Though the majority of information on transposons is in relation to their parasitic effect, it is sometimes unclear as to how exactly they hurt the host organism. To clarify, there are several ways in which a negative effect can be produced by transposable elements.
* Production of siRNA or miRNA that target specific cellular mRNAs, resulting in their destruction or inhibiting their translation through an RNAi-related mechanism
* Production of siRNA or miRNA that stimulates in RNA-Directed DNA Methylation (Rdrm) silencing of a similarly coded gene
* Insertion into a specific gene, interrupting its normal function
Any one of these can have an extreme or minimal effect, depending on what systems the mutation affects. For example, if a transposon were to interrupt the coding for the enzyme which allows for seeds to digest the nourishing endosperm, then the seed would fail to propagate at all, meaning that the mutation was, in essence, fatal. As a counter example, a transposon could be inserted into a non-coding region (which is likely the remnant of a now inactive transposon) and have no effect at all.