Mazumder Tarikul Huda, Chakraborty Supriyo, Paul Prosenjit
Department of Biotechnology, Assam University, Silchar 788011, Assam, India.
Bioinformation. 2014 May 20;10(5):256-62. doi: 10.6026/97320630010256. eCollection 2014.
Oncogenes are the genes that have the potential to induce cancer. The extent and origin of codon usage bias is an important indicator of the forces shaping genome evolution in living organisms.
We observed moderate correlations between gene expression as measured by CAI and GC content at any codon site. The findings of our results showed that there is a significant positive correlation (Spearman's r= 0.45, P<0.01) between GC content at first and second codon position with that of third codon position. Further, striking negative correlation (r = -0.771, P < 0.01) between ENC with the GC3s values of each gene and positive correlation (r=0.644, P<0.01) in between CAI and ENC was also observed.
The mutation pressure is the major determining factor in shaping the codon usage pattern of oncogenes rather than natural selection since its effects are present at all codon positions. The results revealed that codon usage bias determines the level of oncogene expression in human. Highly expressed oncogenes had rich GC contents with high degree of codon usage bias.
癌基因是具有诱发癌症潜力的基因。密码子使用偏好的程度和起源是影响生物基因组进化力量的重要指标。
我们观察到，通过密码子适应指数（CAI）衡量的基因表达与任何密码子位点的GC含量之间存在适度的相关性。我们的研究结果表明，第一和第二密码子位置的GC含量与第三密码子位置的GC含量之间存在显著正相关（斯皮尔曼相关系数r = 0.45，P < 0.01）。此外，还观察到每个基因的有效密码子数（ENC）与GC3s值之间存在显著负相关（r = -0.771，P < 0.01），以及CAI与ENC之间存在正相关（r = 0.644，P < 0.01）。
突变压力是塑造癌基因密码子使用模式的主要决定因素，而非自然选择，因为其影响存在于所有密码子位置。结果表明，密码子使用偏好决定了人类癌基因的表达水平。高表达的癌基因具有丰富的GC含量和高度的密码子使用偏好。
