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Transposons, also called jumping genes, are mobile genetic elements that relocate from one genomic position to another through transposition. Each transposon contains a transposase gene encoding an enzyme that catalyzes movement, plus flanking sequences and other genes. This specialized recombination process can alter genomic structure and potentially affect target DNA function.

Non-replicative transposition involves transposase cleaving inverted flanking sequences to form a DNA loop inserted into a target chromosome without copying. Replicative transposition creates a cointegrate intermediate where the transposon is copied during insertion, resulting in both donor and target DNA retaining one transposon copy after resolvase cleavage.

Retrotransposition first transcribes the transposable element into an RNA intermediate called a retrotransposon. Reverse-transcriptase then copies this RNA back into DNA, which is inserted into a target site. This RNA-mediated mechanism contrasts with direct DNA-based transposition, yet all three transposition types can alter genomic structure and function.

Transposons rarely move because transposition can have deleterious effects on genome stability and gene function. The frequency of transposition correlates with sequence specifications and structural motifs at donor and target sites. This low frequency means genetic selection is required to detect transposition outcomes, such as color variegation in maize or white patches on Snapdragon flowers.

Transposons comprise significant portions of many organism genomes and likely drove speciation by changing genome sizes and modifying gene expression patterns. In bacteria, transposition confers antibiotic resistance by transferring resistant genetic elements. In eukaryotes, transposons regulate target genes under physiological stress conditions, a mechanism extensively studied in plants.

All transposons contain a transposase-encoding gene and short flanking sequences that are reverse complements of each other. These inverted sequences are critical recognition sites where transposase cleaves DNA during movement. Additionally, transposons carry other genes beyond transposase, enabling their diverse functions across different genomic contexts.

During replicative transposition, transposase cleaves both transposon terminals and target DNA. The 3' ends of the transposon are covalently attached to the 5' ends of target DNA through strand transfer, creating a cointegrate where the transposon's 5' end remains attached to donor DNA. DNA polymerase then uses unligated ends as primers to replicate the transposon.