Kyoto, Japan -- Our genes are written in long strings of three-letter units composed of four different nucleotides. These units -- or codons -- specify one of many amino acids, the building blocks of proteins. Multiple codons can encode the same amino acid, which seems to point to some redundancy in our genetic code.
Yet growing evidence suggests that these synonymous codons are not interchangeable: rather, some confer stability to mRNAs and are more efficiently translated in cells, and thus more optimal than others. mRNAs enriched in non-optimal codons are inefficiently translated and subsequently degraded, but how human cells detect and respond to these substandard codons has largely remained a mystery.
A collaborative team of researchers at Kyoto University and RIKEN, led by Osamu Takeuchi and Takuhiro Ito, was determined to unravel this enigma, and conducted several tests to better understand this process.
First, the team performed a genome-wide CRISPR screening to identify factors that regulate codon-dependent gene expression, which led them to identify the RNA-binding protein DHX29 as a central regulator of codon-dependent gene expression. They then utilized RNA sequencing to analyze global mRNA expression, observing that loss of this protein results in the upregulation of mRNAs enriched in non-optimal codons.
Cryo-electron microscopy helped the team visualize the direct interaction between DHX29 and the 80S ribosome. Then with selective ribosome profiling they analyzed the codons read by DHX29-bound ribosomes, which revealed that DHX29 preferentially interacts with ribosomes decoding non-optimal codons. Finally, through proteomic analyses they discovered that DHX29 recruits the GIGYF2•4EHP protein complex to selectively repress mRNAs enriched in non-optimal codons.
"Together, these findings reveal a direct molecular link between synonymous codon choice and the control of gene expression in human cells," says co-corresponding author Masanori Yoshinaga.
This study reshapes our understanding of how codon choice controls gene expression in humans. The DHX29-mediated regulatory mechanism may play a role in key biological processes such as cell differentiation, cellular homeostasis, and the development of cancer, so this study is likely to have broad relevance. Next, the team aims to explore how the influence of DHX29 on gene expression affects health and disease.
"We have long been fascinated by how cells interpret the hidden layer of information embedded within the genetic code, so discovering the molecular factor that allows human cells to read and respond to this hidden code has been particularly rewarding," says team leader Osamu Takeuchi.
