A novel group of families of short interspersed repetitive elements (SINEs) in Xenopus: evidence of a specific target site for DNA-mediated transposition of inverted-repeat SINEs

Abstract

We have isolated from Xenopus borealis members of a family of short interspersed repetitive elements (SINEs) that we have termed Xbr. Xbr elements are also present in other Xenopus genomes and are typically framed by 46 bp terminal inverted repeats (TIRs). These TIRs and those of two previously described families of inverted-repeat SINEs from X. laevis begin with the sequence TTAAAGGRR. Knowledge of this consensus, termed the T2 motif, allowed us to define four previously uncharacterized families of inverted-repeat SINEs from Xenopus database sequences. We estimate that the group of seven SINE families that possess the T2 motif accounts for about 10% of all X. laevis SINEs. Novel evidence for the transposition of inverted-repeat SINEs is provided: (1) by examples of the presence/absence of T2 elements at corresponding locations in either duplicated genes or pseudotetraploid gene homeologues; and (2) by the existence of contiguous elements from different T2 families that are joined precisely by their TIRs. These examples provide novel evidence for a DNA-mediated mechanism of T2 element transposition. They also show that the tetranucleotide, TTAA, which flanks integrated elements on both sides and is present once at unoccupied sites, is the obligate target site for T2 insertion. The use of a specific sequence as a target site for SINE insertion is unexpected, although such specificity is exhibited by a limited number of larger transposable elements that encode their own transposase. The clear evidence for DNA-mediated transposition provided by T2 elements demonstrates that the evolution and maintenance of SINE families in vertebrate genomes results from two distinctive mechanisms.