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PLoS Genet. 2006 Dec 15;2(12):e212. Epub 2006 Nov 1.

Global mapping of transposon location.

Author information

Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America.


Transposable genetic elements are ubiquitous, yet their presence or absence at any given position within a genome can vary between individual cells, tissues, or strains. Transposable elements have profound impacts on host genomes by altering gene expression, assisting in genomic rearrangements, causing insertional mutations, and serving as sources of phenotypic variation. Characterizing a genome's full complement of transposons requires whole genome sequencing, precluding simple studies of the impact of transposition on interindividual variation. Here, we describe a global mapping approach for identifying transposon locations in any genome, using a combination of transposon-specific DNA extraction and microarray-based comparative hybridization analysis. We use this approach to map the repertoire of endogenous transposons in different laboratory strains of Saccharomyces cerevisiae and demonstrate that transposons are a source of extensive genomic variation. We also apply this method to mapping bacterial transposon insertion sites in a yeast genomic library. This unique whole genome view of transposon location will facilitate our exploration of transposon dynamics, as well as defining bases for individual differences and adaptive potential.

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Conflict of interest statement

Competing interests. Some reagents were the gift of Qiagen and others were the gift of Generation Biotech. One author (JD) is the founder of Generation Biotech and an inventor of haplotype-specific extraction (United States 2001–0031467 A1). Qiagen has licensed the commercial rights to haplotype-specific extraction products from Generation Biotech. AG, JD, and MJD have applied for a patent based on this work.

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