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Open AccessArticle

RNA-Seq Analysis Reveals Localization-Associated Alternative Splicing across 13 Cell Lines

by 1,2,* and 1,2,3,4,*
1
AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo 169-8555, Japan
2
Faculty of Science and Engineering, Waseda University, Tokyo 169-8555, Japan
3
Institute for Medical-oriented Structural Biology, Waseda University, Tokyo 162-8480, Japan
4
Graduate School of Medicine, Nippon Medical School, Tokyo 113-8602, Japan
*
Authors to whom correspondence should be addressed.
Genes 2020, 11(7), 820; https://doi.org/10.3390/genes11070820
Received: 19 June 2020 / Revised: 15 July 2020 / Accepted: 17 July 2020 / Published: 18 July 2020
(This article belongs to the Special Issue Splicing: The New Frontier in Therapeutics)
Alternative splicing, a ubiquitous phenomenon in eukaryotes, is a regulatory mechanism for the biological diversity of individual genes. Most studies have focused on the effects of alternative splicing for protein synthesis. However, the transcriptome-wide influence of alternative splicing on RNA subcellular localization has rarely been studied. By analyzing RNA-seq data obtained from subcellular fractions across 13 human cell lines, we identified 8720 switching genes between the cytoplasm and the nucleus. Consistent with previous reports, intron retention was observed to be enriched in the nuclear transcript variants. Interestingly, we found that short and structurally stable introns were positively correlated with nuclear localization. Motif analysis reveals that fourteen RNA-binding protein (RBPs) are prone to be preferentially bound with such introns. To our knowledge, this is the first transcriptome-wide study to analyze and evaluate the effect of alternative splicing on RNA subcellular localization. Our findings reveal that alternative splicing plays a promising role in regulating RNA subcellular localization. View Full-Text
Keywords: alternative splicing; subcellular localization; retained intron alternative splicing; subcellular localization; retained intron
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MDPI and ACS Style

Zeng, C.; Hamada, M. RNA-Seq Analysis Reveals Localization-Associated Alternative Splicing across 13 Cell Lines. Genes 2020, 11, 820. https://doi.org/10.3390/genes11070820

AMA Style

Zeng C, Hamada M. RNA-Seq Analysis Reveals Localization-Associated Alternative Splicing across 13 Cell Lines. Genes. 2020; 11(7):820. https://doi.org/10.3390/genes11070820

Chicago/Turabian Style

Zeng, Chao; Hamada, Michiaki. 2020. "RNA-Seq Analysis Reveals Localization-Associated Alternative Splicing across 13 Cell Lines" Genes 11, no. 7: 820. https://doi.org/10.3390/genes11070820

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