COoperation, COmpensation, COmpetition: the complex interplay between DNA Methylation and Polycomb at Transposable Elements in ArabidopsiS – COMPTES

In plants and many organisms, DNA methylation is a hallmark of transposable elements (TE) that negatively controls TE expression. On the other hand, histone H3 lysine 27 trimethylation (H3K27me3), targeted by the highly conserved Polycomb Group (PcG) proteins, is a hallmark of transcriptional repression associated with protein-coding genes. Nevertheless, there is a growing body of evidence for interplay between these pathways. In particular, many TE sequences, upon their loss of DNA methylation and/or in certain cell types, display H3K27me3 marks. This raises fundamental questions with regards to the differences and commonalities between PcG- and DNA methylation-mediated silencing and the role and mechanistic determinants of PcG targeting at TEs. I propose to address them in Arabidopsis thaliana—a powerful model to study the epigenetic regulation of TEs and its consequences for adaptation—and, when appropriate, in the context of biotic stress to which TEs can be highly sensitive. In this respect, the proposed research program lies for the most part at the interface of plant responses to pathogens and epigenetic control, which confers its originality. It is comprised of three aims that can largely be carried out independently of each other.
First, I propose to address how the different silencing epigenetic marks prevent transcription by studying the crosstalk between transcription factors (TF) and DNA methylation and H3K27me3 respectively, in particular at one model TE. Furthermore, we will study the impact of this crosstalk on TE heritable transposition upon biotic stress, using sensitive TE detection methods.
Second, I propose to get insights into the role of PcG at TEs by implementing epigenome-editing tools which will enable us to assess the impact of H3K27me3 loss at discrete TEs without the confounding effects of PRC2 mutants. These tools will be useful for the investigation of PcG role in biological contexts where TEs are hypomethylated in the wild-type and presumably targeted by H3K27me3, which we will document. We will start by investigating the role of PcG (in cooperation or in competition with de novo DNA methylation) in resilencing hypomethylated TEs after their transposition, a process which remains very elusive.
Third, I propose to unravel the molecular determinants of PRC2 recruitment at TEs which are completely unknown. We will determine whether endogenous and exogenous TEs can recruit PRC2 in cis (instructive recruitment) or become H3K27me3-marked due to spreading from adjacent PcG targets, and by which mechanisms, using TE transgenes and reverse genetic approaches. We will also test the hypothesis that active DNA demethylation can promote PRC2 recruitment at some TEs in the wild-type. Finally, we will set up a reporter system to later identify, through a forward genetic screen, other mechanisms by which PcG recruitment is promoted and sometimes favored over DNA methylation
This research program should lead to impactful discoveries in the field of epigenetics, plant-pathogen interactions, transposon biology and evolution. In the long-term, it could find applications 1) in plant breeding since transposition is increasingly considered as a tool to induce genetic/ epigenetic diversity, and since phenotypic variation between plants regenerated from tissue culture is presumably due to genetic/ epigenetic instabilities that could be modulated if better understood 2) in cancer biology in which the elusive interplay between DNA methylation and PcG plays a central role.