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.

The soybean GmSNAP18 gene underlies two types of resistance to soybean cyst nematode

“…RSE has been successfully applied to yeast, human and zebrafish1112131415, but has not yet been applied to plants. Here we show that RSE-Seq of a targeted 300 kb genomic DNA segment (Gm18: 1480001..1780000) of contrasting chromosomal regions underlying resistance was effective in the direct identification of a candidate rhg1 SCN resistance gene (Table 1 and Fig.…”

“…RSE was performed using the genomic DNA of Essex, Forrest, Peking and PI 88788 as described by Gabriel et al 11. and Dapprich et al 12,.…”

“…We then applied ‘region-specific extraction sequencing' (RSE-Seq), a capture technology developed to enrich a targeted chromosomal segment for genome sequencing111213, to identify SCN resistance genes within the identified 300 kb chromosomal segment carrying the rhg1 locus. RSE-Seq has been applied successfully to study yeast, human and zebrafish1112131415. The SNPs and insertions and deletions (InDels) of four soybean lines (Essex, Forrest, Peking and PI 88788) were analysed using the Williams 82 genomic sequence as a reference16.…”

Calling cards for DNA-binding proteins

“…Of course, the false-positive rate can be reduced by increasing the cutoff, but that comes at the expense of a higher false-negative rate. Advances in the experimental approach are likely to be necessary for significant improvement in the specificity and sensitivity of our method (Gabriel et al 2006;Wheelan et al 2006). One reason for this high false-positive rate might be the large number of cycles of the inverse PCR required to provide enough probe for hybridization to the DNA microarrays, which may result in over-amplification of some of the nonspecific insertions.…”

LINE-1 Elements in Structural Variation and Disease

“…One method to identify dimorphic retrotransposon insertions, transposon insertion profiling by microarray (TIP-chip), employs the principles of transposon display to specifically amplify retrotransposons and their associated flanking sequences (80, 109, 253). The resultant amplicons are hybridized back to oligonucleotide arrays to identify sequences flanking the retrotransposons.…”