Exploring Codon Usage Patterns of Alternatively Spliced Genes in Human Chromosome 1

Introduction A large number of species (prokaryotes and eukaryotes) have been used to study the pattern of codon usage bias, and it has also been demonstrated that inter- and intra-genomic variation of the pattern of codon usage is a widespread phenomenon, which may result from various factors. Alternative synonymous codon usage does not modify the amino acid sequence encoded in DNA among species and often among genes from the same genome. It has been suggested that the pattern of codon usag…

Exploring Codon Usage Patterns of Alternatively Spliced Genes in Human Chromosome 1

In this study, 414 whole protein-coding sequences (238 004 codons) of alternatively spliced genes of human chromosome 1 have been employed to explore the patterns of codon usage bias among genes. Overall codon usage data analysis indicates that G- and C-ending codons are predominant in the genes. The base usage in all three codon positions suggests a selection-mutation balance. Multivariate statistical analysis reveals that the codon usage variation has a strong positive correlation with the expressivities of the genes (r=0.5790, P<0.0001). All 27 codons identified as optimal are G- and C-ending codons. Correlation analysis shows a strong negative correlation between the gene length and codon adaptation index value (r=0.2252, P<0.0001), and a significantly positive correlation between the gene length and Nc values (r=0.1876, P<0.0001). These results suggest that the comparatively shorter genes in the genes have higher codon usage bias to maximize translational efficiency, and selection may also contribute to the reduction of highly expressed proteins.