Analysis of LTR retrotransposon contribution to gene function in C. elegans and D. melanogaster
Ganko, Eric Walter
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Transposons are mobile DNA sequences found in varying abundance within host eukaryotic genomes. One transposon class, the retrotrantransposons, produce RNA copies that are reverse-transcribed into DNA. The DNA copy is then reinserted into the host?s genome. To produce transcripts, retrotransposons encode regulatory features including transcriptional promotion and termination signals. Due to their encoded regulatory features and insertional nature, retrotransposons may influence genes in the host organism. Using the sequenced model organisms Caenorhabditis elegans and Drosophila melanogaster a number of LTR retrotransposons in close promimity to host genes have been identified. In the worm C. elegans, a significantly greater number of transposons are found 500- 1000 bp upstream of genes than predicted by random insertion models. In all, 63% of LTR retrotransposon sequences (79/124) are located within 1 kb of a gene or within gene boundaries. Many genes with a nearby LTR retrotransposon lack homology to other species and may be nematode specific. In the genome of the fruitfly D. melanogaster, 33.4% of LTR retrotransposon sequences (228/682) are within 1 kb of a gene or within gene boundaries. Genes with an external response function were found to have a neighboring transposon more often than expected, while genes with metabolic and cell differentiation functions had fewer neighboring transposons. Results in C. elegans and D. melanogaster are consistent with the hypothesis that LTR retrotransposons may contribute to the structural and/or regulatory evolution of genes.