Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression
Abstract
Transposable elements (TEs) are ubiquitous genomic parasites. The deleterious consequences of the presence and activity of TEs have fueled much debate about the evolutionary forces countering their expansion. Purifying selection is thought to purge TE insertions from the genome, and TE sequences are targeted by hosts for epigenetic silencing. However, the interplay between epigenetic and evolutionary forces countering TE expansion remains unexplored. Here we propose a mechanism for selection against TEs, based on analysis of genomic, epigenetic, and population genetic data from Arabidopsis thaliana. Using genome-wide DNA methylation data, we show that the proportion of methylated TEs is a function of proximity to genes. Using extensive TE polymorphism data, we provide evidence that purifying selection is acting on methylated TEs near genes. We present a model in which host silencing of TEs near genes has deleterious effects on neighboring gene expression, resulting in the preferential loss of methylated TEs from gene rich chromosomal regions. This mechanism implies an evolutionary trade-off in which silencing of TE families imposes a fitness cost via deleterious effects on the expression of nearby genes.
Footnotes
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- Received January 26, 2009.
- Accepted May 20, 2009.
- Copyright © 2009, Cold Spring Harbor Laboratory Press
