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