The primary mutualistic interaction between transposon and host organism is in the formation of epialleles. True to the name, an epiallele is a kind of epigenetic mutant of a certain allelic type that produces distinct morphological differences from the wild type. The predominant research into this subject has been conducted on Arabidopsis thaliana, which has the dual disadvantages of being both TE-poor and an overly genetically stable organism. The manner of formation of epialleles is somewhat unclear, but it is thought to be due to the fact that some transposable elements, in stealing pieces of genetic code from their host organism, blend in so well as to confuse the host cellular machinery into thinking that its own genes are the transposons, which leads to epigenetic silencing of certain alleles, forming an epiallele. Some examples of this are:
* FWA, a dominant allele in arabidopsis, turned off by transposon regulation elements. The overall effect of this heritable silencing is to delay flowering.
* BNS, a recessive allele in arabiopsis, hypermethylated via siRNA co-opting of RISC complex, which results in silencing. The overall effect of this is the loss of a putative anaphase promoting complex gene.
* FLC, the flowering locus C gene, which represses flowering time in arabidopsis, can be partially inactivated by the insertion of a Mu-like element (MULE) into the first intron of the gene, resulting in earlier flowering time.
There is also evidence to suggest that trasposons play a more general role than was previously thought in the formation of miRNAs as well as in the silencing of centromeres.