Nuclear processes that silence plant transgenes are being revealed by
analyses of natural triggers of epigenetic modifications, particularly
cytosine methylation, and by comparisons of the genomic environments
of differentially expressed transgene loci. It is increasingly apparen
t that plant genomes can sense and respond to the presence of foreign
DNA in certain sequence contexts and at multiple dispersed sites. Dete
rmining the basis of this sensitivity and how nuclear defense systems
are activated poses major challenges for the future.