Overview of Transposition and Recombination

Transposition is a specialized form of recombination in which genetic elements, such as chromosomal segments, are relocated from one position in the genome to another. These mobile elements are called transposons, or jumping genes. 

Every transposon contains a coding sequence for an enzyme called transposase, in addition to other genes, as well as short flanking sequences that are reverse complements of each other. There are three types of transposition. 

In the first type, known as non-replicative or conservative transposition, the transposase encoding gene produces the dimeric enzyme that cleaves at short inverted sequences that flank a DNA transposon. Then, the inverted sequences come together to form a DNA loop which can be inserted into a target chromosome by transposase-mediated cuts.

In the second type, called replicative transposition, transposase cleaves both the transposon terminals and the target DNA. Then the 3’ ends of the transposon and the 5’ ends of the target DNA are covalently attached in a step called strand transfer. 

This creates an intermediate where the 5’ end of the transposon is still attached to the donor DNA. The unligated ends are used as primers by DNA polymerase to replicate the transposon. This intermediate is called a cointegrate.

Enzymes called resolvases cleave the intermediate at the internal resolution site, generating donor and target DNAs that each have one copy of the transposon.

In the third type of transposition, the transposable element is first transcribed into an RNA intermediate known as a retrotransposon. The RNA is copied back into a DNA sequence by reverse-transcription and then inserted into a target site. 

Despite their different mechanisms, all three of these processes can alter the genomic structure and potentially the function of the target DNA.