Different codons, same amino acid

The genomes of species from bacteria to Drosophila show unique biases for particular synonymous codons—varying triplet base pairs that code for the same amino acids—but it has been unclear if such codon preferences exist in mammals. In a paper published in PNAS this week, a group led by Joshua B. Plotkin of the Bauer Center for Genomic Research at Harvard shows that cell usage of synonymous codons is systematically different between human tissues. In addition, the authors make a case that these codon choices result from evolutionary selection.

Plotkin and his colleagues analyzed genes expressed preferentially in six human tissues—brain, liver, uterus, testis, ovary, and vulva—and found synonymous codon biases between gene sets. In particular, they compared brain-specific genes to liver-specific genes; uterus genes to testis genes; and ovary genes to vulva genes. All three pairs differed significantly from each other in their synonymous codon usage.

"We can even predict ...