Codon usage is an important determinant of gene expression levels largely through its effects on transcription

Significance

Codon usage bias is an essential feature of all genomes. The effects of codon usage biases on gene expression were previously thought to be mainly due to its impacts on translation. Here, we show that codon usage bias strongly correlates with protein and mRNA levels genome-wide in the filamentous fungus Neurospora, and codon usage is an important determinant of gene expression. Surprisingly, we found that the impacts of codon usage on gene expression are mainly due to effects on transcription and are largely independent of translation. Together, these results uncovered an unexpected role of codon biases in determining transcription levels by affecting chromatin structures and suggest that codon biases are results of genome adaptation to both transcription and translation machineries.

Abstract

Codon usage biases are found in all eukaryotic and prokaryotic genomes, and preferred codons are more frequently used in highly expressed genes. The effects of codon usage on gene expression were previously thought to be mainly mediated by its impacts on translation. Here, we show that codon usage strongly correlates with both protein and mRNA levels genome-wide in the filamentous fungus Neurospora. Gene codon optimization also results in strong up-regulation of protein and RNA levels, suggesting that codon usage is an important determinant of gene expression. Surprisingly, we found that the impact of codon usage on gene expression results mainly from effects on transcription and is largely independent of mRNA translation and mRNA stability. Furthermore, we show that histone H3 lysine 9 trimethylation is one of the mechanisms responsible for the codon usage-mediated transcriptional silencing of some genes with nonoptimal codons. Together, these results uncovered an unexpected important role of codon usage in ORF sequences in determining transcription levels and suggest that codon biases are an adaptation of protein coding sequences to both transcription and translation machineries. Therefore, synonymous codons not only specify protein sequences and translation dynamics, but also help determine gene expression levels.