Targeting Transposition: At Home in the Genome

The completion of the Saccharomyces genome sequence in 1996 signaled the beginning of a new chapter in repetitive element sequence analysis (Cherry et al. 1997). The genomic analysis in the article by Kim et al. (1998) in this issue provides new insights into the nature and distribution of repetitive DNA sequences in theSaccharomyces genome. It not only assesses the repetitive sequences present in the genome but also clarifies what is not found.Saccharomyces has five long terminal repeat (LTR)–retrotransposon families (Ty elements) but no nuclear LINE-like or SINE retroelements and no identifiable DNA-based transposable elements. Remarkably, each Ty family displays insertion specificity. The parallels and differences between the organization of transposable elements in the Saccharomyces genome, and what is thus far known of the organization of elements in the genomes of other eukaryotes, suggest that this chapter will have many interesting sequelae.

The genomic analysis by Kim et al. (1998) further defines the relationships of the Ty families of yeast comprised of four copia-like (Ty1, Ty2, Ty4, and Ty5) and one gypsy-like (Ty3) families. The copia-like families have been divided further based on similarity of encoded proteins and LTRs. Ty1 and Ty2 share significant similarity, particularly in the capsid domain, and share a common LTR, called δ. In addition, Kim et al. showed for the first time, that Ty1 and Ty2 δ elements are distinct—differing consistently at a single position. Unlike retrovirus LTRs, yeast element LTRs flanking the internal domain undergo recombination, thereby deleting one copy of the LTR and the internal domain sequence. Interestingly, among the families, there are widely differing copy numbers of complete elements and LTRs: 32 Ty1 elements and 217 Ty1-type δ elements; 13 Ty2 elements and 34 Ty2-type δ elements; two Ty3 elements and 41 σ elements; 3 Ty4 elements and 32 τ …