Determining the relationship of gene expression and global mRNA stability in Drosophila melanogaster and Escherichia coli using linear models

There are several sequence-dependent factors regulating gene expression. Some of them have been extensively studied, among the most prominent are GC content and codon usage bias. Other factors hypothesized to have an impact on gene expression are gene length and the thermodynamic stability of mRNA secondary structure. In this work, we analyzed two different microarray datasets of Drosophila melanogaster gene expression and one dataset of Escherichia coli. To investigate the relationship between gene expression, codon usage bias and GC content of first, second and third codon position, gene length and mRNA stability we employed a multiple regression analysis using a comprehensive linear model. It is shown that codon usage bias and GC content of the first, second and third codon position show a significant influence on gene expression, whereas no significant effect of mRNA secondary structure stability is observed.