Genome intruder scanning and modulation systems and transgene silencing

The widespread occurrence of transgene inactivation in plants and classical cases of silencing of duplicated sequences in fungi suggest that all genomes contain defense systems that are capable of monitoring and manipulating intrusive DNA. Such DNA might be recognized by its structure, its sequence composition relative to that of its genomic environment and possibly by its disruption of normal biochemical functions. Although methylation, especially of repeated sequences, is widely associated with gene inactivation, other attributes, including chromatin modification, may be involved. Elimination of inactivated intrusive DNA (presently best documented for filamentous fungi) may also contribute to genomic defense mechanisms in plants. Stable integration and expression of introduced genes are essential for genetically engineered crops, and thus transformation constructs must be designed to avoid host surveillance processes.