Crosstalk between DNA methylation, DNA compaction and Polycomb Repressive Complex 2 through an analysis of Arabidopsis ddm1 clf mutants

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), deposited by the highly conserved Polycomb Repressive Complex 2 (PRC2), is a hallmark of transcriptional repression associated with protein-coding and miRNA genes. Nevertheless, there is a growing body of evidence for functional interplay between these pathways. In particular, many TE sequences, upon their loss of DNA methylation, display H3K27me3 marks and this suggests that PcG could serve as a back-up silencing system for hypomethylated TEs. Here, we show that in ddm1 mutants impaired for DNA methylation, hundreds of TEs gain H3K27m3 as previously observed for met1, and that this gain is completely dependent on the PRC2-SET domain protein CURLY LEAF (CLF), with no redundancy of its paralog SWINGER (SWN). Unexpectedly, complete loss of H3K27me3 in ddm1 clf was not associated with further reactivation of TE expression in ddm1 clf as compared to ddm1, nor with a burst of transposition with the notable exception of the ATCOPIA93 retroelement EVD. Instead, ddm1 clf globally exhibited a partial suppression of ddm1 molecular phenotypes with a partial recompaction of DNA coupled with DNA remethylation. Thus, H3K27me3 marks antagonize DNA remethylation and condensation in a ddm1 background. These findings bring valuable information on the mode of PRC2 action and have potential implications for TE control in naturally hypomethylated cell-types such as the pollen vegetative cell or the endosperm, or after their transposition.