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.

Synopsis

Transposons, or mobile DNA sequences—first described by Barbara McClintock—are interesting and important residents of all genomes. They are involved in gene creation and regulation, chromosome evolution, and generation of mutations, events that can occur on hugely varying time scales, from millions of years to mere days in the lab. Some transposons have even been “tamed” by geneticists for use as tools for marking genes and making mutations. In yeast, genome sequencing has given us a snapshot of transposons present in one strain at one particular time. The authors developed a method to easily, accurately, and globally track transposons in order to study how their locations change in different strains or during an experiment. The method involves finding pieces of DNA that contain the ends of transposons along with neighboring DNA and attaching these segments to magnetic beads. A magnet is then used to separate the selected DNAs away from the rest of the genome. The transposon-associated DNA is labeled with dyes and applied to a microarray, a glass slide with over 40,000 unique sequence features of yeast DNA attached. Each feature that lights up with the dye marks a transposon location. This new technique allows investigators to easily identify specific strains, to accurately monitor mobile portions of the genome, and to determine the role of transposons in phenotypic differences.