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.
Highlights
The genomes of all organisms studied have been populated, over evolutionary time, by different classes of transposable elements
In order to isolate DNA fragments containing sequences that flank specific transposons, we digested whole genomic DNA with three different restriction endonucleases, pooled the digested DNA, and combined it with oligonucleotide probes designed to anneal to specific segments of selected transposons (Figure 1, steps 1–3)
The extracted DNA fragments were released from the beads and fluorescently labeled using either Cy3- or Cy5-dUTP in the presence of random primers and exoÀ Klenow fragment (Figure 1, steps 5 and 6), and hybridized to dense whole genome oligonucleotide microarrays of the S. cerevisiae genome (Figure 1, steps 7 and 8)
Summary
The genomes of all organisms studied have been populated, over evolutionary time, by different classes of transposable elements These multicopy genetic elements, first postulated by Barbara McClintock, are regulated at many levels to suppress their movement: such movement has been shown to result in genetic diseases in humans [1], hybrid dysgenesis and sterility in Drosophila [2], spread of antibiotic resistance in bacteria [3], and, generally, insertional activation or inactivation of nearby genes [4,5]. Their effects on host genomes can be more widespread and subtle. Differences in placement of transposons in individual genomes could cause or at least correlate with phenotypic differences
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