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Article

Bioinformatics Analyses of the Transcriptome Reveal Ube3a-Dependent Effects on Mitochondrial-Related Pathways

Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Abba Khoushy Ave 199, Haifa 3498838, Israel
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Int. J. Mol. Sci. 2020, 21(11), 4156; https://doi.org/10.3390/ijms21114156
Received: 5 May 2020 / Revised: 7 June 2020 / Accepted: 8 June 2020 / Published: 10 June 2020
(This article belongs to the Special Issue Mitochondria-Targeted Approaches in Health and Disease)
The UBE3A gene encodes the ubiquitin E3-ligase protein, UBE3A, which is implicated in severe neurodevelopmental disorders. Lack of UBE3A expression results in Angelman syndrome, while UBE3A overexpression, due to genomic 15q duplication, results in autism. The cellular roles of UBE3A are not fully understood, yet a growing body of evidence indicates that these disorders involve mitochondrial dysfunction and increased oxidative stress. We utilized bioinformatics approaches to delineate the effects of murine Ube3a deletion on the expression of mitochondrial-related genes and pathways. For this, we generated an mRNA sequencing dataset from mouse embryonic fibroblasts (MEFs) in which both alleles of Ube3a gene were deleted and their wild-type controls. Since oxidative stress and mitochondrial dysregulation might not be exhibited in the resting baseline state, we also activated mitochondrial functioning in the cells of these two genotypes using TNFα application. Transcriptomes of the four groups of MEFs, Ube3a+/+ and Ube3a−/−, with or without the application of TNFα, were analyzed using various bioinformatics tools and machine learning approaches. Our results indicate that Ube3a deletion affects the gene expression profiles of mitochondrial-associated pathways. We further confirmed these results by analyzing other publicly available human transcriptome datasets of Angelman syndrome and 15q duplication syndrome. View Full-Text
Keywords: Angelman syndrome; mitochondria; oxidative stress; reactive oxygen species; gene expression; machine learning; bioinformatics Angelman syndrome; mitochondria; oxidative stress; reactive oxygen species; gene expression; machine learning; bioinformatics
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MDPI and ACS Style

Panov, J.; Simchi, L.; Feuermann, Y.; Kaphzan, H. Bioinformatics Analyses of the Transcriptome Reveal Ube3a-Dependent Effects on Mitochondrial-Related Pathways. Int. J. Mol. Sci. 2020, 21, 4156. https://doi.org/10.3390/ijms21114156

AMA Style

Panov J, Simchi L, Feuermann Y, Kaphzan H. Bioinformatics Analyses of the Transcriptome Reveal Ube3a-Dependent Effects on Mitochondrial-Related Pathways. International Journal of Molecular Sciences. 2020; 21(11):4156. https://doi.org/10.3390/ijms21114156

Chicago/Turabian Style

Panov, Julia, Lilach Simchi, Yonatan Feuermann, and Hanoch Kaphzan. 2020. "Bioinformatics Analyses of the Transcriptome Reveal Ube3a-Dependent Effects on Mitochondrial-Related Pathways" International Journal of Molecular Sciences 21, no. 11: 4156. https://doi.org/10.3390/ijms21114156

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