High Guanine and Cytosine Content Increases mRNA Levels in Mammalian Cells

Grzegorz Kudla,Aleksandra Helwak,Maciej Zylicz,Leszek Lipinski,Fanny Caffin,Laurence D Hurst

doi:10.1371/journal.pbio.0040180

Abstract

Mammalian genes are highly heterogeneous with respect to their nucleotide composition, but the functional consequences of this heterogeneity are not clear. In the previous studies, weak positive or negative correlations have been found between the silent-site guanine and cytosine (GC) content and expression of mammalian genes. However, previous studies disregarded differences in the genomic context of genes, which could potentially obscure any correlation between GC content and expression. In the present work, we directly compared the expression of GC-rich and GC-poor genes placed in the context of identical promoters and UTR sequences. We performed transient and stable transfections of mammalian cells with GC-rich and GC-poor versions of Hsp70, green fluorescent protein, and IL2 genes. The GC-rich genes were expressed several-fold to over a 100-fold more efficiently than their GC-poor counterparts. This effect was not due to different translation rates of GC-rich and GC-poor mRNA. On the contrary, the efficient expression of GC-rich genes resulted from their increased steady-state mRNA levels. mRNA degradation rates were not correlated with GC content, suggesting that efficient transcription or mRNA processing is responsible for the high expression of GC-rich genes. We conclude that silent-site GC content correlates with gene expression efficiency in mammalian cells.

Highlights

In the standard genetic code, all U$C and almost all A$G substitutions in the third positions of codons are synonymous
We have shown that the efficiency of mRNA production from green fluorescent protein (GFP), IL2, and Hsp70-family genes in mammalian cells correlates with the silent-site guanine and cytosine (GC) content of these genes
The origin of GC content variability in human genes attracts much interest, the effect of GC content on gene expression in mammalian cells has not been previously addressed in a direct experimental way

Summary

Introduction

In the standard genetic code, all U$C and almost all A$G substitutions in the third positions of codons are synonymous. It is believed that this broad variation in nucleotide usage is caused by the large-scale variation of nucleotide composition (isochore structure) of mammalian genomes. Genes located in GC-rich isochores tend to be more GC-rich than genes located in the GC-poor isochores [1,2], and the GC content of pseudogenes increases following their insertion into GC-rich isochores [3]. This suggests that the same evolutionary force is responsible for the isochore structure of mammalian genomes and for the codon usage of genes. The precise mechanism that underlies the formation of isochores and the diversification of nucleotide usage in genes is not yet clear

Methods

Results

Conclusion