Project : Chromatin organization based mechanisms of TE silencing

Transposable Elements (TEs) are “selfish” genetic elements that threaten genomic stability through their capability to move around the genome. Eukaryotic genomes contain the historical records of the successive TE invasions they survived. This is because the host genomes have evolved specific molecular machineries to silence these TE genomic parasites both transcriptionally (TGS) and post-transcriptionally (PTGS). PTGS relies on small RNA-based silencing pathways that either cleave TE transcripts or prevent their translation. TGS leads to reduced TE transcription through an interplay between the P-element induced wimpy testis (Piwi) protein and chromatin factors. Piwi contributes to creating a repressive heterochromatin environment at TE loci by promoting histone H3 lysine (K) 9 trimethylation through the recruitment of the histone methyltransferase SETDB1. However, other studies suggest that H3K9 methylation is not the final silencing mark and the mechanisms by which Piwi induces heterochromatin formation to promote TE silencing remain poorly understood. In addition, the specific roles of chromatin marks and factors in TE silencing still remain to be established. We, and our collaborator, have found new links between Piwi and the chromatin machinery: the histone demethylase dLsd1 and its coREST cofactor, the histone deacetylase Rpd3, as well as the chromatin remodeler Mi-2 and its partner MEP-1, are all required for TE TGS in Drosophila ovaries. Importantly, preliminary results from our teams suggest that these proteins can physically interact together and with Piwi. In this proposal, we propose to:

1. Dissect the mechanisms by which dLsd1, Rpd3 and MEP-1 act together to transcriptionally repress TEs.
2. Study the impact of depletion of these factors on TE mobilization and genome stability
3. Identify novel chromatin factors involved in TE silencing

The goal of the study is to identify fundamental mechanisms by which chromatin regulates TE expression. Importantly, combining genomic and proteomic approaches with genetic analysis in the model organism Drosophila melanogaster will allow us to determine whether the mechanisms that we will characterize in details in vitro are physiologically relevant in vivo during Drosophila development.