Target site analysis of RTE1_LA and its AfroSINE partner in the elephant genome

SINEs retrotranspose using their partner LINE's enzymatic machinery. It has recently been proposed that AfroSINEs ending with GGTTT 3′ tandem repeats were mobilized by RTE elements ending with CAA 3′ tandem repeats in the Afrotherian genome. Using sequences from the elephant genome, we show that AfroSINEs derive from RTE ending with GGTTT-like 3′ tandem repeats, a subgroup of RTE1_LA that only reached low copy number, and confirm that they were most likely mobilized by RTE ending with CAA_(n) tandem repeats (RTE1_LA-CAA_(n)). This partnership is supported by sequence similarity between two regions of the elements, overlap in the timing of their activity, common features of their target site consensus that are not shared by other members of the RTE family, and their high copy number. Detailed analyses of pre-insertion loci reveal that like many other apurinic/apyrimidinic endonuclease encoding elements, RTE1_LA-CAA_(n) shows loose target site specificity. In addition, the RTE1_LA-CAA_(n) target site consensus shares several structural and primary sequence features with that of LINE1, suggesting that these two elements share close functional similarity in the target primed reverse transcription (TPRT) reaction. Interestingly, although globally similar, the target site consensus of AfroSINE(Anc) and RTE1_LA-CAA_(n) differ in several aspects. These differences, not observed among all SINE/LINE pairs so far examined, are most likely due to the fact that AfroSINEs and RTE1_LA-CAA_(n) are terminated by a different tandem repeat motif. We propose that these differences reflect constraints imposed by base pairing interactions between the mRNA 3′ terminal tandem repeats and the target DNA at the onset of TPRT. So in addition to the endonuclease nicking preference, the mRNA of these elements appears to play an important role in integration site choice through a passive, post-nicking, selective process.