The impact of alternative splicing on RNA subcellular localization

Chao Zeng, Michiaki Hamada

Research output: Contribution to journalArticlepeer-review


Background: Alternative splicing, a ubiquitous phenomenon in eukaryotes, provides 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 influence of alternative splicing on the RNA subcellular localization has rarely been studied. Results: By analyzing RNA-seq data from subcellular fractions across thirteen human cell lines, we observed that splicing is apparent to promote cytoplasmic localization. We also discovered that intron retention is preferred by transcripts localized in the nucleus. Short and structurally stable introns show a positive correlation with nuclear localization. Such introns are predicted to be preferentially bound by MBNL1, an RNA-binding protein that contains two nuclear localization signals. Conclusions: Our findings reveal that alternative splicing plays an important role in regulating RNA subcellular localization. This study provides valuable clues for understanding the biological mechanisms of alternative splicing.

Original languageEnglish
JournalUnknown Journal
Publication statusPublished - 2019 Nov 30


  • Alternative splicing
  • Intron retention
  • Localization
  • RNA-binding protein

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • Immunology and Microbiology(all)
  • Neuroscience(all)
  • Pharmacology, Toxicology and Pharmaceutics(all)

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