Third-nucleotide codon bias and synonymous codon bias define functional translational programs that shape human tissue and cancer proteomes.

BackgroundCodon usage bias is a universal feature of the genetic code, yet how synonymous codon bias or third-nucleotide codon bias (A/T-vs G/C-ending) shape translation and proteome composition across tissues and cancer remain unclear. ResultsUsing comparative genomics between human and rodent coding sequences, we uncovered a conserved codon-bias axis. A/T-ending codons consistently marked genes involved in proliferation and RNA processing, whereas G/C-ending codons were enriched for differentiation and neuronal functions. While GC3 scores, measuring the third-nucleotide codon bias, showed differences between humans and rodents due to recombination events, the functional dichotomy was conserved. Isoacceptors frequencies, measuring gene synonymous codon bias, was conserved from rodents to humans. Synonymous codons exhibited distinct functional enrichment patterns, demonstrating functional divergence at the codon level. Two new indices; the ANN-index and mG-index, reflecting codons decoded by the tA and mG tRNA modifications, linked tRNA modification biology to translation. Both indices correlated with proliferative, A/T-biased programs, providing a universal basis for their roles in cancer. Tissue proteomes showed strong RNA-protein discordance and distinct codon biases. Analysis of 21 cancer types revealed a global A/T-ending codon bias in cancer. Analysis of 2,600 cancer cell lines revealed codon bias heterogeneity in cell lines from the same cancer subtype that is not observable between cancer patients. ConclusionsOur results define synonymous codon divergence and tRNA-modification indices as determinants of translational reprogramming. This work establishes a unified framework connecting codon usage, tRNA modifications, and proteome remodeling, providing a basis for rational design of mRNA and gene therapeutics. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/685942v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@161ca0borg.highwire.dtl.DTLVardef@117c3f8org.highwire.dtl.DTLVardef@142d26borg.highwire.dtl.DTLVardef@483f6_HPS_FORMAT_FIGEXP M_FIG C_FIG