Functional impact of transposable elements using bioinformatic analysis and a comparative genomic approach.
A dual coding event, which is the translation of different isoforms from a single gene, is one of the special patterns among the alternative splicing events. This is an important mechanism for the regulation of protein diversity in human and mouse genomes. Although the regulation for dual coding events has been characterized in a few genes, the individual mechanism remains unclear. Numerous studies have described the exonization of transposable elements, which is the splicing mediated insertion of transposable element sequence fragments into mature mRNAs. Therefore, in this study, we investigated the number of transposable element (TE)-derived dual coding genes in human, chimpanzee and mouse genomes. TE fusion exons appeared in the dual coding regions of 309 human genes. Functional protein domain alterations by TE-derived dual coding events were observed in 129 human genes. Comparative TE-derived dual coding events were also analyzed in chimpanzee and mouse orthologs. Seventy chimpanzee orthologs had TE-derived dual coding events, but mouse orthologs did not have any TE-derived dual coding events. Taken together, our analyses listed the number of TE-derived dual coding genes which could be investigated by experimental analysis and suggested that TE-derived dual coding events were major sources for the functional diversity of human genes, but not mouse genes.
Kim
Dae-Soo
DS
National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang 363-883, Korea.
Huh
Jae-Won
JW
Kim
Young-Hyun
YH
Park
Sang-Je
SJ
Chang
Kyu-Tae
KT
D017398:Alternative Splicing; D000818:Animals; D004251:DNA Transposable Elements; D005091:Exons; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D051379:Mice; D002679:Pan troglodytes
D004251:DNA Transposable Elements