R2 and Related Site‐Specific Non‐Long Terminal Repeat Retrotransposons

Abstract

R2 elements are unusual mobile elements because all copies insert into a specific site within the genome, the 28S rRNA genes. The target-primed reverse transcription (TPRT) reaction characterized for R2 elements now serves as the model for studying the mechanism of all non-long terminal repeat (LTR) retrotransposons, and has also been shown to be similar to critical steps in group II intron retrohoming. Among the first eukaryotic genes to be cloned molecularly were the rRNA genes of Drosophila melanogaster. R1 elements were similar in coding capacity to L1 and I elements in that they contained two open reading frames (ORFs). A genomic DNA blotting approach was used initially to score for the presence of R1 and R2 insertions in the 28S rRNA genes of 47 species from nine insect orders. More recently, PCR has been used as the favored assay for the presence of R2 and R1 elements within insect species. In this approach degenerate oligonucleotide primers, designed to anneal to highly conserved regions within the RTencoding region of the elements, are used in combination with a second oligonucleotide that anneals to invariant 28S gene sequences approximately 700 bp downstream of the insertion sites. In summary, R1 and R2 elements have been identified in every major lineage of arthropods examined to date. All R2 elements insert in the 28S gene at a site exactly 74 bp upstream of all R1 insertions.