title: Global mapping of transposon location.
abstract: 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.
authors.affiliation: Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America. gabriel@cabm.rutgers.edu
authors.forename: Abram
authors.initials: A
authors.lastname: Gabriel
authors.forename: Johannes
authors.initials: J
authors.lastname: Dapprich
authors.forename: Mark
authors.initials: M
authors.lastname: Kunkel
authors.forename: David
authors.initials: D
authors.lastname: Gresham
authors.forename: Stephen C
authors.initials: SC
authors.lastname: Pratt
authors.forename: Maitreya J
authors.initials: MJ
authors.lastname: Dunham
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D004251:DNA Transposable Elements; D008954:Models, Biological; D016254:Mutagenesis, Insertional; D020411:Oligonucleotide Array Sequence Analysis; D012441:Saccharomyces cerevisiae / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004251:DNA Transposable Elements