Effect of depletion of CNOT4 on gene transcription in human cells.
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE294397 | GEO | 2025/10/17
REPOSITORIES: GEO
Similar Datasets
Project description:Codon usage bias of an organism plays an important role in determining its gene expression levels. Here, we have identified that a subunit of CCR4-NOT complex, CNOT4, plays a significant role in mediating codon usage effect on gene expression in human cells by affecting mRNA levels in a codon usage dependent manner.
2025-10-17 | GSE261504 | GEO
Project description:Codon usage bias of an organism has been reported to affect the level of gene expression by influencing this process at multiple steps. Here, we have identified a role of poly-A exosome targeting complex (PAXT), which is a substrate adaptor of nuclear RNA exosome, in regulating codon usage effect on gene expression. PAXT complex subunits, ZFC3H1 and PABPN1, regulate stability and subcellular localization of mRNA in a codon usage dependent manner. This suggests that codon usage dependent mRNA stability and nuclear export are important factors of codon usage effect on gene expression in human cells. Also, a subunit of CCR4-NOT complex, CNOT4, was found to play a significant role in this regulation by affecting the nuclear mRNA levels and their subcellular localization in codon usage dependent manner.
2025-10-17 | GSE261505 | GEO
Project description:CCR4-NOT regulates multiple steps in gene regulation, including transcription, mRNA decay, protein ubiquitylation and translation. Originally discovered in yeast, this complex is highly conserved across eukaryotes, although its composition and functions differ between mammals and yeast. For example, unlike yeast Not4, human CNOT4 (E3 Ubiquitin Ligase) does not form a stable complex with CCR4-NOT, and its functions are less clear compared to its yeast counterpart. To investigate the roles of CNOT1 (the central scaffold subunit) and CNOT4, we developed a rapid auxin-induced degron cell culture system that allows for the acute depletion of these proteins. We studied the effects of their absence on complex integrity, cell growth, and mRNA expression and turnover. Our transcriptome-wide analysis revealed that depleting CNOT1 altered the expression of thousands of transcripts, with the majority showing increased abundance and a general decrease in mRNA decay. Although CNOT4 does not associate with the complex through standard biochemical methods, BioID proximity labelling confirmed its association with the complex in cells. However, depleting CNOT4 did not affect the integrity of CCR4-NOT. In contrast to the effects observed with CNOT1 depletion, reducing CNOT4 levels led to only modest changes in RNA steady-state levels and unexpectedly accelerated global mRNA decay. Finally, we show that the changes in mRNA stability in CCR4-NOT depleted cells correlated with the codon optimality of the transcripts. Our data suggest that CNOT4 exerts opposite effects on mRNA metabolism compared to CNOT1, and that CNOT4 may have functions distinct from those of complex subunits that promote mRNA degradation.
2025-10-23 | GSE277237 | GEO
Project description:The CCR4-NOT complex is a major mRNA deadenylase in eukaryotes and comprise CNOT6/6L and CNOT7/8, both of which are two types of catalytic subunits, as well as CNOT4, which is a regulatory subunit with previously undetermined functions. These subunits are previously hypothesized to play synergistic biochemical functions; however, their in vivo functions have remained poorly investigated. In this study, we constructed viable Cnot6/6l double knockout mice and the males were fertile, whereas Cnot7–/– male mice have been reported to be infertile. These results are against canonical viewpoints and indicate that CNOT7 has CNOT6/6L-independent functions in vivo. We also demonstrate that the mouse testis has an endogenous complex that contains CNOT7 and CNOT4, but not CNOT6/6L. CNOT4 is required for post-implantation embryo development and meiosis progression during spermatogenesis. Selective knockout of Cnot4 in male germ cells leads to defective DNA damage repair and homologous crossover formation between X and Y chromosomes in a cell autonomous manner. CNOT4 functions as a previously unrecognized mRNA adaptor of CCR4-NOT by targeting mRNAs to CNOT7 for deadenylation of the poly(A) tails, thereby mediating the degradation of a subset of transcripts from the zygotene to pachytene stage. Therefore, the mRNA removal promoted by CNOT4-regulated CCR4-NOT complex during the zygotene to pachytene transition is crucial for the selection of DNA repair pathways, subsequent activation of meiosis-related genes, sex chromosome paring, and ultimately, male fertility.
2021-02-19 | GSE158471 | GEO
Project description:Usage of synonymous codons represents a characteristic pattern of preference in each organism. It has been inferred that such bias of codon usage has evolved as a result of adaptation for efficient synthesis of proteins. Here we examined synonymous codon usage in genes of the fission yeast Schizosaccharomyces pombe, and compared codon usage bias with expression levels of the gene. In this organism, synonymous codon usage bias was correlated with expression levels of the gene; the bias was most obvious in two-codon amino acids. A similar pattern of the codon usage bias was also observed in Saccharomyces cerevisiae, Arabidopsis thaliana, and Caenorhabditis elegans, but was not obvious in Oryza sativa, Drosophila melanogaster, Takifugu rubripes and Homo sapiens. As codons of the highly expressed genes have greater influence on translational efficiency than codons of genes expressed at lower levels, it is likely that codon usage in the S. pombe genome has been optimized by translational selection through evolution. Relative amounts of mRNA for each ORF were measured by DNA microarray using genomic DNA as a reference, and the copy number of mRNA was calculated using an estimate of the total mRNA number in the cell as 100,000 copies.
2010-06-20 | E-GEOD-13554 | biostudies-arrayexpress
Project description:Usage of synonymous codons represents a characteristic pattern of preference in each organism. It has been inferred that such bias of codon usage has evolved as a result of adaptation for efficient synthesis of proteins. Here we examined synonymous codon usage in genes of the fission yeast Schizosaccharomyces pombe, and compared codon usage bias with expression levels of the gene. In this organism, synonymous codon usage bias was correlated with expression levels of the gene; the bias was most obvious in two-codon amino acids. A similar pattern of the codon usage bias was also observed in Saccharomyces cerevisiae, Arabidopsis thaliana, and Caenorhabditis elegans, but was not obvious in Oryza sativa, Drosophila melanogaster, Takifugu rubripes and Homo sapiens. As codons of the highly expressed genes have greater influence on translational efficiency than codons of genes expressed at lower levels, it is likely that codon usage in the S. pombe genome has been optimized by translational selection through evolution.
2009-04-01 | GSE13554 | GEO
Project description:Codon usage bias is a fundamental aspect of molecular biology, influencing the efficiency and accuracy of protein synthesis. In a recent study, we investigated codon usage patterns across various tissues in mice, revealing a consistent and significant trend.
2025-09-07 | GSE282134 | GEO
Project description:Differences in codon frequency between genomes, genes, or positions along a gene, modulate transcription and translation efficiency, leading to phenotypic and functional differences. Integrative studies quantifying the phenotypic consequences of codon usage bias at different molecular and cellular levels in human cells are lacking. Here, we present a multiscale analysis of the effects of synonymous codon recoding during heterologous gene expression in human cells. Six synonymous versions of an antibiotic resistance gene were generated, fused to a fluorescent reporter, and independently expressed in HEK293 cells. Multiscale phenotype was analysed by means of: quantitative transcriptome and proteome assessment, as proxies for gene expression; cellular fluorescence, as a proxy for single-cell level expression; and real-time cell proliferation in absence or presence of antibiotic, as a proxy for the cell fitness. We show that differences in codon usage bias strongly impact the molecular and cellular phenotype: (i) they result in large differences in mRNA and in protein levels, as well in mRNA-to-protein ratio; (ii) they introduce unpredicted splicing events; (iii) they lead to reproducible phenotypic heterogeneity; and (iv) they lead to a trade-off between the benefit of antibiotic resistance and the burden of heterologous expression. In human cells in culture, codon usage bias modulates gene expression by modifying mRNA availability and suitability for translation, leading to differences in protein levels and eventually eliciting functional phenotypic changes.
2024-05-24 | PXD038324 | Pride
Project description:Effect of depletion of CNOT4 on gene expression in human cells
| PRJNA1087337 | ENA
Project description:Effect of depletion of CNOT4 on gene transcription in human cells.
| PRJNA1249380 | ENA