Human DHX29 detects nonoptimal codon usage to regulate mRNA stability.
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| Title: | Human DHX29 detects nonoptimal codon usage to regulate mRNA stability. |
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| Authors: | Hia, Fabian (AUTHOR), Wu, Yitong (AUTHOR), Yoshinaga, Masanori (AUTHOR), Goto-Ito, Sakurako (AUTHOR), Iwasaki, Wakana (AUTHOR), Imami, Koshi (AUTHOR), Toh, Hirotaka (AUTHOR), Han, Peixun (AUTHOR), Cai, Ting (AUTHOR), Ohira, Takayuki (AUTHOR), Fukao, Akira (AUTHOR), Standley, Daron M. (AUTHOR), Shichino, Yuichi (AUTHOR), Takegawa, Masaki (AUTHOR), Fujiwara, Toshinobu (AUTHOR), Suzuki, Tsutomu (AUTHOR), Iwasaki, Shintaro (AUTHOR), Bassik, Michael C. (AUTHOR), Ito, Takuhiro (AUTHOR), Takeuchi, Osamu (AUTHOR) |
| Source: | Science. 5/7/2026, Vol. 392 Issue 6798, p1-16. 16p. |
| Subjects: | RNA helicase, RNA regulation, Genetic code, Genetic regulation, Protein synthesis, Messenger RNA, Ribosomes |
| Abstract: | Synonymous codon usage controls global gene expression in both prokaryotic and eukaryotic species. Nonoptimal codons are known to induce messenger RNA (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. Cryo–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 nonoptimal mRNAs. These findings establish a mechanistic link between synonymous codon usage and the regulation of gene expression. Editor's summary: The genetic code is redundant, yet the choice of synonymous codons profoundly influences messenger RNA (mRNA) stability and translation. In human cells, mRNAs enriched in nonoptimal (A/U–ending) codons are translated inefficiently and degraded rapidly. Using a genome-wide CRISPR screen, Hia et al. identified the RNA-binding protein DHX29 as a key regulator of codon-dependent gene expression. Cryo–electron microscopy showed that DHX29 preferentially interacts with translating ribosomes during the decoding of nonoptimal codons, suppressing mRNAs enriched in these codons. These findings reveal a direct molecular mechanism linking synonymous codon usage to gene expression in human cells. —Di Jiang INTRODUCTION: The genetic code is degenerate, with multiple synonymous codons encoding the same amino acid, yet these codons are not functionally equivalent. Synonymous codon usage strongly influences mRNA stability and translation efficiency across species. mRNAs enriched in optimal codons are generally stable and efficiently translated, whereas those enriched in nonoptimal codons (nonoptimal mRNAs) are ineffectively translated and rapidly degraded. Despite the pervasive impact of synonymous codon usage on gene expression, the molecular mechanisms by which nonoptimal codons are sensed in human cells remain poorly understood. RATIONALE: To understand how gene expression is regulated in a codon-dependent manner, it is essential to identify cellular factors that sense nonoptimal codon usage and control gene expression. We therefore performed an unbiased, genome-wide CRISPR screen using paired synonymous reporters enriched in either optimal or nonoptimal codons to systematically identify regulators that selectively target nonoptimal mRNA sequences. RESULTS: The genome-wide CRISPR screen identified the RNA binding protein DHX29 as a pivotal regulator of codon-dependent gene expression in human cells. RNA-sequencing analyses revealed transcriptome-wide up-regulation of nonoptimal mRNAs in DHX29-depleted cells across multiple human cell lines. Moreover, degradation of nonoptimal mRNAs was slowed in the absence of DHX29, suggesting a role of DHX29 in regulating nonoptimal mRNA turnover. To investigate the molecular basis of this regulation, we performed proteomic analysis and polysome fractionation, which revealed that DHX29 interacts with translating ribosomes not only during initiation, as previously reported, but also during elongation. Cryo–electron microscopy further showed that DHX29 directly engages with the A-site entrance of the 80S ribosome via its double-stranded RNA binding domain (dsRBD). This structural snapshot showed that binding of the DHX29 dsRBD to the ribosome is mutually exclusive with binding of the eEF1A•GTP•aminoacyl-tRNA ternary complex during the aminoacyl-tRNA sampling. Functional analyses of DHX29 mutants revealed that the dsRBD is required for repression of nonoptimal mRNA expression. We further assessed codon-specific interactions between DHX29 and the translating 80S ribosomes by performing selective ribosome profiling and found that DHX29 preferentially associates with ribosomes decoding nonoptimal codons at the A site. We next investigated the downstream regulatory pathways and found that DHX29 associates with the GIGYF2•4EHP complex, which has been linked to the repression of mRNAs with stalled ribosomes. Depletion of either GIGYF2 or 4EHP resulted in transcriptome-wide up-regulation of nonoptimal mRNAs, phenocopying loss of DHX29. Moreover, 4EHP knockdown in DHX29-depleted cells did not further enhance nonoptimal mRNA expression, indicating that these factors act within the same regulatory pathway. CONCLUSION: This study identifies DHX29 as an essential molecular link between synonymous codon usage and gene expression in human cells, acting by selectively associating with translating 80S ribosomes that decode nonoptimal codons and recruiting the GIGYF2•4EHP complex. These findings provide a mechanistic framework for understanding codon-dependent regulation of gene expression in human cells. Model of DHX29-mediated regulation of mRNAs enriched in nonoptimal codons.: During aminoacyl-tRNA sampling at nonoptimal codons, DHX29 preferentially associates with the 80S ribosome adjacent to the vacant A site. Subsequently, DHX29 recruits the 4EHP•GIGYF2 complex, thereby triggering the repression of nonoptimal mRNA expression. [ABSTRACT FROM AUTHOR] |
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| Database: | Psychology and Behavioral Sciences Collection |
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| Abstract: | Synonymous codon usage controls global gene expression in both prokaryotic and eukaryotic species. Nonoptimal codons are known to induce messenger RNA (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. Cryo–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 nonoptimal mRNAs. These findings establish a mechanistic link between synonymous codon usage and the regulation of gene expression. Editor's summary: The genetic code is redundant, yet the choice of synonymous codons profoundly influences messenger RNA (mRNA) stability and translation. In human cells, mRNAs enriched in nonoptimal (A/U–ending) codons are translated inefficiently and degraded rapidly. Using a genome-wide CRISPR screen, Hia et al. identified the RNA-binding protein DHX29 as a key regulator of codon-dependent gene expression. Cryo–electron microscopy showed that DHX29 preferentially interacts with translating ribosomes during the decoding of nonoptimal codons, suppressing mRNAs enriched in these codons. These findings reveal a direct molecular mechanism linking synonymous codon usage to gene expression in human cells. —Di Jiang INTRODUCTION: The genetic code is degenerate, with multiple synonymous codons encoding the same amino acid, yet these codons are not functionally equivalent. Synonymous codon usage strongly influences mRNA stability and translation efficiency across species. mRNAs enriched in optimal codons are generally stable and efficiently translated, whereas those enriched in nonoptimal codons (nonoptimal mRNAs) are ineffectively translated and rapidly degraded. Despite the pervasive impact of synonymous codon usage on gene expression, the molecular mechanisms by which nonoptimal codons are sensed in human cells remain poorly understood. RATIONALE: To understand how gene expression is regulated in a codon-dependent manner, it is essential to identify cellular factors that sense nonoptimal codon usage and control gene expression. We therefore performed an unbiased, genome-wide CRISPR screen using paired synonymous reporters enriched in either optimal or nonoptimal codons to systematically identify regulators that selectively target nonoptimal mRNA sequences. RESULTS: The genome-wide CRISPR screen identified the RNA binding protein DHX29 as a pivotal regulator of codon-dependent gene expression in human cells. RNA-sequencing analyses revealed transcriptome-wide up-regulation of nonoptimal mRNAs in DHX29-depleted cells across multiple human cell lines. Moreover, degradation of nonoptimal mRNAs was slowed in the absence of DHX29, suggesting a role of DHX29 in regulating nonoptimal mRNA turnover. To investigate the molecular basis of this regulation, we performed proteomic analysis and polysome fractionation, which revealed that DHX29 interacts with translating ribosomes not only during initiation, as previously reported, but also during elongation. Cryo–electron microscopy further showed that DHX29 directly engages with the A-site entrance of the 80S ribosome via its double-stranded RNA binding domain (dsRBD). This structural snapshot showed that binding of the DHX29 dsRBD to the ribosome is mutually exclusive with binding of the eEF1A•GTP•aminoacyl-tRNA ternary complex during the aminoacyl-tRNA sampling. Functional analyses of DHX29 mutants revealed that the dsRBD is required for repression of nonoptimal mRNA expression. We further assessed codon-specific interactions between DHX29 and the translating 80S ribosomes by performing selective ribosome profiling and found that DHX29 preferentially associates with ribosomes decoding nonoptimal codons at the A site. We next investigated the downstream regulatory pathways and found that DHX29 associates with the GIGYF2•4EHP complex, which has been linked to the repression of mRNAs with stalled ribosomes. Depletion of either GIGYF2 or 4EHP resulted in transcriptome-wide up-regulation of nonoptimal mRNAs, phenocopying loss of DHX29. Moreover, 4EHP knockdown in DHX29-depleted cells did not further enhance nonoptimal mRNA expression, indicating that these factors act within the same regulatory pathway. CONCLUSION: This study identifies DHX29 as an essential molecular link between synonymous codon usage and gene expression in human cells, acting by selectively associating with translating 80S ribosomes that decode nonoptimal codons and recruiting the GIGYF2•4EHP complex. These findings provide a mechanistic framework for understanding codon-dependent regulation of gene expression in human cells. Model of DHX29-mediated regulation of mRNAs enriched in nonoptimal codons.: During aminoacyl-tRNA sampling at nonoptimal codons, DHX29 preferentially associates with the 80S ribosome adjacent to the vacant A site. Subsequently, DHX29 recruits the 4EHP•GIGYF2 complex, thereby triggering the repression of nonoptimal mRNA expression. [ABSTRACT FROM AUTHOR] |
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| ISSN: | 00368075 |
| DOI: | 10.1126/science.adw0288 |
