RNA-Seq Analysis Reveals Localization-Associated Alternative Splicing across 13 Cell Lines
RNA-Seq Analysis Reveals Localization-Associated Alternative Splicing across 13 Cell Lines
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DOI：
10.3390/genes11070820
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发表时间：
2019-11
期刊：
影响因子：
3.5
通讯作者：
Chao Zeng;Michiaki Hamada
中科院分区：
文献类型：
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作者：
Chao Zeng;Michiaki Hamada
选择性剪接是真核生物中普遍存在的一种现象，是个体基因生物多样性的调节机制。大多数研究都集中在选择性剪接对蛋白质合成的影响上。然而，选择性剪接对RNA亚细胞定位的转录组范围的影响很少被研究。通过分析从13个人类细胞系的亚细胞组分中获得的RNA-seq数据，我们确定了8720个在细胞质和细胞核之间转换的基因。与以前的报道一致，观察到内含子保留在核转录变体中富集。有趣的是，我们发现短的和结构稳定的内含子与核定位呈正相关。模体分析表明，14个RNA结合蛋白（RBP）倾向于优先与这些内含子结合。据我们所知，这是第一个转录组范围内的研究，分析和评估选择性剪接对RNA亚细胞定位的影响。我们的研究结果表明，选择性剪接在调节RNA亚细胞定位中起着很有前途的作用。
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.