Inactivation of foreign genes, e.g. viral genes and transgenes

Gene silencing is a natural reaction of plants to high levels of foreign gene expression. Not all foreign gene expression, however, leads to gene silencing.

Many factors contribute to gene silencing including the nature and orientation of the foreign transgenes, expression levels, and phase of development.

Gene silencing is sometimes sorted into three categories:

• Mutual inactivation of tandemly introduced transgenes (cis inactivation)
•  A newly introduced transgene can inactivate an existing copy of the same gene (transinactivation)
•  Inactivation of a plant's own gene by transgenically introducing another copy (cosuppression)

The actual inactivation happens through various mechanisms, some working directly affecting DNA, while others affect RNA levels after the genes are read (transcribed). In transcriptional gene silencing, DNA can be chemically modified (methylated) to inactivate the transgene. In addition, RNA-RNA interactions can create double stranded RNA, which is rapidly targeted for degradation.