Global analysis of pre-mRNA subcellular localization following splicing inhibition by spliceostatin A

Rei Yoshimoto, Daisuke Kaida, Masaaki Furuno, A. Maxwell Burroughs, Shohei Noma, Harukazu Suzuki, Yumi Kawamura, Yoshihide Hayashizaki, Akila Mayeda, Minoru Yoshida

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

Spliceostatin A (SSA) is a methyl ketal derivative of FR901464, a potent antitumor compound isolated from a culture broth of Pseudomonas sp. no. 2663. These compounds selectively bind to the essential spliceosome component SF3b, a subcomplex of the U2 snRNP, to inhibit pre-mRNA splicing. However, the mechanism of SSA-fs antitumor activity is unknown. It is noteworthy that SSA causes accumulation of a truncated form of the CDK inhibitor protein p27 translated from CDKN1B premRNA, which is involved in SSA-induced cell-cycle arrest. However, it is still unclear whether pre-mRNAs are uniformly exported from the nucleus following SSA treatment. We performed RNA-seq analysis on nuclear and cytoplasmic fractions of SSA-treated cells. Our statistical analyses showed that intron retention is the major consequence of SSA treatment, and a small number of intron-containing pre-mRNAs leak into the cytoplasm. Using a series of reporter plasmids to investigate the roles of intronic sequences in the pre-mRNA leakage, we showed that the strength of the 5′ splice site affects pre-mRNA leakage. Additionally, we found that the level of pre-mRNA leakage is related to transcript length. These results suggest that the strength of the 5′ splice site and the length of the transcripts are determinants of the pre-mRNA leakage induced by SF3b inhibitors.

Original languageEnglish
Pages (from-to)47-57
Number of pages11
JournalRNA
Volume23
Issue number1
DOIs
Publication statusPublished - 01-2017

All Science Journal Classification (ASJC) codes

  • Molecular Biology

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    Yoshimoto, R., Kaida, D., Furuno, M., Burroughs, A. M., Noma, S., Suzuki, H., Kawamura, Y., Hayashizaki, Y., Mayeda, A., & Yoshida, M. (2017). Global analysis of pre-mRNA subcellular localization following splicing inhibition by spliceostatin A. RNA, 23(1), 47-57. https://doi.org/10.1261/rna.058065.116