1. Functional Impact of Transposable Element using Bioinformatic Analysis
Dae-Soo Kim1, Un-Jong Jo1,Jae-Won Huh2 and Heui-Soo Kim1, 2
1PBBRC, Interdisciplinary Research Program of Bioinformatics, College of Natural Sciences, Pusan National
University, Busan
2Division of Biological Sciences, College of Natural Sciences,Pusan National University, Busan
Dae-Soo Kim1 ,Jae-Won Huh2 and Heui-Soo Kim1, 2
1PBBRC, Interdisciplinary Research Program of Bioinformatics, College of Natural Sciences, Pusan National University, Busan
Functional Impact of Transposable Element using Bioinformatic Analysis
and Comparative Genomic Approach
Pusan National University
ABSTRACT
METHODS
RESULTS
Alternative splicing is an important mechanism for regulating protein diversity in higher eukaryotes. Although the regulation for alternative splicing event in a few genes is characterized, the general regulation mechanism for alternative splicing remains to be unclear. Numerous studies describe exonization of transposable elements, which is, splicing mediated insertion of fragments of transposable elements sequence into mature mRNAs. In this study, we investigate the number of transposable elements expression in protein coding region from the alternative splicing events. We searched currently available human, chimpanzee and mouse RefSeq sequences, including proteome complement for the presence of transposable elements. The transposable elements fusion exons appeared within the coding region of human 309 genes caused related insert protein domains or unrelated protein domains. Thus, we can compare with the numbers of orthologs in terms of protein diversity event in chimpanzee and mouse orthologs gene pairs and the transposable elements conservation. Most of 309 genes can be found in chimpanzee orthologs gene pairs, but can’t be found in mouse orthologs gene pairs. The transposable elements within protein coding sequence of gene have been a major source of
variation and novel genes during human evolution.
The human genome is disappointing:
It is small
It is empty
It is unoriginal
It is repetitive
K-value paradox
Complexity does not correlate with chromosome number.
C-value paradox
Complexity does not correlate with genome size.
N-value paradox
Complexity does not correlate
with gene number.
The genome contains a large number of genetic pseudogenes.
Transposable element
fusion screen
BLAST
Figure 1. Location of transposable element integration
Table 1. Distribution of transposable element
within human protein coding regions
Transposable element insertion within protein
coding regions
Functional analysis of transposable elements in the coding regions
Comparative analysis of transposable elements within coding region
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By generalization, a large number of transposable elements
might not be junk, but could have had a significant role in
gene evolution or species divergence.
Genome Information Lab