Plant DNA methylation: An evolutionary perspective

Plants methylate the DNA of both transposable elements (TEs) and genes.  For the former, DNA methylation and other epigenetic modifications suppress TE activity.  From studies in several systems, it is now clear that the epigenetic modification of TEs can affect the expression of nearby genes and also that the epigenetic interaction between TEs and their hosts is evolutionarily consequential.  Many of the epigenetic mechanisms that plants use to modify TEs have been characterized, but an important mystery remains: how is a naïve TE recognized by the plant host in the first place?  We believe we have uncovered a clue to this important interaction for one type of element, Sirevirus LTR retrotransposons. By analyzing a set of carefully annotated, full-length elements from maize, we show that small RNAs map to specific regions of the element, particularly a complex palindrome-rich region that forms hairpins and acts as a cis-regulatory elements.  We hypothesize that the palindromes aid the silencing of active elements and influence transposition potential, siRNA targeting levels, and ultimately the fate of an element within the genome. Just as TEs are methylated in plants, so is a subset of genes.  Several recent papers have demonstrated that the presence of genic DNA methylation within an individual gene is conserved across plant lineages.  These genes tend to evolve slowly and are expressed broadly. However, the function of genic DNA methylation remains unclear, if indeed it has a function. Genic DNA methylation does correlate weakly with gene expression, but it has been difficult to separate cause from effect.  As a result, the function and evolution of genic methylation remains mysterious.