Synonymous codon bias has been examined in 78 human genes (19967 codons) and measured by relative synonymous codon usage (RSCU). Relative frequencies of all kinds of dinucleotides in 2,3 or 3,4 codon positions have been calculated, and codon-anticodon binding strength has been estimated by the stacking energies of codon-anticodon bases in Watson-Crick pairs. The data show common features in synonymous codon bias for all codon families in human genes: all C-ending codons, which possess the strongest codon-anticodon binding energies, are the most favored codons in almost all codon families, and those codons with medium codon-anticodon binding energies are avoided. Data analysis suggests that besides isochore and genome signature, codon-anticodon binding strength may be closely related to synonymous codon choice in human genes. The join-effect of these factors on human genes results in the common features in codon bias.
Xiufan ShiJingfei HuangChongrong LiangShuqun LiuJun XieCiquan Liu
Here we report the codon bias and the mRNA secondary structural features of the hemagglutinin(HA)cleavage site basic amino acid regions of avian influenza virus H5N1 subtypes.We have developed a dynamic extended folding strategy to predict RNA secondary structure with RNAstructure 4.1 program in an iterative extension process.Statistical analysis of the sequences showed that the HA cleavage site basic amino acids favor the adenine-rich codons,and the corresponding mRNA fragments are mainly in the folding states of single-stranded loops.Our sequential and structural analyses showed that to prevent and control these highly pathogenic viruses,that is,to inhibit the gene expression of avian influenza virus H5N1 subtypes,we should consider the single-stranded loop regions of the HA cleavage site-coding sequences as the targets of RNA interference.
