RT Journal Article
SR Electronic
T1 RNA-Seq Analysis Reveals Localization-Associated Alternative Splicing across 13 Cell Lines
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 860783
DO 10.1101/860783
A1 Chao Zeng
A1 Michiaki Hamada
YR 2020
UL http://biorxiv.org/content/early/2020/07/18/860783.abstract
AB 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 StatementThe authors have declared no competing interest.