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

13 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

Fingerprint

RNA Precursors
RNA Splice Sites
Introns
U2 Small Nuclear Ribonucleoproteins
Cyclin-Dependent Kinase Inhibitor p27
Spliceosomes
Pseudomonas
Cell Cycle Checkpoints
spliceostatin A
Cytoplasm
Plasmids
RNA
Proteins

All Science Journal Classification (ASJC) codes

  • Molecular Biology

Cite this

Yoshimoto, R., Kaida, D., Furuno, M., Burroughs, A. M., Noma, S., Suzuki, H., ... 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
Yoshimoto, Rei ; Kaida, Daisuke ; Furuno, Masaaki ; Burroughs, A. Maxwell ; Noma, Shohei ; Suzuki, Harukazu ; Kawamura, Yumi ; Hayashizaki, Yoshihide ; Mayeda, Akila ; Yoshida, Minoru. / Global analysis of pre-mRNA subcellular localization following splicing inhibition by spliceostatin A. In: RNA. 2017 ; Vol. 23, No. 1. pp. 47-57.
@article{92d864c66a6f491aaa7a3d42486c718f,
title = "Global analysis of pre-mRNA subcellular localization following splicing inhibition by spliceostatin A",
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.",
author = "Rei Yoshimoto and Daisuke Kaida and Masaaki Furuno and Burroughs, {A. Maxwell} and Shohei Noma and Harukazu Suzuki and Yumi Kawamura and Yoshihide Hayashizaki and Akila Mayeda and Minoru Yoshida",
year = "2017",
month = "1",
doi = "10.1261/rna.058065.116",
language = "English",
volume = "23",
pages = "47--57",
journal = "RNA",
issn = "1355-8382",
publisher = "Cold Spring Harbor Laboratory Press",
number = "1",

}

Yoshimoto, R, Kaida, D, Furuno, M, Burroughs, AM, 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, vol. 23, no. 1, pp. 47-57. https://doi.org/10.1261/rna.058065.116

Global analysis of pre-mRNA subcellular localization following splicing inhibition by spliceostatin A. / Yoshimoto, Rei; Kaida, Daisuke; Furuno, Masaaki; Burroughs, A. Maxwell; Noma, Shohei; Suzuki, Harukazu; Kawamura, Yumi; Hayashizaki, Yoshihide; Mayeda, Akila; Yoshida, Minoru.

In: RNA, Vol. 23, No. 1, 01.2017, p. 47-57.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Global analysis of pre-mRNA subcellular localization following splicing inhibition by spliceostatin A

AU - Yoshimoto, Rei

AU - Kaida, Daisuke

AU - Furuno, Masaaki

AU - Burroughs, A. Maxwell

AU - Noma, Shohei

AU - Suzuki, Harukazu

AU - Kawamura, Yumi

AU - Hayashizaki, Yoshihide

AU - Mayeda, Akila

AU - Yoshida, Minoru

PY - 2017/1

Y1 - 2017/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85006986581&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85006986581&partnerID=8YFLogxK

U2 - 10.1261/rna.058065.116

DO - 10.1261/rna.058065.116

M3 - Article

C2 - 27754875

AN - SCOPUS:85006986581

VL - 23

SP - 47

EP - 57

JO - RNA

JF - RNA

SN - 1355-8382

IS - 1

ER -