R1 retrotransposition models based on the standard target primed reverse transcription reaction. The uninserted 28S gene is shown at the top. The various regions upstream and downstream of the target site are colored as in Figure 7. Left side: ancestral type R1 transcripts (wavy line) do not contain upstream 28S gene sequences. Ancestral type R1s cleave the top DNA strand 14 bp downstream of the bottom cleavage site. Nucleotide variation at the 5' junctions corresponds to the imprecise nature by which the R1 polymerase uses the top strand of the DNA target to prime second-strand DNA synthesis. Right side: full length melanogaster-type R1 transcripts include 28S sequences starting upstream of position -9. Cleavage of the top strand occurs at one of two sites. If top-strand cleavage occurs 9 bp upstream of the bottom-strand site, then the upstream RNA sequences can anneal to the end of the cDNA strand, resulting in a precise 9 bp deletion of the target site. If top-strand cleavage occurs downstream of the bottom-strand site, then the annealing of cDNA to the target site is not possible, generating variation at the junction of the target site duplication.
Stage and Eickbush Genome Biology 2009 10:R49 doi:10.1186/gb-2009-10-5-r49