAs (piRNAs) act as a guardian of our genome and promote genome stability by repressing selfish DNA elements. Our recent studies reveal that C. elegans piRNAs trigger remarkably stable silencing of their targets that can last for generations, and that cells have evolved a mechanism to protect endogenous genes from piRNA silencing. Our study will shed light on the fundamental mechanisms of gene regulation and has the potential to reveal underlying mechanisms behind some infertility and developmental defects in humans.