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Babaylova ES, Gopanenko AV, Tupikin AE, et al. Deficiency of the Ribosomal Protein uL5 Leads to Significant Rearrangements of the Transcriptional and Translational Landscapes in Mammalian Cells. Int J Mol Sci. 2021;22(24)doi: 10.3390/ijms222413485.
Babaylova, E. S., Gopanenko, A. V., Tupikin, A. E., Kabilov, M. R., Malygin, A. A., & Karpova, G. G. (2021). Deficiency of the Ribosomal Protein uL5 Leads to Significant Rearrangements of the Transcriptional and Translational Landscapes in Mammalian Cells. International journal of molecular sciences, 22(24), . https://doi.org/10.3390/ijms222413485
Babaylova, Elena S, et al. "Deficiency of the Ribosomal Protein uL5 Leads to Significant Rearrangements of the Transcriptional and Translational Landscapes in Mammalian Cells." International journal of molecular sciences vol. 22,24 (2021). doi: https://doi.org/10.3390/ijms222413485
Babaylova ES, Gopanenko AV, Tupikin AE, Kabilov MR, Malygin AA, Karpova GG. Deficiency of the Ribosomal Protein uL5 Leads to Significant Rearrangements of the Transcriptional and Translational Landscapes in Mammalian Cells. Int J Mol Sci. 2021 Dec 15;22(24). doi: 10.3390/ijms222413485. PMID: 34948282.
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Int J Mol Sci. 2021 Dec 15;22(24). doi: 10.3390/ijms222413485.

Deficiency of the Ribosomal Protein uL5 Leads to Significant Rearrangements of the Transcriptional and Translational Landscapes in Mammalian Cells.

International journal of molecular sciences

Elena S Babaylova, Alexander V Gopanenko, Alexey E Tupikin, Marsel R Kabilov, Alexey A Malygin, Galina G Karpova

Affiliations

  1. Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, 630090 Novosibirsk, Russia.

PMID: 34948282 DOI: 10.3390/ijms222413485

Abstract

Protein uL5 (formerly called L11) is an integral component of the large (60S) subunit of the human ribosome, and its deficiency in cells leads to the impaired biogenesis of 60S subunits. Using RNA interference, we reduced the level of uL5 in HEK293T cells by three times, which caused an almost proportional decrease in the content of the fraction corresponding to 80S ribosomes, without a noticeable diminution in the level of polysomes. By RNA sequencing of uL5-deficient and control cell samples, which were those of total mRNA and mRNA from the polysome fraction, we identified hundreds of differentially expressed genes (DEGs) at the transcriptome and translatome levels and revealed dozens of genes with altered translational efficiency (GATEs). Transcriptionally up-regulated DEGs were mainly associated with rRNA processing, pre-mRNA splicing, translation and DNA repair, while down-regulated DEGs were genes of membrane proteins; the type of regulation depended on the GC content in the 3' untranslated regions of DEG mRNAs. The belonging of GATEs to up-regulated and down-regulated ones was determined by the coding sequence length of their mRNAs. Our findings suggest that the effects observed in uL5-deficient cells result from an insufficiency of translationally active ribosomes caused by a deficiency of 60S subunits.

Keywords: HEK293T cells; RNA-seq; differential gene expression; knockdown of ribosomal protein uL5; next-generation sequencing; polysome profiling; uL5-dependent genes; uL5-related processes

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