What Is the Role of Transposable Elements in Genome Evolution?

KEY CONCEPT
-Transposable elements tend to increase in copy number when introduced to a genome but are kept in check by negative selection and transposition regulation mechanisms.
Transposable elements (TEs) are mobile genetic elements that can be integrated into the genome at multiple sites and (for some elements) also excised from an integration site.  The insertion of a TE at a new site in the genome is called transposition. One type of TE, the retrotransposon, transposes via an RNA intermediate; a new copy of the element is created by transcription, followed by reverse transcription to DNA and subsequent integration at a new site.
Most TEs integrate at sequences that are random (at least with respect to their functions). As such, they are a major source of the problems associated with insertion mutations: frameshifts if inserted into coding regions and altered gene expression if inserted into regulatory regions. The number of copies of a particular TE in a species’ genome therefore depends on several factors: the rate of integration of the TE, its rate of excision (if any), selection on individuals with phenotypes altered by TE integration, and regulation of transposition.
TEs effectively act as intracellular parasites and, like other parasites, might need to strike an evolutionary balance between their own proliferation and the detrimental effects on the “host” organism. Studies on Drosophila TEs confirm that the mutational integration of TEs generally has deleterious, sometimes lethal, phenotypic effects. This suggests that negative selection plays an important role in the regulation of transposition; individuals with high levels of transposition are less likely to survive and reproduce.
However, we might expect that both TEs and their hosts might evolve mechanisms to limit transposition, and in fact both are observed. In one example of TE self-regulation, the Drosophila P element encodes a transposition repressor protein that is active in somatic tissue . In addition, there are two major cellular mechanisms for transposition regulation:
-In an RNA interference-like mechanism  involving piRNAs, the RNA intermediates of retrotransposons can be selectively degraded.
-In mammals, plants, and fungi, a DNA methyltransferase methylates cytosines within TEs, resulting in transcriptional silencing .
In any case, it is rare for TE proliferation to continue unchecked but rather to be limited by negative selection and/or regulation of transposition. However, following introduction of a TE to a genome, the copy number can increase to many thousands or millions before some equilibrium is achieved, particularly if TEs are integrated into introns or intergenic DNA where phenotypic effects will be absent or minimal. As a result, genomes might contain a high proportion of moderately or highly repetitive sequences .