Bioinformatic analysis of TE-spliced new exons within human, mouse and zebrafish genomes

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Title
Bioinformatic analysis of TE-spliced new exons within human, mouse and zebrafish genomes
Author(s)
Dae Soo KimJae Won HuhYoung-Hyun KimSang Je Park; H S Kim; Kyu Tae Chang
Bibliographic Citation
Genomics, vol. 96, no. 5, pp. 266-271
Publication Year
2010
Abstract
Recent studies indicate major roles for transposable elements (TEs) in alternative splicing. In this study, we conducted genome-wide alternative splicing analyses focusing on new internal exon birth derived from TEs in human, mouse, and zebrafish genomes. We identified two different exon sets, TE-spliced exons and non-TE-spliced exons. The proportion of TE-spliced exons was nearly twice as high as the proportion of non-TE-spliced exons in the coding sequence (CDS) region. Detailed analysis of various families of TEs in three different species of TE-spliced exons revealed a different pattern in zebrafish. In our analysis, we could identify the functional role of TE insertions in the vertebrate genome affecting mRNA splicing machinery. Their effects can be directly linked to the shift from constitutive to alternative splicing during primate evolution. Our results indicate that TEs have a significant effect on shaping new internal exons in human, mouse, and zebrafish transcriptomes.
Keyword
BioinformaticsTE-spliced exonTransposable element
ISSN
0888-7543
Publisher
Elsevier
DOI
http://dx.doi.org/10.1016/j.ygeno.2010.08.004
Type
Article
Appears in Collections:
Ochang Branch Institute > Division of National Bio-Infrastructure > National Primate Research Center > 1. Journal Articles
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