Knockdown of the Ribosomal Protein eL29 in Mammalian Cells Leads to Significant Changes in Gene Expression at the Transcription Level
An imbalance in the synthesis of ribosomal proteins can lead to the disruption of various cellular processes. For mammalian cells, it has been shown that the level of the eukaryote-specific ribosomal protein eL29, also known as the one interacting with heparin/heparan sulfate, substantially affects...
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MDPI AG
2020-05-01
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| Series: | Cells |
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| Online Access: | https://www.mdpi.com/2073-4409/9/5/1228 |
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| author | Alexander V. Gopanenko Alena V. Kolobova Maria I. Meschaninova Alya G. Venyaminova Alexey E. Tupikin Marsel R. Kabilov Alexey A. Malygin Galina G. Karpova |
| author_facet | Alexander V. Gopanenko Alena V. Kolobova Maria I. Meschaninova Alya G. Venyaminova Alexey E. Tupikin Marsel R. Kabilov Alexey A. Malygin Galina G. Karpova |
| author_sort | Alexander V. Gopanenko |
| collection | DOAJ |
| description | An imbalance in the synthesis of ribosomal proteins can lead to the disruption of various cellular processes. For mammalian cells, it has been shown that the level of the eukaryote-specific ribosomal protein eL29, also known as the one interacting with heparin/heparan sulfate, substantially affects their growth. Moreover, in animals lacking this protein, a number of anatomical abnormalities have been observed. Here, we applied next-generation RNA sequencing to HEK293 cells transfected with siRNAs specific for the mRNA of eL29 to determine what changes occur in the transcriptome profile with a decrease in the level of the target protein. We showed that an approximately 2.5-fold decrease in the content of eL29 leads to statistically significant changes in the expression of more than a thousand genes at the transcription level, without a noticeable effect on cell viability, rRNA level, and global translation. The set of eL29-dependent genes included both up-regulated and down-regulated ones, among which there are those previously identified as targets for proteins implicated in oncogenesis. Thus, our findings demonstrate that an insufficiency of eL29 in mammalian cells causes a significant reorganization of gene expression, thereby highlighting the relationship between the cellular balance of eL29 and the activities of certain genes. |
| first_indexed | 2024-03-10T19:48:24Z |
| format | Article |
| id | doaj.art-2565d5009ed042579fb20aa20bddd8ea |
| institution | Directory Open Access Journal |
| issn | 2073-4409 |
| language | English |
| last_indexed | 2024-03-10T19:48:24Z |
| publishDate | 2020-05-01 |
| publisher | MDPI AG |
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| series | Cells |
| spelling | doaj.art-2565d5009ed042579fb20aa20bddd8ea2023-11-20T00:36:02ZengMDPI AGCells2073-44092020-05-0195122810.3390/cells9051228Knockdown of the Ribosomal Protein eL29 in Mammalian Cells Leads to Significant Changes in Gene Expression at the Transcription LevelAlexander V. Gopanenko0Alena V. Kolobova1Maria I. Meschaninova2Alya G. Venyaminova3Alexey E. Tupikin4Marsel R. Kabilov5Alexey A. Malygin6Galina G. Karpova7Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, RussiaInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, RussiaInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, RussiaInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, RussiaInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, RussiaInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, RussiaInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, RussiaInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, Novosibirsk 630090, RussiaAn imbalance in the synthesis of ribosomal proteins can lead to the disruption of various cellular processes. For mammalian cells, it has been shown that the level of the eukaryote-specific ribosomal protein eL29, also known as the one interacting with heparin/heparan sulfate, substantially affects their growth. Moreover, in animals lacking this protein, a number of anatomical abnormalities have been observed. Here, we applied next-generation RNA sequencing to HEK293 cells transfected with siRNAs specific for the mRNA of eL29 to determine what changes occur in the transcriptome profile with a decrease in the level of the target protein. We showed that an approximately 2.5-fold decrease in the content of eL29 leads to statistically significant changes in the expression of more than a thousand genes at the transcription level, without a noticeable effect on cell viability, rRNA level, and global translation. The set of eL29-dependent genes included both up-regulated and down-regulated ones, among which there are those previously identified as targets for proteins implicated in oncogenesis. Thus, our findings demonstrate that an insufficiency of eL29 in mammalian cells causes a significant reorganization of gene expression, thereby highlighting the relationship between the cellular balance of eL29 and the activities of certain genes.https://www.mdpi.com/2073-4409/9/5/1228HEK293 cellsknockdown of ribosomal protein eL29next-generation sequencingRNA-seqdifferential gene expressioneL29-dependent genes |
| spellingShingle | Alexander V. Gopanenko Alena V. Kolobova Maria I. Meschaninova Alya G. Venyaminova Alexey E. Tupikin Marsel R. Kabilov Alexey A. Malygin Galina G. Karpova Knockdown of the Ribosomal Protein eL29 in Mammalian Cells Leads to Significant Changes in Gene Expression at the Transcription Level Cells HEK293 cells knockdown of ribosomal protein eL29 next-generation sequencing RNA-seq differential gene expression eL29-dependent genes |
| title | Knockdown of the Ribosomal Protein eL29 in Mammalian Cells Leads to Significant Changes in Gene Expression at the Transcription Level |
| title_full | Knockdown of the Ribosomal Protein eL29 in Mammalian Cells Leads to Significant Changes in Gene Expression at the Transcription Level |
| title_fullStr | Knockdown of the Ribosomal Protein eL29 in Mammalian Cells Leads to Significant Changes in Gene Expression at the Transcription Level |
| title_full_unstemmed | Knockdown of the Ribosomal Protein eL29 in Mammalian Cells Leads to Significant Changes in Gene Expression at the Transcription Level |
| title_short | Knockdown of the Ribosomal Protein eL29 in Mammalian Cells Leads to Significant Changes in Gene Expression at the Transcription Level |
| title_sort | knockdown of the ribosomal protein el29 in mammalian cells leads to significant changes in gene expression at the transcription level |
| topic | HEK293 cells knockdown of ribosomal protein eL29 next-generation sequencing RNA-seq differential gene expression eL29-dependent genes |
| url | https://www.mdpi.com/2073-4409/9/5/1228 |
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