Paramutation and transgene silencing: A common response to invasive DNA?

Some cases of paramutation of endogenous plant genes and silencing of introduced genes suggest the action of a genomic defence system that inactivates and methylates invasive DNA sequences such as transposable elements and multiple copies of transgenes. Paramutation can occur when promoters of repeated endogenous genes contain transposable elements that are highly homologous to other elements in the genome; the endogenous gene is then mistakenly identified as invasive. Transgenes can be recognized as being invasive either during integration or after integration if multiple copies are present. Because transposable elements are often associated with plant genes, the dividing line between endogenous and 'foreign' genes is not always clear cut. The blurring of this distinction could account for the similar epigenetic behaviour of many transgenes and paramutable endogenous genes, and might have broader implications for the regulation of plant gene expression.