Despite the major role it played in plant evolution, interspecific hybridization is generally thought to cause dramatic changes in gene regulation. This so called “genomic shock” might be mediated by epigenetic deregulation and the concomitant reactivation of transposable elements (TEs). Indeed, the epigenetic profiles reflect variation in TE content across plant genomes. Previous work in Arabidopsis thaliana x Arabidopsis lyrata interspecific hybrids showed that orthologous TEs present a preferential expression of the A. lyrata allele, which was associated to the reduced presence of silencing epigenetic marks.
To study the effect of interspecific hybridization on the epigenomic landscape, we used ChIP-Seq to characterize the profiles of H3K9me2 and H3K27me3 epigenetic marks in A. thaliana, A. lyrata, and in three hybrids between different accessions of these species. The distribution of H3K27me3 silencing marks, which normally labels genes that are developmentally or environmentally regulated, coincided in all three hybrids with regions typified in A. thaliana as H3K27me3 rich. By contrast, two hybrids showed a distribution of TE silencing H3K9me2 marks similar to the pattern observed in the parents, while the third showed a markedly modified pattern. These results suggest the existence of within-species variation in the potential to reprogram epigenetic marks associated to TE silencing in hybrids.