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Volume 23
Issue 17
10.3390/ijms23179740
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Article

Reorganization of the Landscape of Translated mRNAs in NSUN2-Deficient Cells and Specific Features of NSUN2 Target mRNAs

by
Olga A. Kossinova
,
Alexander V. Gopanenko
,
Elena S. Babaylova
,
Alexey E. Tupikin
,
Marsel R. Kabilov
,
Alexey A. Malygin
and
Galina G. Karpova
*
Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2022, 23(17), 9740; https://doi.org/10.3390/ijms23179740
Submission received: 14 July 2022 / Revised: 22 August 2022 / Accepted: 24 August 2022 / Published: 28 August 2022
(This article belongs to the Special Issue Selected Papers from the HSG-2022 Conference)
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Abstract

The RNA cytosine C5 methyltransferase NSUN2 has a variety of RNA substrates and plays an important role in mRNA metabolism. NSUN2 binds to specific sequences enriched in exosomal mRNAs, suggesting its possible involvement in the sorting of mRNAs into exosomes. We applied the photoactivatable.4-thiouridine-enhanced cross-linking and immunoprecipitation assay involving high-throughput RNA sequencing (RNA-seq) to HEK293T cells to determine NSUN2 mRNA targets. NSUN2 cross-linking sites were found in more than one hundred relatively abundant mRNAs with a high GC content and a pronounced secondary structure. Then, utilizing RNA-seq for the total and polysome-associated mRNA from HEK293T cells with and without the knockdown of NSUN2, we identified differentially expressed genes, as well as genes with altered translational efficiency (GATEs). It turned out that the up-regulated GATE mRNAs were much shorter on average than the down-regulated ones, and their GC content was higher; moreover, they contained motifs with C residues located in GC-rich environments. Our findings reveal the specific features of mRNAs that make them potential targets for NSUN2 and expand our understanding of the role of NSUN2 in controlling translation and, possibly, in mRNA sorting into exosomes implemented through the methylation of cytosine residues.
Keywords: HEK293T cells; knockdown of NSUN2; PAR-CLIP; RNA-seq; polysome profiling; NSUN2 target mRNAs; NSUN2-dependent differentially expressed genes HEK293T cells; knockdown of NSUN2; PAR-CLIP; RNA-seq; polysome profiling; NSUN2 target mRNAs; NSUN2-dependent differentially expressed genes

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MDPI and ACS Style

Kossinova, O.A.; Gopanenko, A.V.; Babaylova, E.S.; Tupikin, A.E.; Kabilov, M.R.; Malygin, A.A.; Karpova, G.G. Reorganization of the Landscape of Translated mRNAs in NSUN2-Deficient Cells and Specific Features of NSUN2 Target mRNAs. Int. J. Mol. Sci. 2022, 23, 9740. https://doi.org/10.3390/ijms23179740

AMA Style

Kossinova OA, Gopanenko AV, Babaylova ES, Tupikin AE, Kabilov MR, Malygin AA, Karpova GG. Reorganization of the Landscape of Translated mRNAs in NSUN2-Deficient Cells and Specific Features of NSUN2 Target mRNAs. International Journal of Molecular Sciences. 2022; 23(17):9740. https://doi.org/10.3390/ijms23179740

Chicago/Turabian Style

Kossinova, Olga A., Alexander V. Gopanenko, Elena S. Babaylova, Alexey E. Tupikin, Marsel R. Kabilov, Alexey A. Malygin, and Galina G. Karpova. 2022. "Reorganization of the Landscape of Translated mRNAs in NSUN2-Deficient Cells and Specific Features of NSUN2 Target mRNAs" International Journal of Molecular Sciences 23, no. 17: 9740. https://doi.org/10.3390/ijms23179740

APA Style

Kossinova, O. A., Gopanenko, A. V., Babaylova, E. S., Tupikin, A. E., Kabilov, M. R., Malygin, A. A., & Karpova, G. G. (2022). Reorganization of the Landscape of Translated mRNAs in NSUN2-Deficient Cells and Specific Features of NSUN2 Target mRNAs. International Journal of Molecular Sciences, 23(17), 9740. https://doi.org/10.3390/ijms23179740

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