Codon usage in mammalian genes is biased by sequence slippage mechanisms

Abstract

The codons for some conserved amino acids are found to be the same between homologous genes from different species when the statistics of codon usage would suggest that they should be different. I examine whether this ‘coincidence’ of codon usage could be due to genetic mechanisms homogenising the DNA around specific sites. This paper describes the further analysis of the coincident codons in 19 genes (a total of 96 homologues) for slippage. Coincident codons arise in contexts of increased sequence simplicity, and have a high chance of occuring within sequences similar to the recombination-prone minisatellite ‘core’ sequence. This suggests a role of genetic homogenisation in their generation.

Key Words:

• codon usage
• cryptic simplicity
• gene expression
• slippage