RNA-seq analysis reveals localization-associated alternative splicing across 13 cell lines

Chao Zeng*, Michiaki Hamada

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

8 Citations (Scopus)


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.

Original languageEnglish
Article number820
Pages (from-to)1-14
Number of pages14
Issue number7
Publication statusPublished - 2020 Jul


  • Alternative splicing
  • Retained intron
  • Subcellular localization

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


Dive into the research topics of 'RNA-seq analysis reveals localization-associated alternative splicing across 13 cell lines'. Together they form a unique fingerprint.

Cite this