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

View ORCID ProfileChao Zeng, View ORCID ProfileMichiaki Hamada
doi: https://doi.org/10.1101/860783
Chao Zeng
1AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, 169-8555, Japan
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Michiaki Hamada
2Faculty of Science and Engineering, Waseda University, Tokyo, 169-8555, Japan
1AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, 169-8555, Japan
3Institute for Medical-oriented Structural Biology, Waseda University, Tokyo, 162-8480, Japan
4Graduate School of Medicine, Nippon Medical School, Tokyo, 113-8602, Japan
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ABSTRACT

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.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵* CZ (zeng.chao{at}aist.go.jp) or MH (mhamada{at}waseda.jp)

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted July 18, 2020.
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RNA-Seq Analysis Reveals Localization-Associated Alternative Splicing across 13 Cell Lines
Chao Zeng, Michiaki Hamada
bioRxiv 860783; doi: https://doi.org/10.1101/860783
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RNA-Seq Analysis Reveals Localization-Associated Alternative Splicing across 13 Cell Lines
Chao Zeng, Michiaki Hamada
bioRxiv 860783; doi: https://doi.org/10.1101/860783

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