Figure 3

Analysis of ten sites that are polymorphic for DINE-1 insertions in natural populations of D. yakuba. For each site, the sequence from a strain containing a DINE-1 insertion is shown at the top, and the sequence from a strain lacking the insertion is shown at the bottom. Only the terminal sequences of DINE-1 and its flanking sequences are shown. The 5' subTIR is shown in bold italics. Insertions 1-3 were previously reported in [23]. The interpretation of these data depends on the designation of the DINE-1 termini and whether insertion causes a TSD. (a) Analysis using the annotation of DINE-1 structure presented in this paper. This annotation places the subTIR of D. yakuba 1 bp internal to the 5' end. It also assumes that no TSD is created, in accord with the proposed mechanism of Helitron-type replication [24]. Under these stipulations, all ten insertions occur between the dinucleotide TT in the consensus sequence WTT (where W = A or T), and eight of ten match a longer consensus sequence of insertion after the second nucleotide in the sequence of WTTTT. (b) Analysis assuming the DINE-1 termini of [28], and Helitron-type replication. Only sites 1 and 10 are shown. Under this annotation, DINE-1 would have an insertion preference for WT dinucleotides. (c) Analysis assuming that the DINE-1 5' end begins at its inverted repeat, inserts between the dinucleotide TT and causes a 2 bp TSD, as in MITE-like DNA transposons. The TSDs caused by DINE-1 are boxed.