Get the jump - Do 3'UTRs protect transposable elements from silencing?

Eukaryotic genomes contain large numbers of transposable elements and repetitive sequences that are subjected to silencing through epigenetic mechanisms. These involve primarily DNA methylation, chromatin modifications and small RNA. It is known that these transposable elements can affect the expression of neighboring genes; however, little is known about how transposable element silencing depends on the general chromosomal environment at the insertion site. Taking advantage of the vast genomic resources available in Arabidopsis thaliana, a recent report begins to unravel these interactions by identifying insertion sites of one specific MULE element, AtMu1c across the A. thaliana lineage. Among over 30 insertion sites analyzed, a correlation between the loss of epigenetic silencing and the insertion into the 3'end of protein coding genes was found. Here, we discuss details, implications and potential mechanisms of these findings that may be applicable to a much wider set of transposable elements and across diverse species.