Isolation of a sequence-specific RNA binding protein, polypyrimidine tract binding protein, using RNA affinity chromatography

Methods in Molecular Biology

Volumn 488, Issue , 2008, Pages 1-8

  Sharma, Shalini ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Affinity chromatography; c src N1 exon; Intronic splicing silencer; Polypyrimidine tract binding protein; RNA binding proteins

Indexed keywords

EID: 84934434641     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-60327-475-3_1     Document Type: Article

References (27)

1. Black, D. L. (2003) Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem. 72, 291-336.
2. Reed, R., and Hurt, E. (2002) A conserved mRNA export machinery coupled to pre-mRNA splicing. Cell 108, 523-531.
3. Maniatis, T., and Reed, R. (2002) An extensive network of coupling among gene expression machines. Nature 416, 499-506.
4. Graveley, B. R. (2000) Sorting out the complexity of SR protein functions. RNA 6, 1197-211.
5. Krecic, A. M., and Swanson, M. S. (1999) hnRNP complexes: composition, structure, and function. Curr. Opin. Cell Biol. 11, 363-371.
6. Dreyfuss, G., Kim, V. N., and Kataoka, N. (2002) Messenger-RNA-binding proteins and the messages they carry. Nat. Rev. Mol. Cell Biol. 3, 195-205.
7. Belsham, G. J., and Sonenberg, N. (1996) RNA-protein interactions in regulation of picornavirus RNA translation. Microbiol. Rev. 60, 499-511.
8. Wagner, E. J., and Garcia-Blanco, M. A. (2001) Polypyrimidine tract binding protein antagonizes exon definition. Mol. Cell. Biol. 21, 3281-3288.
9. Valcarcel, J., and Gebauer, F. (1997) Post-transcriptional regulation: the dawn of PTB. Curr. Biol. 7, R705-R708.
10. Castelo-Branco, P., Furger, A., Wollerton, M., et al. (2004) Polypyrimidine tract binding protein modulates efficiency of polyadenylation. Mol. Cell. Biol. 24, 4174-4183.
11. Chou, M. Y., Underwood, J. G., Nikolic, J., Luu, M. H., and Black, D.L. (2000) Multisite RNA binding and release of polypyrimidine tract binding protein during the regulation of c-src neural-specific splicing. Mol. Cell 5, 949-957.
12. Chan, R. C., and Black, D. L. (1997) The polypyrimidine tract binding protein binds upstream of neural cell-specific c-src exon N1 to repress the splicing of the intron downstream. Mol. Cell. Biol. 17, 4667-4676.
13. Perez, I., McAfee, J. G., and Patton, J. G. (1997) Multiple RRMs contribute to RNA binding specificity and affinity for polypyrimidine tract binding protein. Biochemistry 36, 11881-11890.
14. Liu, H., Zhang, W., Reed, R. B., Liu, W., and Grabowski, P. J. (2002) Mutations in RRM4 uncouple the splicing repression and RNA-binding activities of polypyrimidine tract binding protein. RNA 8, 137-149.
15. Yuan, X., Davydova, N., Conte, M. R., Curry, S., and Matthews, S. (2002) Chemical shift mapping of RNA interactions with the polypyrimidine tract binding protein. Nucleic Acids Res. 30, 456-462.
16. Amir-Ahmady, B., Boutz, P. L., Markovtsov, V., Phillips, M. L., and Black, D. L. (2005) Exon repression by polypyrimidine tract binding protein. RNA 11, 699-716.
17. Caputi, M., and Zahler, A. M. (2001) Determination of the RNA binding specificity of the heterogeneous nuclear ribonucleoprotein (hnRNP) H/H′/F/2H9 family. J. Biol. Chem. 276, 43850-43859.
18. Kaminski, A., Ostareck, D. H., Standart, N. M., and Jackson, R. J. (1998) Affinity methods for isolating RNA binding proteins. In: RNA: Protein Interactions (Smith, C. W. J., ed.), Oxford University Press, New York, pp. 137-160.
19. Siebel, C. W., Kanaar, R., and Rio, D. C. (1994) Regulation of tissue-specific P-element pre-mRNA splicing requires the RNA-binding protein PSI. Genes Dev. 8, 1713-1725.
20. Hartmuth, K., Vornlocher, H. P., and Luhrmann, R. (2004) Tobramycin affinity tag purification of spliceosomes. Methods Mol. Biol. 257, 47-64.
21. Bachler, M., Schroeder, R., and von Ahsen, U. (1999) StreptoTag: a novel method for the isolation of RNA-binding proteins. RNA 5, 1509-1516.
22. Zhou, Z., Sim, J., Griffith, J., and Reed, R. (2002) Purification and electron microscopic visualization of functional human spliceosomes. Proc. Natl. Acad. Sci. U. S. A. 99, 12203-12207.
23. Rodgers, J. T., Patel, P., Hennes, J. L., Bolognia, S. L., and Mascotti, D. P. (2000) Use of biotin-labeled nucleic acids for protein purification and agarose-based chemiluminescent electromobility shift assays. Anal. Biochem. 277, 254-259.
24. Hall, M. P., Huang, S., and Black, D. L. (2004) Differentiation-induced colocalization of the KH-type splicing regulatory protein with polypyrimidine tract binding protein and the c-src pre-mRNA. Mol. Biol. Cell 15, 774-786.
25. Dignam, J. D. (1990) Preparation of extracts from higher eukaryotes. Methods Enzymol. 182, 194-203.
26. Black, D. L., Chan, R., Min, H., Wang, J., and Bell, L. (1998) The electrophoretic mobility shift assay for RNA binding proteins. In: RNA:Protein Interactions (Smith, C. W. J., ed.), Oxford University Press, New York, pp. 109-136.
27. Rooke, N., and Underwood, J. (2003) In vitro RNA splicing in mammalian cell extracts. Curr. Protoc. Cell Biol. 2, 11.17.1-11.17.20.