Effect of DHX29 depletion on mRNA stability in HEK293T cells

Synonymous codon usage controls global gene expression in both prokaryotic and eukaryotic species. Non-optimal codons are known to induce mRNA decay; however, the underlying molecular mechanism remains poorly understood in human cells. Through genome-wide CRISPR screening, we identified the RNA-binding protein DHX29 as a critical regulator of codon-dependent gene expression. Cryogenic electron microscopy and selective ribosome profiling demonstrated that DHX29 directly interacts with the A-site entrance of the translating 80S ribosome, the binding site for the eEF1A•GTP•aminoacyl-tRNA ternary complex, suggesting a role in monitoring aminoacyl-tRNA sampling. Proteomic analysis further revealed that DHX29 recruits the GIGYF2•4EHP complex to mediate global suppression of non-optimal mRNAs. These findings establish a mechanistic link between synonymous codon usage and the regulation of gene expression.