Birth and Activation of a piRNA cluster – BiopiC

Transposable elements (TEs) make up half of our genome and induce DNA damages when active. In recent years, an adaptive immune system against TE transposition has been uncovered. In the germline, a dedicated pathway based on small non-coding piRNAs targets TEs at the transcriptional and post-transcriptional levels through base-pair complementarity. The piRNAs are produced by discrete genomic loci called piRNA clusters, which are made of multiple and intermingled TE fragments and constitute the memory of this immune system. Our global objective is to understand how this defense system is generated and how it evolves and adapts to novel TE invasions and external stresses, without triggering an “autoimmune” response against endogenous genes. Based on findings from a previous ANR project, our main hypothesis is that DNA loci encoding for tRNA (tDNA) and subtelomeric sequences play major roles in the genesis of such genome defenses both at short and long term.
We will focus on Drosophila oogenesis, in particular on one of its periods of which we have previously discovered the importance for the control of TEs, the "pilp" (piwiless pocket).

Our first objective is to test whether clustered transfer RNA (tRNA) loci (tDNA clusters) and subtelomeric regions of chromosomes can induce piRNA cluster formation by promoting multiple TEs insertions in their vicinity.
Our second objective is to identify the cis- and trans-acting factors required for the activation and maintenance of these nascent or dormant piRNA clusters. In particular, we will analyze maternally inherited piRNAs and their involvement in the initiation and/or maintenance of the activity of piRNA clusters. On the other hand, a Histone DeMethylase (HDM) recently discovered in the laboratory for its role in maintaining the extinct or dormant state of piRNA clusters will be characterized in detail in this biopiC project using multi-omic approaches. Finally, we have a unique tool that allows us to turn a piRNA cluster ON or OFF without affecting the levels of its primary transcripts. We wish to investigate the effect of RNA methylation on the quality/stability of these primary transcripts and establish a molecular mechanism linking the activity or inactivity of these piRNA clusters as recently suggested by our preliminary data.

Our project is both original and ambitious. In the past decade, many studies have sought to describe the biogenesis and functions of piRNAs in the repression of TEs. Here, we rather focus on studying the genomic plasticity of this “immune system” and the complementary functions of TEs and piRNAs in the birth and activation/maintenance of piRNA clusters, respectively.

Our consortium is built with the partners that participated in ANR “PlasTiSiPi” (PRC-2013). Under this program, members of the consortium published and co-signed 20 peer-reviewed articles or reviews in high impact journals. The success of the consortium is based on the complementarity of expertises between the labs in the fields of genetics, epigenetics, cell biology and bioinformatics tools development and analysis as well as on frequent meetings between partners. The complementarity between our labs allows us to propose an integrated project from biochemistry to bioinformatics. Our consortium is among the pioneers in the field, and our tools, generated in a previous program, give us a strong competitive advantage.
Defending against TEs and adapting to external stresses are problems that almost all organisms face. Thus, our results will benefit basic research as well as reproductive medicine and oncology.