Nearly all eukaryotic genomes contain selfish genetic elements such as transposons. Their devastating impact on the host is illustrated by the phenomenon of “hybrid dysgenesis” in Drosophila melanogaster: Intercrosses between laboratory strain females and males caught in the wild result in progeny with severe sterility. This is caused by the uncontrolled activity of a single transposon, which is present (and silenced) in wild populations but absent in stocks that have been kept in laboratories since ~100 years. The Drosophila genome, however, contains not only one, but more than one hundred transposon families, whose transposition strategies vary widely. To ensure reproductive fitness, flies (and all other organisms) have thus been under evolutionary pressure to evolve a generic transposon silencing system. Work over the past decade has demonstrated that the piRNA pathway, a specialized small RNA silencing pathway is the major silencing system that keeps transposons under control in animal gonads.

The piRNA pathway is a wonderful example of how much more sophisticated nature devises a solution to a problem compared to what we would theoretically design. In essence, the piRNA pathway acts as an RNA-based genome immune system. It comprises an inheritable genetic component and an acute response system, which specifically targets active transposons. Briefly, the transcription of discrete heterochromatic loci (termed piRNA clusters) provides a template, from which primary piRNAs are produced. piRNA clusters contain vast collections of immobile and broken copies of transposons, which are or have been active in a population and therefore act as a long term storage system for transposon sequence information.  If a primary piRNA encounters a target (active transposon), cleavage of the transposon RNA by the piRNA-complex leads to the synthesis of a novel, complementary piRNA. This piRNA in turn guides the production of more antisense piRNAs derived from the piRNA cluster transcript. Thus, piRNA clusters act not only as a genetically inherited memory component but also as relay stations to boost the production of silencing competent piRNAs.
Recent studies have elucidated the conceptual framework of this pathway described above. These were mostly based on the bioinformatics analysis of piRNA populations in the light of decades of genetic work on transposon control in flies. At a mechanistic level, however, our understanding of the piRNA pathway is rudimentary at best. The only thing that is clear at the moment is that this pathway is by far more complex than the related microRNA and siRNA pathways.
To further understand this fascinating silencing system, we use Drosophila melangaster as a model system. Here, we can combine genetics, biochemistry, cell biology and bioinformatics in unique ways. Moreover, roughly 35 years of genetic studies on transposons and host-strategies to silence them provide us with a wide range of observations, which we can now connect to this pathway.

1. Identifying and characterizing novel piRNA pathway members: We have established very robust RNAi conditions for both, the somatic ovarian cells where a simplified piRNA pathway is active, but also for germline cells, where many piRNA pathway factors are acting specifically. Using these in vivo RNAi systems we performed genome wide screens towards the identification of novel piRNA pathway genes in Drosophila. The preliminary results from these screens promise a deeper understanding of essentially all levels of this pathway, from piRNA cluster biology to piRNA biogenesis and to piRNA mediated silencing.  

2. Systems level analysis of gene/transposon expression in wildtype and piRNA pathway mutants: Till today, no systematic analysis on transposon activity and transposition frequency and patterns has been conducted in flies lacking the piRNA pathway. Using our established RNAi conditions we will probe the genome wide consequences of deficiencies in the somatic and germline piRNA pathways. We are taking advantage of deep sequencing technologies coupled to bioinformatics to obtain novel insight into these questions.  

3. Understanding the enigmatic piRNA clusters: piRNA clusters are typically located at telomeres or at the border between euchromatin and heterochromatin. Their transcripts are believed to traverse large (up to several hundreds of kb) heterochromatic regions. We are interested in the regulation and processing of piRNA clusters. Ultimately, we want to understand how the cell is able to discriminate cluster transcripts from other RNAs in the cell.