Knockdown of the mRNA encoding the ribosomal protein eL38 in mammalian cells causes a substantial reorganization of genomic transcription

Gopanenko, Alexander V.; Kolobova, Alena V.; Meschaninova, Mariya I.; Venyaminova, Alya G.; Tupikin, Alexey E.; Kabilov, Мarsel R.; Malygin, Alexey A.; Карпова, Г. Г.

doi:10.1016/j.biochi.2021.02.017

Cited by 4 publications

(14 citation statements)

References 47 publications

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“…To determine the effects of eL38 deficiency on the translatome profile, the Ribo-seq was performed in combination with the high throughput sequencing of the total cellular mRNA (RNA-seq) [ 11 ]. The TE parameters of genes were calculated taking into account the Ribo-seq and RNA-seq data obtained for cell samples treated with specific siRNAs against eL38 mRNA and with non-targeting siRNA.…”

Section: Resultsmentioning

confidence: 99%

“…Although differentiating cells seem to be the most suitable models for investigating the causes of congenital anomalies associated with eL38 haploinsufficiency in mutant mice, the use of standard HEK293 cells allowed us to determine the general consequences of a deficiency of this protein on the cellular translatome. As mentioned in the Introduction, we have previously shown that a decrease in the eL38 level in HEK293 cells leads to a change in the expression (activation or suppression) of more than 1500 genes at the transcriptional level [ 11 ]. This means that the cellular response to eL38 deficiency is more pronounced at the transcriptional level, rather than at the translational one.…”

Section: Discussionmentioning

confidence: 99%

“…These are, first of all, the processes related to translation and splicing. At the same time, among the translationally activated genes, there are no those involved in translation in mitochondria, which are present in the set of transcriptionally activated genes [ 11 ]. On the other hand, the expression of genes associated with protein folding was increased at the level of translation, while they have been shown not to be included in the number of transcriptionally activated genes.…”

Section: Discussionmentioning

confidence: 99%

“…However, not all skeletal anomalies observed in these animals can be attributed to impaired Hox gene expression. For example, excessive ossification is most likely related to the enhanced transcription of the BMP2 and BMP6 genes revealed in [ 11 ], which are involved in skeletal regeneration and the morphogenesis of cartilage and bones. In addition, decreased translational efficiencies of the collagen genes COL2A1 and COL6A1 can also contribute to the disruption of the process that regulates bone formation during development [ 18 , 19 , 20 ].…”

Section: Discussionmentioning

confidence: 99%

“…In our previous work using the RNA-seq approach, we have shown that the knockdown of eL38 in HEK293 cells caused a substantial reorganization of genomic transcription, resulting in the altered expression of nearly 1500 genes [ 11 ]. An analogous effect of eL38 deficiency on gene expression has been demonstrated in HepG2 cells using RT-qPCR for a group of genes identical to those whose transcriptional activities were reduced or enhanced in HEK293 cells with the decreased level of eL38, which suggests that the response of different cell types to eL38 insufficiency is generally similar [ 11 ]. In this study, using the ribosome profiling method (Ribo-seq), we investigated how the reduced content of eL38 in HEK293 cells affects gene expression at the level of translation.…”

Section: Introductionmentioning

confidence: 99%

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Knockdown of the Ribosomal Protein eL38 in HEK293 Cells Changes the Translational Efficiency of Specific Genes

Gopanenko

Kolobova

Tupikin

et al. 2021

IJMS

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The protein eL38 is one of the smallest proteins of the mammalian ribosome, which is a component of its large (60S) subunit. The haploinsufficiency of eL38 in mice leads to the Tail-short mutant phenotype characterized by defects in the development of the axial skeleton caused by the poor translation of mRNA subsets of Hox genes. Using the ribosome profiling assay applied to HEK293 cells knocked down of eL38, we examined the effects of the lack of eL38 in 60S subunits on gene expression at the level of translation. A four-fold decrease in the cell content of eL38 was shown to result in significant changes in the translational efficiencies of 150 genes. Among the genes, whose expression at the level of translation was enhanced, there were mainly those associated with basic metabolic processes; namely, translation, protein folding, chromosome organization, splicing, and others. The set of genes with reduced translation efficiencies contained those that are mostly involved in the processes related to the regulation of transcription, including the activation of Hox genes. Thus, we demonstrated that eL38 insufficiency significantly affects the expression of certain genes at the translational level. Our findings facilitate understanding the possible causes of some anomalies in eL38-deficient animals.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Knockdown of the Ribosomal Protein eL38 in HEK293 Cells Changes the Translational Efficiency of Specific Genes

Gopanenko

Kolobova

Tupikin

et al. 2021

IJMS

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Deficiency of the ribosomal protein uS10 (RPS20) reorganizes human cells translatome according to the abundance, CDS length and GC content of mRNAs

Tian,

Babaylova,

Gopanenko

et al. 2024

Open Biol.

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Ribosomal protein uS10, a product of the RPS20 gene, is an essential constituent of the small (40S) subunit of the human ribosome. Disruptive mutations in its gene are associated with a predisposition to hereditary colorectal carcinoma. Here, using HEK293T cells, we show that a deficiency of this protein leads to a decrease in the level of ribosomes (ribosomal shortage). RNA sequencing of the total and polysome-associated mRNA samples reveals hundreds of genes differentially expressed in the transcriptome (t)DEGs and translatome (p)DEGs under conditions of uS10 deficiency. We demonstrate that the (t)DEG and (p)DEG sets partially overlap, determine genes with altered translational efficiency (TE) and identify cellular processes affected by uS10 deficiency-induced ribosomal shortage. We reveal that translated mRNAs of upregulated (p)DEGs and genes with altered TE in uS10-deficient cells are generally more abundant and that their GC contents are significantly lower than those of the respective downregulated sets. We also observed that upregulated (p)DEGs have longer coding sequences. Based on our findings, we propose a combinatorial model describing the process of reorganization of mRNA translation under conditions of ribosomal shortage. Our results reveal rules according to which ribosomal shortage reorganizes the transcriptome and translatome repertoires of actively proliferating cells.

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Changes in the Transcriptome Caused by Mutations in the Ribosomal Protein uS10 Associated with a Predisposition to Colorectal Cancer

Tian

Babaylova

Gopanenko

et al. 2022

IJMS

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A number of mutations in the RPS20 gene encoding the ribosomal protein uS10 have been found to be associated with a predisposition to hereditary non-polyposis colorectal carcinoma (CRC). We transfected HEK293T cells with constructs carrying the uS10 minigene with mutations identical to those mentioned above and examined the effects of the produced proteins on the cellular transcriptome. We showed that uS10 with mutations p.V50SfsX23 or p.L61EfsX11 cannot be incorporated into 40S ribosomal subunits, while the protein with the missense mutation p.V54L functionally replaces the respective endogenous protein in the 40S subunit assembly and the translation process. The comparison of RNA-seq data obtained from cells producing aberrant forms of uS10 with data for those producing the wild-type protein revealed overlapping sets of upregulated and downregulated differently expressed genes (DEGs) related to several pathways. Among the limited number of upregulated DEGs, there were genes directly associated with the progression of CRC, e.g., PPM1D and PIGN. Our findings indicate that the accumulation of the mutant forms of uS10 triggers a cascade of cellular events, similar to that which is triggered when the cell responds to a large number of erroneous proteins, suggesting that this may increase the risk of cancer.

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Knockdown of the mRNA encoding the ribosomal protein eL38 in mammalian cells causes a substantial reorganization of genomic transcription

Cited by 4 publications

References 47 publications

Knockdown of the Ribosomal Protein eL38 in HEK293 Cells Changes the Translational Efficiency of Specific Genes

Knockdown of the Ribosomal Protein eL38 in HEK293 Cells Changes the Translational Efficiency of Specific Genes

Deficiency of the ribosomal protein uS10 (RPS20) reorganizes human cells translatome according to the abundance, CDS length and GC content of mRNAs

Changes in the Transcriptome Caused by Mutations in the Ribosomal Protein uS10 Associated with a Predisposition to Colorectal Cancer

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