The Anti-tumor Drug E7107 Reveals an Essential Role for SF3b in Remodeling U2 SnRNP to Expose the Branch Point-binding Region

Overview

Journal Genes Dev

Specialty Molecular Biology

Date 2011 Mar 3

PMID 21363962

Citations 108

Authors

Eric G Folco

Kaitlyn E Coil

Robin Reed

Affiliations

Soon will be listed here.

Abstract

Duplex formation between the branch point-binding region (BBR) of U2 snRNA and the branch point sequence (BPS) in the intron is essential for splicing. Both the BBR and BPS interact with the U2 small nuclear ribonucleoprotein (snRNP)-associated SF3b complex, which is the target of the anti-tumor drug E7107. We show that E7107 blocks spliceosome assembly by preventing tight binding of U2 snRNP to pre-mRNA. E7107 has no apparent effect on U2 snRNP integrity. Instead, E7107 abolishes an ATP-dependent conformational change in U2 snRNP that exposes the BBR. We conclude that SF3b is required for this remodeling, which exposes the BBR for tight U2 snRNP binding to pre-mRNA.

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References

Newnham C, Query C . The ATP requirement for U2 snRNP addition is linked to the pre-mRNA region 5' to the branch site. RNA. 2001; 7(9):1298-309. PMC: 1370173. DOI: 10.1017/s1355838201010561. View

Das R, Dufu K, Romney B, Feldt M, Elenko M, Reed R . Functional coupling of RNAP II transcription to spliceosome assembly. Genes Dev. 2006; 20(9):1100-9. PMC: 1472470. DOI: 10.1101/gad.1397406. View

Stoilov P, Lin C, Damoiseaux R, Nikolic J, Black D . A high-throughput screening strategy identifies cardiotonic steroids as alternative splicing modulators. Proc Natl Acad Sci U S A. 2008; 105(32):11218-23. PMC: 2516208. DOI: 10.1073/pnas.0801661105. View

Smith D, Query C, Konarska M . "Nought may endure but mutability": spliceosome dynamics and the regulation of splicing. Mol Cell. 2008; 30(6):657-66. PMC: 2610350. DOI: 10.1016/j.molcel.2008.04.013. View

REED R . Initial splice-site recognition and pairing during pre-mRNA splicing. Curr Opin Genet Dev. 1996; 6(2):215-20. DOI: 10.1016/s0959-437x(96)80053-0. View

Roybal G, Jurica M . Spliceostatin A inhibits spliceosome assembly subsequent to prespliceosome formation. Nucleic Acids Res. 2010; 38(19):6664-72. PMC: 2965229. DOI: 10.1093/nar/gkq494. View

OBrien K, Matlin A, Lowell A, Moore M . The biflavonoid isoginkgetin is a general inhibitor of Pre-mRNA splicing. J Biol Chem. 2008; 283(48):33147-54. PMC: 2586251. DOI: 10.1074/jbc.M805556200. View

Muraki M, Ohkawara B, Hosoya T, Onogi H, Koizumi J, Koizumi T . Manipulation of alternative splicing by a newly developed inhibitor of Clks. J Biol Chem. 2004; 279(23):24246-54. DOI: 10.1074/jbc.M314298200. View

Dybkov O, Will C, Deckert J, Behzadnia N, Hartmuth K, Luhrmann R . U2 snRNA-protein contacts in purified human 17S U2 snRNPs and in spliceosomal A and B complexes. Mol Cell Biol. 2006; 26(7):2803-16. PMC: 1430325. DOI: 10.1128/MCB.26.7.2803-2816.2006. View

10.

Das R, REED R . Resolution of the mammalian E complex and the ATP-dependent spliceosomal complexes on native agarose mini-gels. RNA. 1999; 5(11):1504-8. PMC: 1369872. DOI: 10.1017/s1355838299991501. View

11.

Will C, Schneider C, MacMillan A, Katopodis N, Neubauer G, Wilm M . A novel U2 and U11/U12 snRNP protein that associates with the pre-mRNA branch site. EMBO J. 2001; 20(16):4536-46. PMC: 125580. DOI: 10.1093/emboj/20.16.4536. View

12.

Donmez G, Hartmuth K, Kastner B, Will C, Luhrmann R . The 5' end of U2 snRNA is in close proximity to U1 and functional sites of the pre-mRNA in early spliceosomal complexes. Mol Cell. 2007; 25(3):399-411. DOI: 10.1016/j.molcel.2006.12.019. View

13.

Konarska M, Query C . Insights into the mechanisms of splicing: more lessons from the ribosome. Genes Dev. 2005; 19(19):2255-60. DOI: 10.1101/gad.1363105. View

14.

Kuhn A, van Santen M, Schwienhorst A, Urlaub H, Luhrmann R . Stalling of spliceosome assembly at distinct stages by small-molecule inhibitors of protein acetylation and deacetylation. RNA. 2008; 15(1):153-75. PMC: 2612777. DOI: 10.1261/rna.1332609. View

15.

Wahl M, Will C, Luhrmann R . The spliceosome: design principles of a dynamic RNP machine. Cell. 2009; 136(4):701-18. DOI: 10.1016/j.cell.2009.02.009. View

16.

Sumanasekera C, Watt D, Stamm S . Substances that can change alternative splice-site selection. Biochem Soc Trans. 2008; 36(Pt 3):483-90. DOI: 10.1042/BST0360483. View

17.

Kotake Y, Sagane K, Owa T, Mimori-Kiyosue Y, Shimizu H, Uesugi M . Splicing factor SF3b as a target of the antitumor natural product pladienolide. Nat Chem Biol. 2007; 3(9):570-5. DOI: 10.1038/nchembio.2007.16. View

18.

Ruby S, Chang T, Abelson J . Four yeast spliceosomal proteins (PRP5, PRP9, PRP11, and PRP21) interact to promote U2 snRNP binding to pre-mRNA. Genes Dev. 1993; 7(10):1909-25. DOI: 10.1101/gad.7.10.1909. View

19.

Kaida D, Motoyoshi H, Tashiro E, Nojima T, Hagiwara M, Ishigami K . Spliceostatin A targets SF3b and inhibits both splicing and nuclear retention of pre-mRNA. Nat Chem Biol. 2007; 3(9):576-83. DOI: 10.1038/nchembio.2007.18. View

20.

Younis I, Berg M, Kaida D, Dittmar K, Wang C, Dreyfuss G . Rapid-response splicing reporter screens identify differential regulators of constitutive and alternative splicing. Mol Cell Biol. 2010; 30(7):1718-28. PMC: 2838070. DOI: 10.1128/MCB.01301-09. View