Dissimilar substitution rates between two strands of DNA influence codon usage pattern in some human genes

Abstract

We illustrated the descriptive aspects of codon usage of some important human genes and their expression potential in E. coli. By comparing the results of various codon usage parameters, effects that are due to selection and mutational pressures have been deciphered. The variation in GC3s explains a significant proportion of the variation in codon usage patterns. The codons CGC, CGG, CTG and GCG showed strong positive correlation with GC3, which suggested that codon usage had been influenced by GC bias. We also found that ACC (Thr, RSCU-1.77), GCC (Ala, RSCU-1.67), CCC (Pro, RSCU-1.54), TCC (Ser, RSCU-1.47) were frequently used which signified that C was common at 2nd and 3rd codon positions. Correspondence analysis revealed that F1 axis had significant correlation with various GC contents suggesting that compositional properties under mutation pressure might affect codon usage bias. Nc-GC3 plot analysis suggested that both mutation pressure and natural selection might affect the codon usage bias which is also supported by neutrality plot analysis. The dinucleotide CT, TG and AG were significantly over-represented and CG, TA, AT, TT, and GT were underrepresented due to high rate of spontaneous mutation resulting from cytosine deamination.