Differentiation of epigenetic modifications between transposons and genes

Transposable elements (TEs) and repeats are methylated and silenced epigenetically in a variety of organisms including plants. Recent results in Arabidopsis suggest that the TE silencing can be reprogrammed by small RNA during gametogenesis. On the other hand, TE-specific DNA methylation independent of small RNA can be induced by H3K9 methylation through mechanisms conserved between plants and fungi. Methylation of CG sites is found not only in TEs but also in the body of constitutively transcribed genes. Although the function of gene-body methylation is still elusive, the distribution and control of this type of DNA methylation are very similar between plants and animals. Possible interactions of these multiple layers of epigenetic marks and their evolution are discussed.

Research highlights▶ Transposons are marked by specific epigenetic modifications in the plant genome. ▶ Small RNAs reprogram the epigenetic marking of transposons during gametogenesis. ▶ Transcribed sequences lose H3K9 methylation by active demethylation. ▶ CG sites are methylated in the body of transcribed genes.