Retroposons and transposable elements

Transposable elements are relatively long DNA sequences in prokaryotic and eukaryotic genomes that act as mobile genetic elements. These elements, which represent a large part of the genomes of many species transpose by a mechanism that involves DNA synthesis followed by random integration at a new target site in the genome.

All transposable elements encode for transposase, the special enzyme activity that helps in the insertion of transposons at a new site, and most of them contain inverted repeats at their ends. The major difference between bacterial transposable elements and their eukaryotic counterparts is the mechanism of transposition . Only eukaryotic genomes contain a special type of transposable elements, called retroposons, which use reverse transcriptase to transpose through an RNA intermediate.

Transposition may result in splicing of DNA fragments into or out of the genome. During replicative transposition, the transposon is first replicated giving a new copy that is transferred to a new site, with the old copy being left at the original site. Nonreplicative transposition however describes the movement of a transposon that is excised from a donor site, usually generating a double, and is integrated in a new site.

The most basic transposable elements in bacteria are insertion sequences , which encode only for one enzyme, the transposase. Longer bacterial transposons contain at least one more protein-coding gene , which most frequently is an antibiotic resistance gene. In eukaryotes , retroposons are more common than transposons. They are either retroviral or nonviral. Viral retroposons encode for the enzymes reverse transcriptase and integrase and are flanked by long terminal repeats (LTRs) in the same way as retroviruses . The typical and most abundant nonviral retroposons are the short interspersed elements (SINEs) and the long interspersed elements (LINEs), which are usually repeated, many times in the mammalian genome. Both SINEs and LINEs lack LTRs and are thought to transpose through a special retrotransposition mechanism that involves transcription of one strand of the retroposon into RNA. This RNA undergoes conformation change (looping) and provides a primer for the synthesis of single stranded cDNA. The cDNA later serve as template for the synthesis of a double stranded DNA that is inserted in the genome by yet unknown mechanisms.

Transposons and retroposons seem to play a role in evolution and biology by promoting rearrangement and restructuring of genomes. Transposition may directly cause both deletion and inversion mutagenesis. Furthermore, transposable elements mediate the movement of host DNA sequences to new locations, enrich the genome with identical sequences positioned at different locations, and promote homologous recombination . Such recombination may eventually result in deletions, inversions, and translocations.

Transposons usually influence the expression of the genes in proximity of their insertion sites. They have therefore been extensively used as tools to create random insertion mutants in bacteria, yeast and higher eukaryotes. They are also used in large-scale functional genomic studies. They are valuable both during the cloning of genes and the generation of transgenic animals.

See also Microbial genetics; Transposition