Comparing synonymous codon usage of alternatively spliced genes with non-alternatively spliced genes in human genome
Zhuang, YL（Institute of Bioinformatics, Tsinghua University）
Li, YD（Institute of Bioinformatics, Tsinghua University）
Xu, XF（Life Science College, Nanjing Normal University, Nanjing ）
Chen, XP（College of Economics and Technology, University of Science and Technology of China）
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It is becoming clear that alternative splicing plays an important role in expanding protein diversity. However, the previous studies an codons usage did not distinguish alternative splicing from non-alternative splicing. Do codon usage patterns hold distinctions between them? Thus, we attempted to systematically compare the differences of synonymous codon usage patterns between alternatively and non-alternatively spliced genes by analyzing the large datasets from human genome. The results indicated: (1) There are highly significant differences in the average Nc values between non-alternatively spliced genes and the longer isoform genes as well as the shorter isoform genes, and the level of codon usage bias of non-alternatively spliced genes is to some extent higher than that in alternatively spliced genes. (2) Very extensive heterogeneity of G+C content in silent third codon position (GC3s) was evident among these genes, and it could be also shown there are highly significant differences in the average GC3s values between non-alternatively spliced genes and the longer isoform genes as well as the shorter isoform genes. (3) The Nc-plots and correspondence analysis reveal that codon usage bias are mainly dominated by mutation bias, and no correlation between gene expression level and synonymous codon biased usage is found in human genes. (4) Overall codon usage data analysis indicated that the C-ending codons usage has a highly significant differences between the longer isoform genes and non-alternatively spliced genes as well as the shorter isoform genes, it further found out that there is no significant differences of C-ending codons usage between the shorter isoform genes and non-alternatively spliced genes. Finally, our results seem to imply that alternative splicing gene may originate from non-alternative splicing gene, and may be created by DNA mutation or gene fusion, and be retained through nature selection and adaptive evolution.
出处Volume: 12, Issue: 1(2004) pp. 91-103