Epigenetic regulation and functional exaptation of transposable elements in higher plants

• TEs constitute major parts and are closely associated with genes in a complex genome.
• Epigenetic mechanisms coordinately silence TEs in the host genome.
• During evolution, TEs regulate host genes both genetically and epigenetically.
• TE-derived epialleles can further increase the plant genome diversity.

Transposable elements (TEs) are mobile genetic elements that can proliferate in their host genomes. Because of their robust amplification, TEs have long been considered ‘selfish DNA’, harmful insertions that can threaten host genome integrity. The idea of TEs as junk DNA comes from analysis of epigenetic silencing of their mobility in plants and animals. This idea contrasts with McClintock's characterization of TEs as ‘controlling elements’. Emerging studies on the regulatory functions of TEs in plant genomes have updated McClintock's characterization, indicating exaptation of TEs for genetic regulation. In this review, we summarize recent progress in TE silencing, particularly in Arabidopsis and rice, and show that TEs provide an abundant, natural source of regulation for the host genome.