Most organisms do not have the high transposon load that we have. For those like us, and given a general tendency of transposons to insert at random into new DNA loci, how come we exist at all? Isn’t the danger of transposition into essential gene sequences magnified by the possibility of multiple simultaneous transpositions of elements generated by cut-and-paste and especially replicative mechanisms? Indeed, transposons have been found in genes that are inactive as a result.
An obvious explanation for our survival of transposon activity is that most transposition is into the >90% percent of the genome that does not code for proteins. Another is that eukaryotic organisms have two copies of every gene, so that if one is inactive, the other may sustain us. Beyond this, several mechanisms exist to silence a transposon after transposition has occurred, mitigating the dangers of rampant transposition. As long as a transposition is not lethal (e.g., because its integration disrupts an activity essential to life), the cell and organisms can survive the event. In time, mutations at the ends of CMB3e 344 transposons or in genes responsible for transposition would render them inactive. Finally, there may be a more direct curb on transposition. The small interfering RNAs (siRNAs) we encountered earlier could complement and target viral RNAs for destruction (see the Transcription chapter for more information on siRNAs). There is some evidence that siRNAs similarly target transposon transcripts.
Summing up, transposon activity is moderated by mutational loss of function and/or by more direct mechanisms that limit transposition and thus genetic damage. If an accumulation of transposons to a high load, as occurs in many species, were deleterious, they would be limited or eliminated from genomes. Instead, persistent transposons and acts of transposition are largely neutral, increasing options for diversity in the selection of new genotypes and phenotypic characteristics. We also know now that transposons can function in genetic regulation. Thus, transposons are neither selfish nor junk DNA. Check out these links for more: Not junk after all? and Eulogy for Junk DNA.
256 Transposons- Junk or Not