INTEGRATION OF RETROPOSABLE ELEMENTS IN MAMMALS - SELECTION OF TARGETSITES

Genomic DNA fragments generated by the reverse transcription of cellul ar RNA are called retroposons. Because they are flanked by short repea ts, mammalian retroposons are believed to integrate at staggered chrom osomal breaks. Recently, a significant sequence pattern associated wit h the integration of Alu and ID repeats was identified (Jurka 1996). I t is represented by the 5' TTAAAA consensus sequence around the 5' end s of flanking repeats of Alu, ID, as well as, of B1 and B2 retroposed elements as shown in this paper. This consensus is a potential target for enzymatic nicking which probably occurs in the complementary stran d between 3' AA and the following 3' TTTT bases. The first four bases of the flanking repeats corresponding to the 3' TTTT consensus sequenc e show some sequence variations that may be affected by complementary base pairing between the A-rich RNA tails and the DNA target sequences prior to nicking and reverse transcription. We discuss potential evid ence for such base pairing based on correlated variations in nucleotid e composition of different tail and target regions.