All eukaryotic genomes contain mobile genetic elements called transposons. They can be described as “endo-parasites” at the genomic level and come in a variety of classes including endogenous retroviruses. The uncontrolled spread of transposons to new genomic sites poses a serious threat, e.g. due to insertional mutagenesis. How the host functionally silences transposons remained mysterious for a long time. Recently, the piRNA pathway, a germline specific RNAi pathway has been shown to be at the heart of the animal transposon control system. In Drosophila two separate piRNA pathways exist: One is active in germline cells and the other in somatic cells of the gonad. Interestingly, the somatic piRNA pathway protects the neighboring germline from endogenous retroviruses that invade the developing gamete via viral particles. Only two loci have a described role in this pathway: the Argonaute protein Piwi and the heterochromatic flamenco locus, source of the involved small RNAs (piRNAs). We entirely lack a mechanistic understanding of the biogenesis of somatic piRNAs and how the Piwi complex silences transposons. Here, we first propose to identify new components of the somatic piRNA pathway by two RNAi screens, one in cell culture and one in flies. Our long-term goal is to dissect the mechanistic makeup of the somatic piRNA pathway, its molecular constituents and their biochemical function. Secondly, we will set out to investigate the consequences for gene expression and genome integrity caused by ablating the somatic piRNA pathway. We will use high throughput sequencing technologies to address the following questions: Which retroviral elements become functionally expressed in the absence of Piwi? What is the damage for the host genome caused by uncontrolled retroviral activity? This will be the first systematic, qualitative and quantitative description of the threat posed by endogenous retroviruses and the importance of the somatic piRNA pathway in silencing them.
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