PUBLICATION
Bioinformatic analysis of TE-spliced new exons within human, mouse and zebrafish genomes
- Authors
- Kim, D.S., Huh, J.W., Kim, Y.H., Park, S.J., Kim, H.S., and Chang, K.T.
- ID
- ZDB-PUB-100826-9
- Date
- 2010
- Source
- Genomics 96(5): 266-271 (Journal)
- Registered Authors
- Keywords
- none
- MeSH Terms
-
- Alternative Splicing*
- Animals
- Computational Biology/methods*
- DNA Transposable Elements/genetics*
- Exons/genetics*
- Gene Expression Profiling
- Genome/genetics
- Genome, Human/genetics
- Humans
- Mice/genetics
- Vertebrates/genetics*
- Zebrafish/genetics
- PubMed
- 20728532 Full text @ Genomics
Citation
Kim, D.S., Huh, J.W., Kim, Y.H., Park, S.J., Kim, H.S., and Chang, K.T. (2010) Bioinformatic analysis of TE-spliced new exons within human, mouse and zebrafish genomes. Genomics. 96(5):266-271.
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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping