Genes enriched in A/T-ending codons are co-regulated and conserved across mammals

Codon usage influences gene expression distinctly depending on the cell context. Yet, the importance of codon bias in the simultaneous turnover of specific groups of protein-coding genes remains to be investi-gated. Here, we find that genes enriched in A/T-ending codons are expressed more coordinately in general and across tissues and development than those enriched in G/C-ending codons. tRNA abundance measure-ments indicate that this coordination is linked to the expression changes of tRNA isoacceptors reading A/T-ending codons. Genes with similar codon composition are more likely to be part of the same protein complex, especially for genes with A/T-ending codons. The codon preferences of genes with A/T-ending codons are conserved among mammals and other vertebrates. We suggest that this orchestration contributes to tissue -specific and ontogenetic-specific expression, which can facilitate, for instance, timely protein complex for-mation.

Automated summary

Codon usage bias affects gene expression, with genes enriched in A/T-ending codons being more coordinately expressed across different tissues and developmental stages. This coordination is linked to the abundance of tRNA isoacceptors reading A/T-ending codons. Genes with similar codon composition, especially those with A/T-ending codons, are more likely to be part of the same protein complex. The codon preferences of genes with A/T-ending codons are conserved among mammals and other vertebrates, contributing to tissue-specific and ontogenetic-specific gene expression.