Origin and evolution of eukaryotic gene sequences derived from transposable elements
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My dissertation encompasses five different studies that are linked by a common theme the investigation of transposable element (TE) contributions to eukaryotic gene sequences. A detailed analysis of exonization events of LTR elements in the human genome shows the preference towards the fixation of LTR elements in gene untranslated regions, which supports the existing concept of a major role of LTR elements as a natural source of regulatory sequences. The ability of different classes of sequence similarity search methods to detect TE-derived sequences was evaluated. In general, the different search methods are found to be complementary, and combined search approaches are needed to systematically check any data set for all potential TE-associated coding sequences. On average, TE-derived exon sequences have low protein coding potential. In particular, non-coding TEs, are frequently exonized but unlikely to encode protein sequences. Many of these non-coding exonized TEs may be actually involved in gene regulation via the formation of double stranded RNA complexes with complementary TE-derived exons. The investigation of the relationship between human miRNAs and TEs shows that 55 experimentally verified human miRNA genes (~12%) originated from TEs. Overall, TE-derived miRNA genes are less conserved than non TE-derived miRNAs. The potential regulatory and functional significance of TE-derived miRNAs was explored. An ab initio prediction algorithm I developed was used to discover putative cases of novel TE-derived miRNA genes. A miRNA gene family, hsa-mir-548, was found to be derived from Made1 family of MITEs. The palindromic structure of the Made1 elements, and MITEs in general, points to a specific mechanism by which these sequences can be recognized and processed by the miRNA biogenesis pathway. MITEs may also represent an evolutionary link between siRNAs and miRNAs. An original model for a siRNA-to-miRNA evolutionary transition mediated by DNA-type TEs is proposed. This model is supported by the presence of evolutionary intermediate TE sequences that encode both siRNAs and miRNAs in the Arabidopsis and rice genomes. The siRNA-to-miRNA evolutionary transition is representative of a number of other regulatory mechanisms that evolved to silence TEs and were later co-opted to serve as regulators of host gene expression.