Echolocation: a PCR-based strategy for reliably and rapidly mapping transposon insertion sites

The technique of isolating and defining genes by transposon tagging has been widely exploited in classical genetic organisms (1 —3). However, it is also useful to know the location of insertion sites relative to the established structure of the gene. For example, insertions in exons indicate probable null alleles, while insertions upstream or downstream of the transcript can identify potential as-acting regulatory sequences. Traditional methods to determine insertion sites rely on molecular cloning of the transposon-induced allele or extensive analysis of the genomic DNA by Southern blotting, both of which are laborious. Here I describe a novel strategy ('echolocation') to obtain quite precise (±10 bp) estimates of the site of insertion by the porymerase chain reaction (PCR; ref. 4). The ends of most transposons are defined by short sequences that are inverted with respect to each other. Thus a singl