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Preparation of Efficient Splicing Extracts From Whole Cells, Nuclei, and Cytoplasmic Fractions

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Book cover RNA-Protein Interaction Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 488))

Summary

Pre-mRNA (messenger RNA) splicing is an essential step for gene expression in higher eukaryotes. Splicing reactions have been well studied in vitro using extracts prepared from cultured cells. We describe protocols for the preparation of splicing-competent extracts from whole cells, nuclei, and cytoplasmic fractions. The nuclear and whole-cell extracts are fully active in splicing, while S100 extracts are able to support splicing only when SR (Serine/Arginine-rich) proteins are supplied. The simple method described here to prepare splicing active extracts from whole cells is particularly useful in studying pre-mRNA splicing in many different cell types.

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References

  1. Reed, R. (2000) Mechanisms of fidelity in pre-mRNA splicing. Curr. Opin. Cell Biol. 12, 340–345.

    Article  CAS  PubMed  Google Scholar 

  2. Hastings, M. L., and Krainer, A. R. (2001) Pre-mRNA splicing in the new millennium. Curr. Opin. Cell Biol. 13, 302–309.

    Article  CAS  PubMed  Google Scholar 

  3. Jurica, M. S., and Moore, M. J. (2003) Pre-mRNA splicing: awash in a sea of proteins. Mol. Cell. 12, 5–14.

    Article  CAS  PubMed  Google Scholar 

  4. Rio, D. C. (1988) Accurate and efficient pre-mRNA splicing in Drosophila cell-free extracts. Proc. Natl. Acad. Sci. U. S. A. 85, 2904–2908.

    Article  CAS  PubMed  Google Scholar 

  5. Lin, R. J., Newman, A. J., Cheng, S. C., and Abelson, J. (1985) Yeast mRNA splicing in vitro. J. Biol. Chem. 260, 14780–14792.

    CAS  PubMed  Google Scholar 

  6. Dignam, J. D., Lebovitz, R. M., and Roeder, R. G. (1983) Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 11, 1475–1489.

    Article  CAS  PubMed  Google Scholar 

  7. Kataoka, N., and 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.

    Article  CAS  PubMed  Google Scholar 

  8. Krainer, A. R., Conway, G. C., and Kozak, D. (1990) The essential pre-mRNA splicing factor SF2 influences 5′ splice site selection by activating proximal sites. Cell 62, 35–42.

    Article  CAS  PubMed  Google Scholar 

  9. Fu, X. D. (1995) The superfamily of arginine/serine-rich splicing factors. RNA 1, 663–680.

    CAS  PubMed  Google Scholar 

  10. Graveley, B. R. (2000) Sorting out the complexity of SR protein functions. RNA 6, 1197–1211.

    Article  CAS  PubMed  Google Scholar 

  11. Mayeda, A., and Krainer, A. R. (1992) Regulation of alternative pre-mRNA splicing by hnRNP A1 and splicing factor SF2. Cell 68, 365–375.

    Article  CAS  PubMed  Google Scholar 

  12. Mayeda, A., Screaton, G. R., Chandler, S. D., Fu, X. D., and Krainer, A. R. (1999) Substrate specificities of SR proteins in constitutive splicing are determined by their RNA recognition motifs and composite pre-mRNA exonic elements. Mol. Cell. Biol. 19, 1853–1863.

    CAS  PubMed  Google Scholar 

  13. Tarn, W. Y., and Steitz, J. A. (1996) A novel spliceosome containing U11, U12, and U5 snRNPs excises a minor class (AT-AC) intron in vitro. Cell 84, 801–811.

    Article  CAS  PubMed  Google Scholar 

  14. Wu, Q., and Krainer, A. R. (1996) U1-mediated exon definition interactions between AT-AC and GT-AG introns. Science 274, 1005–1008.

    Article  CAS  PubMed  Google Scholar 

  15. Pellizzoni, L., Kataoka, N., Charroux, B., and Dreyfuss, G. (1998) A novel function for SMN, the spinal muscular atrophy disease gene product, in pre-mRNA splicing. Cell 95, 615–624.

    Article  CAS  PubMed  Google Scholar 

  16. Kataoka, N., Yong, J., Kim, V. 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.

    Article  CAS  PubMed  Google Scholar 

  17. Kataoka, N., Diem, M. D., Kim, V. N., Yong, J., and Dreyfuss, G. (2001) Magoh, a human homolog of Drosophila mago nashi protein, is a component of splicing-dependent exon-exon junction complex. EMBO J. 20, 6424–6433.

    Article  CAS  PubMed  Google Scholar 

  18. Kim, V. N., Kataoka, N., and Dreyfuss, G. (2001) Role of the nonsense-mediated decay factor hUpf3 in the splicing-dependent exon-exon junction complex. Science 293, 1832–1836.

    Article  CAS  PubMed  Google Scholar 

  19. Chan, C. C., Dostie, J., Diem, M. D., et al. (2004) eIF4A3 is a novel component of the exon junction complex. RNA 10, 200–209.

    Article  CAS  PubMed  Google Scholar 

  20. Sakamoto, H., Ohno, M., Yasuda, K., Mizumoto, K., and Shimura, Y. (1987) In vitro splicing of a chicken delta-crystallin pre-mRNA in a mammalian nuclear extract. J. Biochem. (Tokyo) 102, 1289–1301.

    CAS  Google Scholar 

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© 2008 Humana Press, a part of Springer Science + Business Media, LLC

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Kataoka, N., Dreyfuss, G. (2008). Preparation of Efficient Splicing Extracts From Whole Cells, Nuclei, and Cytoplasmic Fractions. In: Lin, RJ. (eds) RNA-Protein Interaction Protocols. Methods in Molecular Biology, vol 488. Humana Press. https://doi.org/10.1007/978-1-60327-475-3_23

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  • DOI: https://doi.org/10.1007/978-1-60327-475-3_23

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-419-7

  • Online ISBN: 978-1-60327-475-3

  • eBook Packages: Springer Protocols

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