GC2 Biology Dictates Gene Expressivity in Camellia sinensis  

Supriyo Chakraborty , Prosenjit Paul
Department of Biotechnology, Assam University, Silchar-788011, Assam, India
Author    Correspondence author
Computational Molecular Biology, 2014, Vol. 4, No. 2   doi: 10.5376/cmb.2014.04.0002
Received: 27 Dec., 2013    Accepted: 15 Jan., 2014    Published: 27 Feb., 2014
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This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Chakraborty and Paul, 2014, GC2 Biology Dictates Gene Expressivity in Camellia sinensis, Computational Molecular Biology, Vol.4, No.2 18-25 (doi: 10.5376/cmb.2014.04.0002)

Abstract

The effectiveness of the gene expression is influenced by the nature of codons used throughout the gene. This is due to the fact that most genes and organisms do not use synonymous codons uniformly; certain synonymous codons are used preferentially, a phenomenon called codon usage bias (CUB). Based on the hypothesis that highly expressed genes are often characterized by strong compositional bias in terms of codon usage, there are a number of measures currently in use that quantify codon usage bias in genes, and hence provide numerical indices to predict the expression level of genes. We analyzed normalized AT and GC frequency at each codon site. We observed that correlations between gene expression as measured by CAI and GC content at any codon site are very weak. GC2s showed moderate positive correlation with gene expression. We also measured the correlations between CAI and AT content at three codon sites. AT2s showed moderate negative correlation with gene expression. We further observed a strong correlation between RCBS and protein length indicating natural selection operating in favor of shorter genes to be expressed at higher level. Our analysis revealed that the second position of synonymous codons in Camellia sinensis plays a more prominent role than the third position in determining gene expressivity as evident from CUB and correlation analysis on ten genes.

Keywords
Gene expression; Relative codon usage bias (RCBS); Codon adaptation index (CAI); Codon usage bias (CUB)
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