Drosophila genetics and epigenetics

Three classes of small RNAs, piRNAs, miRNAs and siRNAs, are at the core of a vast regulatory network in animals involved in gene regulation, defense against viral pathogens and transposable elements as well as in chromatin dynamics.

Through genetic, biochemical as well as bioinformatic approaches, the GED lab studies the mechanisms of small RNA biogenesis and activity, using the fruit fly Drosophila melanogaster as an experimental model.

High throughput sequencing experiments are at the core of our research activity. Thus, we are developing in parallel Mississippi, a public Galaxy-based server dedicated to computational analyses of sequencing datasets.

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Three classes of small RNAs, piRNAs, miRNAs and siRNAs, are at the core of a vast RNA silencing network in animals. They trigger the silencing of complementary mRNA targets or of genomic loci, and are involved in numerous processes including gene regulation, defense against viral pathogens and transposable elements as well as chromatin dynamics. The variety of mechanistic and functional outputs reflects the multiplicity of intertwined RNA silencing pathways that potentially interact or compete with each other. We are focusing on the mechanisms of small RNA biogenesis and activity using genetic, biochemical as well as bioinformatic approaches, and Drosophila melanogaster as an experimental model. We study:

  • the genomic determinants that make specific loci able to produce piRNA and siRNA
  • the contribution of small RNAs to the control of chromatin states in somatic adult tissues
  • novel factors involved in the biogenesis and/or the stability of small RNAs which have been previously identified in a genetic screen.

High throughput sequencing experiments is at the core of our research activity. Thus, we are developing in parallel Mississippi, a public Galaxy-based server dedicated to computational analyses of sequencing datasets.

Highlights

  • Over the past years, our characterization of a battery of Viral Suppressors of RNAi (VSRs) established RNAi as the main line of antiviral defense in insects.
  • Using one of these VSRs, p19, as a genetic tool coupled to small RNA sequencing analysis, we showed that endogenous siRNAs are involved in the maintenance of heterochromatin, as well as transposable element (TE) silencing in the Drosophila somatic tissues.
  • In ovaries, TE repression is mediated by piRNAs. In collaboration with the S. Ronsseray’s team, we demonstrated that maternal piRNAs, in addition, are responsible for a trans-generational transmission of homology-dependent silencing referred to as paramutation.
  • Recently, we have also shown that TE transcriptional silencing by piRNAs during early development is maintained independently of Piwi until adulthood. TEs that escape silencing by Piwi are controlled by the siRNA pathway in adult somatic tissues. Consequently, we show that TE expression increases in flies defective for both pathways beyond what can be observed for either piRNA or siRNA mutants.
  • Using a reporter system based on the silencing of the GFP by artificial miRNAs in a genome-wide screen, we identified 17 new genes involved in miRNA silencing pathway. Many of them are also required for siRNA or piRNA silencing further demonstrating the overlap between those pathways.
  • A beta version of our Galaxy sequencing analysis server was launched in June 2014 and is publically available at http://mississippi.fr. A more advanced version of this analysis server is available to the members of the IBPS or upon request.

Future directions

  • One objective is to identify the cis-acting sequences that contribute to piRNA loci determination as well as to characterize the combination of trans-acting factors required to trigger and sustain piRNA loci activity.
  • We are also going to characterize host/virus interactions upon persistent infections by the Nora Drosophila virus as well as their long-term genetic and epigenetic effects. Viral persistent infections constitute a major threat to human health and we wish to contribute to new strategies to control them, using D. melanogaster as a powerful genetic model.
  • We will pursue the characterization of the set of genes identified using our automiG biosensor. We are also interested in characterizing their function in human, in the perspective of identifying therapeutics targets in pathologies linked to small RNA pathways disorders.
  • Importantly, we wish to further contribute to the international Galaxy project, through the development and public implementation of bioinformatics tools to analyze high-throughput sequencing datasets.