A transposable element can be used as probes to clone genes that are mutated by insertion of a particular element. Firstly, the mutation caused by the transposon has to be identified via genetic screening. As a result, the gene can be isolated molecularly by cloning the DNA sequences flanking the transposable element insertion. This technique, known as transposon tagging, has been widely used to isolate genes from several species. It requires no knowledge of the nature of the product of the tagged gene, instead, it depends only on the expression patterns of a mutant phenotype. There are two approaches that are used: targeted and non targeting transposon tagging. (Gierl and Saedler, 1992)

Targeted transposon tagging is the procedure of choice if only one particular gene is desired. Although targeted tagging leads to a relatively direct identification of a particular gene, it requires a very large number of crosses, and a large population of plants must be screened in order to isolate a gene. If, instead of a particular gene, a group of genes are to be isolated, for example from a particular physiological pathway, non-targetted transposon tagging is an alternative. (Gierl and Saedler, 1992)

Activation Tagging

Activation tagging inserts are designed to carry strong activation sequences that can act on genes adjacent to the insertion site and thus modify their expression. The Cauliflower Mosaic Virus (CaMV) 35S enhancer or promoter sequences are used as transcriptional activators in this type of insertion system. The primary function of the enhancer or promoter sequence is to overexpress the tagged genes to reveal dominant gain-of-function phenotypes. (Marsch-Martinez et. al., 2002)

Enhancer / Gene Traps

Enhancer trap or gene trap elements carry a report gene construct that can respond to cis-acting transcriptional signals at the site of insertion. These elements allow the identification of gene by their pattern of expression and their subsequent cloning using the inserted element as a tag. A particular advantage of such a system is that it permits the identification of genes that would have been missed in conventional mutagenesis screens. (Sundaresan et. al., 1995)