Abstract
Comparative analysis of 12 Drosophila genomes reveals insights into the evolution and mechanism of integration of R1 and R2 retrotransposons.
Highlights
Most arthropods contain R1 and R2 retrotransposons that insert into the 28S rRNA genes
The current model for their integration, called target primed reverse transcription (TPRT), has four basic steps: first, the bottom DNA strand of the target site is cleaved; second, the released 3' hydroxyl is used to prime cDNA synthesis by the element's reverse transcriptase; third, the top DNA strand is cleaved; and fourth, the released 3' hydroxyl is used to prime second-strand DNA synthesis [11]
R2 elements have been previously documented in several species groups of the Drosophila subgenus [25]; our failure to detect R2 sequences in D. virilis and D. grimshawi suggests R2 elements are frequently lost from this subgenus
Summary
Most arthropods contain R1 and R2 retrotransposons that insert into the 28S rRNA genes. The rRNA genes provide a microcosm within the genome that is amenable to a detailed description of the interactions between TEs and their host. In eukaryotes these genes are organized into one or more loci, the rDNA loci, containing hundreds to thousands of copies of the 18S, 5.8S and 28S genes (Figure 1) [3]. The current model for their integration, called target primed reverse transcription (TPRT), has four basic steps: first, the bottom DNA strand of the target site is cleaved; second, the released 3' hydroxyl is used to prime cDNA synthesis by the element's reverse transcriptase; third, the top DNA strand is cleaved; and fourth, the released 3' hydroxyl is used to prime second-strand DNA synthesis [11] This basic mechanism is likely used by R1 [12,13] and most other non-LTR retrotransposons [14]
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