Bioinformatic analysis of TE-spliced new exons within human, mouse and zebrafish genomes.
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.
Kim
Dae-Soo
DS
National Primate Research Center (NPRC), KRIBB, Ochang, Chungbuk 363-883, Republic of Korea.
Huh
Jae-Won
JW
Kim
Young-Hyun
YH
Park
Sang-Je
SJ
Kim
Heui-Soo
HS
Chang
Kyu-Tae
KT
D017398:Alternative Splicing; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D004251:DNA Transposable Elements / Q000235:genetics*; D005091:Exons / Q000235:genetics*; D020869:Gene Expression Profiling; D016678:Genome / Q000235:genetics; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D051379:Mice / Q000235:genetics; D014714:Vertebrates / Q000235:genetics*; D015027:Zebrafish / Q000235:genetics
D004251:DNA Transposable Elements