Despite their abundance in the genome, transposable elements (TEs) and their derivatives are major targets of epigenetic silencing mechanisms, which restrain TE mobility at different stages of the life cycle. DNA methylation, post-translational modification of histone tails and small RNA-based pathways contribute to maintain TE silencing; however, some of these epigenetic marks are tightly interwoven and this complicates the delineation of the exact contribution of each in TE silencing. Recent studies have confirmed that host genomes have evolved versatility in the use of these mechanisms to individualize silencing of particular TEs. These studies also revealed that silencing of TEs is much more dynamic than had been previously thought and can be reversed on the genomic scale in particular cell types or under special environmental conditions. This article is part of a Special Issue entitled "Epigenetic control of cellular and developmental processes in plants".
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