As in many aspects of life, curing the genome of transposable elements (TEs) may be a trade-off. To stop TEs from bouncing all over the genome, cells often resort to small RNA-mediated methylation. But researchers at UC Irvine have discovered that silencing TEs that settle in close to coding regions can reduce the expression of neighboring genes.
Such negative effects could explain why methylated TEs are usually absent from gene-dense regions. Basically, these TEs seem to be preferentially removed from the genome by a process called purifying selection, one of the more common faces of natural selection where the extremities of a given trait are selected against.
Armed with data on ~6,000 TEs from Arabidopsis thaliana, the team noticed several interesting patterns.
- Gene expression decreased as the density of methylated TEs increased.
- Evidence of purifying selection was observed for methylated TEs that were close to genes.
- Typically, methylated TEs were farther away from coding regions than under-methylated TEs.
- Older methylated TEs were farther away from genes than newer methylated TEs.
Taken together, these observations suggest that silencing TEs may be bad for the health of nearby genes. To get the full story on how good silencing goes bad, check out Genome Research, May 2009.