As mentioned in the previous section, transposition is the movement of a transposable element from one location to another. Several different mechanisms are used for transposition in both prokaryotic and eukaryotic cells. Nevertheless, all types of transposition have several features in common: (1) staggered breaks are made in the target DNA (see Figure 13.22); (2) the transposable element is joined to single-stranded ends of the target DNA; and (3) DNA is replicated at the single-stranded gaps.

Some transposable elements transpose as DNA (instead of being first copied into RNA, as retrotransposons are) and are referred to as DNA transposons (also called Class II transposable elements). Other transposable elements transpose through an RNA intermediate. In this case, RNA is transcribed from the transposable element (DNA) and is then copied back into DNA by a special enzyme called reverse transcriptase. Elements that transpose through an RNA intermediate are called retrotransposons (also called Class I transposons). Most transposable elements found in bacteria are DNA transposons. Both DNA transposons and retrotransposons are found in eukaryotes, although retrotransposons are more common.

Among DNA transposons, transposition may be replicative or nonreplicative. In replicative transposition, a new copy of the transposable element is introduced at a new site while the old copy remains behind at the original site, so the number of copies of the transposable element increases as a result of transposition. In nonreplicative transposition, the transposable element excises from the old site and inserts at a new site without any increase in the number of its copies. Nonreplicative transposition requires the replication of only the few nucleotides that constitute the flanking direct repeats. Retrotransposons use replicative transposition only.