NEUTRAL MUTATION AND SELECTIVE CONSTRAINT PLAY MAJOR ROLE IN DICTATING THE CODON BIAS IN BREAST CANCER RISK GENES

T.H. MAZUMDER¹, S. CHAKRABORTY²*
¹Department of Biotechnology, Assam University, Silchar- 788 011, Assam, India.
²Department of Biotechnology, Assam University, Silchar- 788 011, Assam, India.
* Corresponding Author : supriyoch_2008@rediffmail.com

Received : 24-09-2014     Accepted : 30-10-2014     Published : 06-11-2014
Volume : 5     Issue : 1       Pages : 61 - 67
Int J Comput Biol 5.1 (2014):61-67

Keywords : Codon usage, Synonymous codon, Breast cancer, Gene expression, Mutation pressure, Amino acid usage, Nucleotide skewness, Relative codon usage bias
Academic Editor : Dr. Probodh Borah, Dr. Han Wu
Conflict of Interest : None declared

Breast cancer is ranked the first cancer in women worldwide and the second leading cause of death after cervical cancer particularly in developing countries. Specific genes are associated with breast cancer risk in human genome. Understanding the codon usage bias (CUB) with compositional dynamics of coding sequence is of great importance in gaining clues to predict the level of gene expression and genome characterization. In this study, we have analyzed the complete nucleotide coding sequences of fifteen breast cancer risk genes with the help of various genetic indices. Our analysis revealed that both neutral mutation and selective constraint play major roles in the codon usage patterns of breast cancer risk genes. Our results further show that gene expression level is linked with alterations in the nucleotide skewness. Breast cancer gene products showed the dominance of three amino acids namely serine, leucine and glutamate in their composition but the least usage of two amino acids namely tryptophan and methionine. Moreover, the level of breast cancer gene expression measured by RCBS revealed a significant negative correlation with highly used amino acids. In addition, highly used amino acids had negative impact on the expression of breast cancer risk genes.