Silencing of transposon transcripts can vary in completeness of silencing as well as in duration of alteration. Plants employ a number of methods, which range from elimination of transcripts to complete epigenetic silencing. In general, these can be sorted into two strategies:
* Gene silencing#Post-transcriptional gene silencing PTGS], post-transcriptional gene silencing, in which siRNA or miRNA derived from transposon activity are loaded onto an RNA-induced silencing complex (RISC), which cleaves targeted mRNA transcripts
* Gene silencing#Transcriptional gene silencing TGS], transcriptional gene silencing, in which siRNA transposon transcript is loaded onto an RNA-Directed DNA Methylation complex, which methylates the region of DNA which is reactive to the siRNA used in the complex. This can lead to histone modification and, if further epigenetic modification occurs, heterochromatin formation. This process is not well understood, as almost all information regarding it comes to us from the study of the FWA gene in Arabidopsis thaliana, a relatively TE-poor example in the plant kingdom. This paucity of information is further complicated by the relatively small genome and the low variability of the Arabidopsis epigenetic code.
In general, initiation of transposon silencing has yet to be fully explained. For example, there have been recorded incidences of spontaneous silencing in maize, which carries a high number of transposons (~85% of the genome), though the mechanism by which this occurs is unknown. While it is known that heritable methylation occurs, and must occur with frequency, and must be initiated, triggered by some distinct factor, the only known example of this is in the case of Mu killer (Muk), a gene in maize that silences MuDR, a class II autonomous transposable element. Muk encodes a natural inverted derivative of the transposase coding sequence in MuDR, which, when transcribed, forms a dsRNA that is subsequently cut into siRNA, which renders MUDR incapable of cutting and pasting itself by way of RNAi interference of the transposase. Muk also engages RNAi-Directed Methylation to create a stable and heritable suppression.