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

• Published in: Cell systems Vol. 14; no. 4; pp. 312 - 323.e3
• Main Authors: Benisty, Hannah, Hernandez-Alias, Xavier, Weber, Marc, Anglada-Girotto, Miquel, Mantica, Federica, Radusky, Leandro, Senger, Gökçe, Calvet, Ferriol, Weghorn, Donate, Irimia, Manuel, Schaefer, Martin H., Serrano, Luis
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 19.04.2023
• Subjects: A/T-ending codons; Animals; co-regulation; Codon - genetics; Codon Usage; conservation; development; mammals; Mammals - genetics; RAS genes; RNA, Transfer - genetics; synonymous codons; translation efficiency; tRNA; Vertebrates - genetics; RAS genes; conservation; development; mammals; tRNA; synonymous codons; translation efficiency; A/T-ending codons; codon usage; co-regulation
• ISSN: 2405-4712; 2405-4720; 2405-4720
• DOI: 10.1016/j.cels.2023.02.002

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 investigated. 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 measurements 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 formation. [Display omitted] •A/T-ending codons are highly conserved in mammals in comparison with G/C-ending codons•AT3-rich genes are more co-regulated across development and tissues than GC3-rich genes•Codon preferences of AT3-rich genes are conserved among mammals and other vertebrates We found that genes with a certain type of codon (A/T-ending) are more coordinated in their expression across tissues and during development than genes with another type of codon (G/C-ending). This coordination may play a role in cellular processes such as helping the formation of protein complexes.