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
N1 - Funding Information:
This work was supported in part by Grants-in-Aid for Scientific Research (S) from the Ministry of Education, Culture, Sports, Science and Technology of Japan (M.Y.), the Japan Science and Technology Corporation, the CREST Research Project (M.Y.), and the Hori Information Science Promotion Foundation (R.Y.). We also thank Dr. Yuko Kimura and Dr. Shinichi Nakagawa for discussions and careful reading of the manuscript.
Publisher Copyright:
© 2016 Yoshimoto et al.
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.
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U2 - 10.1261/rna.058065.116
DO - 10.1261/rna.058065.116
M3 - Article
C2 - 27754875
AN - SCOPUS:85006986581
SN - 1355-8382
VL - 23
SP - 47
EP - 57
JO - RNA
JF - RNA
IS - 1
ER -