Knockdown of the Ribosomal Protein eL29 in Mammalian Cells Leads to Significant Changes in Gene Expression at the Transcription Level
Abstract
:1. Introduction
2. Materials and Methods
2.1. Preparation of siRNAs
2.2. Cell Culture and eL29 Knockdown
2.3. Determination of eL29 and rRNA Contents in eL29-Knocked Down Cells
2.4. Estimation of the Effect of eL29 Knockdown on Cellular Surveillance and Proliferation
2.5. Analysis of the Content of Ribosomal Proteins in the Lysate and Polysome Profile Fractions of Knockdown Cells
2.6. RNA-Seq Analysis
2.7. Validation of RNA-Seq Data by Reverse Transcription-qPCR
2.8. Bioinformatic Analysis
3. Results
3.1. Knockdown of the Ribosomal Protein eL29 in HEK293 Cells
3.2. RNA-Seq Analysis of eL29-Knocked Down HEK293 Cells
3.3. Cellular Processes Associated with eL29-Dependent DEGs
3.4. DEGs as Targets for p53 and c-Myc
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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GO Term | Definition | Fold Enrichment |
---|---|---|
For up-regulated DEGs: | ||
GO:0006515 | protein quality control for misfolded or incompletely synthesized proteins | 6.54 |
GO:0034976 | response to endoplasmic reticulum stress | 2.76 |
GO:0007005 | mitochondrion organization | 2.39 |
GO:0043087 | regulation of GTPase activity | 2.09 |
GO:0007346 | regulation of mitotic cell cycle | 2.09 |
For down-regulated DEGs: | ||
GO:0006413 | translational initiation | 3.37 |
GO:0022613 | ribonucleoprotein complex biogenesis | 2.87 |
GO:0008654 | phospholipid biosynthetic process | 2.70 |
GO:0051169 | nuclear transport | 2.61 |
GO:0090407 | organophosphate biosynthetic process | 2.52 |
GO:0006417 | regulation of translation | 2.48 |
GO:0031346 | positive regulation of cell projection organization | 2.35 |
GO:0072657 | protein localization to membrane | 2.17 |
GO:0016032 | viral process | 2.11 |
GO:0006396 | RNA processing | 2.08 |
GO:0055086 | nucleobase-containing small molecule metabolic process | 2.08 |
GO:0031329 | regulation of cellular catabolic process | 2.07 |
GO:0007015 | actin filament-based process | 2.03 |
GO:0080135 | regulation of cellular response to stress | 2.01 |
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Gopanenko, A.V.; Kolobova, A.V.; Meschaninova, M.I.; Venyaminova, A.G.; Tupikin, A.E.; Kabilov, M.R.; Malygin, A.A.; Karpova, G.G. Knockdown of the Ribosomal Protein eL29 in Mammalian Cells Leads to Significant Changes in Gene Expression at the Transcription Level. Cells 2020, 9, 1228. https://doi.org/10.3390/cells9051228
Gopanenko AV, Kolobova AV, Meschaninova MI, Venyaminova AG, Tupikin AE, Kabilov MR, Malygin AA, Karpova GG. Knockdown of the Ribosomal Protein eL29 in Mammalian Cells Leads to Significant Changes in Gene Expression at the Transcription Level. Cells. 2020; 9(5):1228. https://doi.org/10.3390/cells9051228
Chicago/Turabian StyleGopanenko, Alexander V., Alena V. Kolobova, Maria I. Meschaninova, Alya G. Venyaminova, Alexey E. Tupikin, Marsel R. Kabilov, Alexey A. Malygin, and Galina G. Karpova. 2020. "Knockdown of the Ribosomal Protein eL29 in Mammalian Cells Leads to Significant Changes in Gene Expression at the Transcription Level" Cells 9, no. 5: 1228. https://doi.org/10.3390/cells9051228