A Quantitative High-Throughput In Vitro Splicing Assay Identifies Inhibitors of Spliceosome Catalysis

REFERENCES

• Achsel T, Ahrens K, Brahms H, Teigelkamp S, Luhrmann R. 1998. The human U5-220kD protein (hPrp8) forms a stable RNA-free complex with several U5-specific proteins, including an RNA unwindase, a homologue of ribosomal elongation factor EF-2, and a novel WD-40 protein. Mol. Cell. Biol. 18:6756–6766.
   PubMedGoogle Scholar
• Albert BJ, et al. 2009. Meayamycin inhibits pre-messenger RNA splicing and exhibits picomolar activity against multidrug-resistant cells. Mol. Cancer Ther. 8:2308–2318.
   PubMed Web of Science ®Google Scholar
• Arenas JE, Abelson JN. 1997. Prp43: an RNA helicase-like factor involved in spliceosome disassembly. Proc. Natl. Acad. Sci. U. S. A. 94:11798–11802.
   PubMed Web of Science ®Google Scholar
• Ballut L, et al. 2005. The exon junction core complex is locked onto RNA by inhibition of eIF4AIII ATPase activity. Nat. Struct. Mol. Biol. 12:861–869.
   PubMed Web of Science ®Google Scholar
• Bessonov S, et al. 2010. Characterization of purified human Bact spliceosomal complexes reveals compositional and morphological changes during spliceosome activation and first step catalysis. RNA 16:2384–2403.
   PubMedGoogle Scholar
• Bessonov S, Anokhina M, Will CL, Urlaub H, Luhrmann R. 2008. Isolation of an active step I spliceosome and composition of its RNP core. Nature 452:846–850.
   PubMed Web of Science ®Google Scholar
• Blencowe BJ. 2006. Alternative splicing: new insights from global analyses. Cell 126:37–47.
   PubMed Web of Science ®Google Scholar
• Bottner CA, Schmidt H, Vogel S, Michele M, Kaufer NF. 2005. Multiple genetic and biochemical interactions of Brr2, Prp8, Prp31, Prp1 and Prp4 kinase suggest a function in the control of the activation of spliceosomes in Schizosaccharomyces pombe. Curr. Genet. 48:151–161.
   PubMedGoogle Scholar
• Brezak MC, et al. 2005. Inhibition of human tumor cell growth in vivo by an orally bioavailable inhibitor of CDC25 phosphatases. Mol. Cancer Ther. 4:1378–1387.
   PubMed Web of Science ®Google Scholar
• Brisson M, et al. 2004. Discovery and characterization of novel small molecule inhibitors of human Cdc25B dual specificity phosphatase. Mol. Pharmacol. 66:824–833.
   PubMed Web of Science ®Google Scholar
• Chan CC, et al. 2004. eIF4A3 is a novel component of the exon junction complex. RNA 10:200–209.
   PubMed Web of Science ®Google Scholar
• Chan SP, Kao DI, Tsai WY, Cheng SC. 2003. The Prp19p-associated complex in spliceosome activation. Science 302:279–282.
   PubMed Web of Science ®Google Scholar
• Contour-Galcera MO, Sidhu A, Prevost G, Bigg D, Ducommun B. 2007. What's new on CDC25 phosphatase inhibitors. Pharmacol. Ther. 115:1–12.
   PubMed Web of Science ®Google Scholar
• Cooper TA, Wan L, Dreyfuss G. 2009. RNA and disease. Cell 136:777–793.
   PubMed Web of Science ®Google Scholar
• Dreyfuss G, Kim VN, Kataoka N. 2002. Messenger-RNA-binding proteins and the messages they carry. Nat. Rev. Mol. Cell Biol. 3:195–205.
   PubMed Web of Science ®Google Scholar
• Fukuhara T, et al. 2006. Utilization of host SR protein kinases and RNA-splicing machinery during viral replication. Proc. Natl. Acad. Sci. U. S. A. 103:11329–11333.
   PubMed Web of Science ®Google Scholar
• Galisson F, Legrain P. 1993. The biochemical defects of prp4-1 and prp6-1 yeast splicing mutants reveal that the PRP6 protein is required for the accumulation of the [U4/U6.U5] tri-snRNP. Nucleic Acids Res. 21:1555–1562.
   PubMedGoogle Scholar
• Hagiwara M. 2005. Alternative splicing: a new drug target of the post-genome era. Biochim. Biophys. Acta 1754:324–331.
   PubMedGoogle Scholar
• Horowitz DS, Lee EJ, Mabon SA, Misteli T. 2002. A cyclophilin functions in pre-mRNA splicing. EMBO J. 21:470–480.
   PubMed Web of Science ®Google Scholar
• Jurica MS, Moore MJ. 2003. Pre-mRNA splicing: awash in a sea of proteins. Mol. Cell 12:5–14.
   PubMed Web of Science ®Google Scholar
• Kaida D, et al. 2007. Spliceostatin A targets SF3b and inhibits both splicing and nuclear retention of pre-mRNA. Nat. Chem. Biol. 3:576–583.
   PubMed Web of Science ®Google Scholar
• Kar S, Wang M, Yao W, Michejda CJ, Carr BI. 2006. PM-20, a novel inhibitor of Cdc25A, induces extracellular signal-regulated kinase 1/2 phosphorylation and inhibits hepatocellular carcinoma growth in vitro and in vivo. Mol. Cancer Ther. 5:1511–1519.
   PubMed Web of Science ®Google Scholar
• Kataoka N, Dreyfuss G. 2008. Preparation of efficient splicing extracts from whole cells, nuclei, and cytoplasmic fractions. Methods Mol. Biol. 488:357–365.
   PubMedGoogle Scholar
• Kataoka N, Dreyfuss G. 2004. A simple whole cell lysate system for in vitro splicing reveals a stepwise assembly of the exon-exon junction complex. J. Biol. Chem. 279:7009–7013.
   PubMedGoogle Scholar
• Kataoka N, et al. 2000. Pre-mRNA splicing imprints mRNA in the nucleus with a novel RNA-binding protein that persists in the cytoplasm. Mol. Cell 6:673–682.
   PubMedGoogle Scholar
• Kim SH, Lin RJ. 1996. Spliceosome activation by PRP2 ATPase prior to the first transesterification reaction of pre-mRNA splicing. Mol. Cell. Biol. 16:6810–6819.
   PubMed Web of Science ®Google Scholar
• Kim VN, et al. 2001. The Y14 protein communicates to the cytoplasm the position of exon-exon junctions. EMBO J. 20:2062–2068.
   PubMed Web of Science ®Google Scholar
• Konarska MM, Sharp PA. 1986. Electrophoretic separation of complexes involved in the splicing of precursors to mRNAs. Cell 46:845–855.
   PubMed Web of Science ®Google Scholar
• Kotake Y, et al. 2007. Splicing factor SF3b as a target of the antitumor natural product pladienolide. Nat. Chem. Biol. 3:570–575.
   PubMed Web of Science ®Google Scholar
• Krawczak M, Reiss J, Cooper DN. 1992. The mutational spectrum of single base-pair substitutions in mRNA splice junctions of human genes: causes and consequences. Hum. Genet. 90:41–54.
   PubMed Web of Science ®Google Scholar
• Kuhn AN, van Santen MA, Schwienhorst A, Urlaub H, Luhrmann R. 2009. Stalling of spliceosome assembly at distinct stages by small-molecule inhibitors of protein acetylation and deacetylation. RNA 15:153–175.
   PubMed Web of Science ®Google Scholar
• Lazo JS, et al. 2001. Discovery and biological evaluation of a new family of potent inhibitors of the dual specificity protein phosphatase Cdc25. J. Med. Chem. 44:4042–4049.
   PubMed Web of Science ®Google Scholar
• Lazo JS, et al. 2002. Identification of a potent and selective pharmacophore for Cdc25 dual specificity phosphatase inhibitors. Mol. Pharmacol. 61:720–728.
   PubMed Web of Science ®Google Scholar
• LE Hir H, Izaurralde E, Maquat LE, Moore MJ. 2000. The spliceosome deposits multiple proteins 20–24 nucleotides upstream of mRNA exon-exon junctions. EMBO J. 19:6860–6869.
   PubMed Web of Science ®Google Scholar
• Le Hir H, Nott A, Moore MJ. 2003. How introns influence and enhance eukaryotic gene expression. Trends Biochem. Sci. 28:215–220.
   PubMed Web of Science ®Google Scholar
• Li YM, Casida JE. 1992. Cantharidin-binding protein: identification as protein phosphatase 2A. Proc. Natl. Acad. Sci. U. S. A. 89:11867–11870.
   PubMed Web of Science ®Google Scholar
• Lutzelberger M, et al. 2010. The N terminus of Prp1 (Prp6/U5-102 K) is essential for spliceosome activation in vivo. Nucleic Acids Res. 38:1610–1622.
   PubMedGoogle Scholar
• Makarov EM, et al. 2002. Small nuclear ribonucleoprotein remodeling during catalytic activation of the spliceosome. Science 298:2205–2208.
   PubMed Web of Science ®Google Scholar
• Makarova OV, Makarov EM, Liu S, Vornlocher HP, Luhrmann R. 2002. Protein 61K, encoded by a gene (PRPF31) linked to autosomal dominant retinitis pigmentosa, is required for U4/U6*U5 tri-snRNP formation and pre-mRNA splicing. EMBO J. 21:1148–1157.
   PubMed Web of Science ®Google Scholar
• Maquat LE. 2004. Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics. Nat. Rev. Mol. Cell Biol. 5:89–99.
   PubMed Web of Science ®Google Scholar
• Mermoud JE, Cohen P, Lamond AI. 1992. Ser/Thr-specific protein phosphatases are required for both catalytic steps of pre-mRNA splicing. Nucleic Acids Res. 20:5263–5269.
   PubMed Web of Science ®Google Scholar
• Muraki M, et al. 2004. Manipulation of alternative splicing by a newly developed inhibitor of Clks. J. Biol. Chem. 279:24246–24254.
   PubMed Web of Science ®Google Scholar
• Nagradova N. 2007. Enzymes catalyzing protein folding and their cellular functions. Curr. Protein Pept. Sci. 8:273–282.
   PubMed Web of Science ®Google Scholar
• Nakajima H, et al. 1996. New antitumor substances, FR901463, FR901464 and FR901465. II. Activities against experimental tumors in mice and mechanism of action. J. Antibiot. ( Tokyo) 49:1204–1211.
   PubMed Web of Science ®Google Scholar
• O'Brien K, Matlin AJ, Lowell AM, Moore MJ. 2008. The biflavonoid isoginkgetin is a general inhibitor of Pre-mRNA splicing. J. Biol. Chem. 283:33147–33154.
   PubMed Web of Science ®Google Scholar
• Pilch B, et al. 2001. Specific inhibition of serine- and arginine-rich splicing factors phosphorylation, spliceosome assembly, and splicing by the antitumor drug NB-506. Cancer Res. 61:6876–6884.
   PubMed Web of Science ®Google Scholar
• Schaffert N, Hossbach M, Heintzmann R, Achsel T, Luhrmann R. 2004. RNAi knockdown of hPrp31 leads to an accumulation of U4/U6 di-snRNPs in Cajal bodies. EMBO J. 23:3000–3009.
   PubMed Web of Science ®Google Scholar
• Schmittgen TD, Ju JF, Danenberg KD, Danenberg PV. 2003. Inhibition of pre-mRNA splicing by cisplatin and platinum analogs. Int. J. Oncol. 23:785–789.
   PubMedGoogle Scholar
• Schneider M, et al. 2010. Human PRP4 kinase is required for stable tri-snRNP association during spliceosomal B complex formation. Nat. Struct. Mol. Biol. 17:216–221.
   PubMed Web of Science ®Google Scholar
• Shi Y, Reddy B, Manley JL. 2006. PP1/PP2A phosphatases are required for the second step of Pre-mRNA splicing and target specific snRNP proteins. Mol. Cell 23:819–829.
   PubMed Web of Science ®Google Scholar
• Shibuya T, Tange TO, Sonenberg N, Moore MJ. 2004. eIF4AIII binds spliced mRNA in the exon junction complex and is essential for nonsense-mediated decay. Nat. Struct. Mol. Biol. 11:346–351.
   PubMed Web of Science ®Google Scholar
• Soret J, et al. 2005. Selective modification of alternative splicing by indole derivatives that target serine-arginine-rich protein splicing factors. Proc. Natl. Acad. Sci. U. S. A. 102:8764–8769.
   PubMed Web of Science ®Google Scholar
• Staley JP, Guthrie C. 1998. Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell 92:315–326.
   PubMed Web of Science ®Google Scholar
• Stoilov P, Lin CH, Damoiseaux R, Nikolic J, Black DL. 2008. A high-throughput screening strategy identifies cardiotonic steroids as alternative splicing modulators. Proc. Natl. Acad. Sci. U. S. A. 105:11218–11223.
   PubMedGoogle Scholar
• Swanson MS, Dreyfuss G. 1988. RNA binding specificity of hnRNP proteins: a subset bind to the 3′ end of introns. EMBO J. 7:3519–3529.
   PubMed Web of Science ®Google Scholar
• Tamura K, et al. 2000. Cdc25 inhibition and cell cycle arrest by a synthetic thioalkyl vitamin K analogue. Cancer Res. 60:1317–1325.
   PubMed Web of Science ®Google Scholar
• Tazi J, et al. 2005. Selective inhibition of topoisomerase I and various steps of spliceosome assembly by diospyrin derivatives. Mol. Pharmacol. 67:1186–1194.
   PubMed Web of Science ®Google Scholar
• Tazi J, Bakkour N, Stamm S. 2009. Alternative splicing and disease. Biochim. Biophys. Acta 1792:14–26.
   PubMed Web of Science ®Google Scholar
• Tazi J, Durand S, Jeanteur P. 2005. The spliceosome: a novel multi-faceted target for therapy. Trends Biochem. Sci. 30:469–478.
   PubMed Web of Science ®Google Scholar
• Wahl MC, Will CL, Luhrmann R. 2009. The spliceosome: design principles of a dynamic RNP machine. Cell 136:701–718.
   PubMed Web of Science ®Google Scholar
• Wan L, et al. 2005. The survival of motor neurons protein determines the capacity for snRNP assembly: biochemical deficiency in spinal muscular atrophy. Mol. Cell. Biol. 25:5543–5551.
   PubMed Web of Science ®Google Scholar
• Wan L, Ottinger E, Cho S, Dreyfuss G. 2008. Inactivation of the SMN complex by oxidative stress. Mol. Cell 31:244–254.
   PubMed Web of Science ®Google Scholar
• Wang ET, et al. 2008. Alternative isoform regulation in human tissue transcriptomes. Nature 456:470–476.
   PubMed Web of Science ®Google Scholar
• Will CL, Luhrmann R. 2010. Spliceosome structure and function. Cold Spring Harb. Perspect. Biol. 3:a003707
   Google Scholar
• Younis I, et al. 2010. Rapid-response splicing reporter screens identify differential regulators of constitutive and alternative splicing. Mol. Cell. Biol. 30:1718–1728.
   PubMedGoogle Scholar