Email this article IDENTIFICATION OF SIGNIFICANT RNA-BINDING PROTEINS IN THE PROCESS OF CD44 SPLICING USING THE BOOSTED BETA REGRESSION ALGORITHM
- Authors: Novosad V.O.1,2
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Affiliations:
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics,
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences
- Issue: Vol 510, No 1 (2023)
- Pages: 316-321
- Section: Articles
- URL: https://journals.rcsi.science/2686-7389/article/view/135704
- DOI: https://doi.org/10.31857/S2686738922601023
- EDN: https://elibrary.ru/QFUIKM
- ID: 135704
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Abstract
The expression of RNA-binding proteins and their interaction with the spliced pre-mRNA are the key factors in determining the final isoform profile. Transmembrane protein CD44 is involved in differentiation, invasion, motility, growth and survival of tumor cells, and is also a commonly accepted marker of cancer stem cells and epithelial-mesenchymal transition. However, the functions of the isoforms of this protein differ significantly. In this paper, we developed a method based on the boosted beta regression algorithm for identification of the significant RNA-binding proteins in the splicing process by modeling the isoform ratio. The application of this method to the analysis of CD44 splicing in colorectal cancer cells revealed 20 significant RNA-binding proteins. Many of them were previously shown as EMT regulators, but for the first time presented as potential CD44 splicing factors.
Keywords
About the authors
V. O. Novosad
Faculty of Biology and Biotechnology, National Research University Higher School of Economics, ; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences
Author for correspondence.
Email: vnovosad@hse.ru
Russian Federation, Moscow; Russian Federation, Moscow
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