A Specific RNA Hairpin Loop Structure Binds the RNA Recognition Motifs of the Drosophila SR Protein B52

REFERENCES

• Allain, F. H.-T., C. C. Gubser, P. W. A. Howe, K. Nagai, D. Neuhaus, and G. Varani. 1996. Specificity of ribonucleoprotein interaction determined by RNA folding during complex formation. Nature 380:646–650.
   PubMed Web of Science ®Google Scholar
• Bartel, D. P., and J. W. Szostak. 1993. Isolation of new ribozymes from a large pool of random sequences. Science 261:1411–1418.
   PubMed Web of Science ®Google Scholar
• Bartel, D. P., M. L. Zapp, M. R. Green, and J. W. Szostak. 1991. HIV-1 Rev regulation involves recognition of non-Watson-Crick base pairs in viral RNA. Cell 67:529–536.
   PubMed Web of Science ®Google Scholar
• Burd, C. G., and G. Dreyfuss. 1994. Conserved structures and diversity of functions of RNA-binding proteins. Science 265:615–621.
   PubMed Web of Science ®Google Scholar
• Burd, C. G., and G. Dreyfuss. 1994. RNA binding specificity of hnRNP A1: significance of hnRNP A1 high-affinity binding sites in pre-mRNA splicing. EMBO J. 13:1197–1204.
   PubMed Web of Science ®Google Scholar
• Cavaloc, Y., M. Popielarz, J. P. Fuchs, R. Gattoni, and J. Stevenin. 1994. Characterization and cloning of the human splicing factor 9G8: a novel 35kDa factor of the serine/arginine protein family. EMBO J. 13:2639–2649.
   PubMed Web of Science ®Google Scholar
• Champlin, D. T., M. Frasch, H. Saumweber, and J. T. Lis. 1991. Characterization of a Drosophila protein associated with boundaries of transcriptionally active chromatin. Genes Dev. 5:1611–1621.
   PubMedGoogle Scholar
• Chaudhary, N. C., C. McMahon, and G. Blobel. 1991. Primary structure of a human arginine-rich nuclear protein that colocalizes with spliceosome components. Proc. Natl. Acad. Sci. USA 88:8189–8193.
   PubMedGoogle Scholar
• Christiansen, J., J. Egebjerg, N. Larsen, and R. A. Garret. 1990. Analysis of rRNA structure: experimental and theoretical considerations, p. 229–252. In G. Spedding (ed.), Ribosomes and protein synthesis: a practical approach. IRL Press, New York, N.Y.
   Google Scholar
• Conrad, R., L. M. Keranen, A. D. Ellington, and A. C. Newton. 1994. Isozyme-specific inhibition of protein kinase C by RNA aptamers. J. Biol. Chem. 269:32051–32054.
   PubMed Web of Science ®Google Scholar
• Dignam, J. D., R. M. Lebovitz, and R. G. Roeder. 1983. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acid Res. 11:1475–1489.
   PubMed Web of Science ®Google Scholar
• Fu, X.-D. 1993. Specific commitment of different pre-mRNAs to splicing by single SR proteins. Nature 365:82–85.
   PubMed Web of Science ®Google Scholar
• Fu, X.-D. 1995. The superfamily of arginine/serine-rich splicing factors. RNA 1:663–680.
   PubMed Web of Science ®Google Scholar
• Fu, X.-D., and T. Maniatis. 1992. Isolation of a complementary DNA that encodes the mammalian splicing factor SC35. Science 256:535–538.
   PubMed Web of Science ®Google Scholar
• Fu, X. D., and T. Maniatis. 1992. The 35-kDa mammalian splicing factor SC35 mediates specific interactions between U1 and U2 small nuclear ribonucleoprotein particles at the 3′ splice site. Proc. Natl. Acad. Sci. USA 89:1725–1729.
   PubMedGoogle Scholar
• Ge, H., and J. L. Manley. 1990. A protein factor, ASF, controls cell-specific alternative splicing of SV40 early pre-mRNA in vitro. Cell 62:25–34.
   PubMed Web of Science ®Google Scholar
• Ge, H., P. Zuo, and J. L. Manley. 1991. Primary structure of the human splicing factor ASF reveals similarities with Drosophila regulators. Cell 66:373–382.
   PubMedGoogle Scholar
• Gold, L., B. Polisky, O. Uhlenbeck, and M. Yarus. 1995. Diversity of oligonucleotide functions. Annu. Rev. Biochem. 64:763–797.
   PubMed Web of Science ®Google Scholar
• Green, R., A. D. Ellington, D. P. Bartel, and J. W. Szostak. 1991. In vitro genetic analysis: selection and amplification of rare functional nucleic acids. Methods 2:75–86.
   Google Scholar
• Groebe, D. R., A. E. Chung, and C. Ho. 1990. Cationic lipid-mediated co-transfection of insect cells. Nucleic Acids Res. 18:4033.
   PubMedGoogle Scholar
• Heinrichs, V., and B. S. Baker. 1995. The Drosophila SR protein RBP1 contributes to the regulation of doublesex alternative splicing by recognizing RBP1 RNA target sequences. EMBO J. 14:3987–4000.
   PubMedGoogle Scholar
• Hoffman, B. E., and J. T. Lis. Unpublished results.
   Google Scholar
• Jaeger, J. A., D. H. Turner, and M. Zuker. 1989. Improved predictions of secondary structures for RNA. Proc. Natl. Acad. Sci. USA 86:7706–7710.
   PubMed Web of Science ®Google Scholar
• Kim, Y. J., P. Zuo, J. L. Manley, and B. S. Baker. 1992. The Drosophila RNA-binding protein RBP1 is localized to transcriptionally active sites of chromosomes and shows a functional similarity to human splicing factor ASF/SF2. Genes Dev. 6:2569–2579.
   PubMedGoogle Scholar
• Krainer, A. R., G. C. Conway, and D. Kozak. 1990. Purification and characterization of pre-mRNA splicing factor SF2 from HeLa cells. Genes Dev. 4:1158–1171.
   PubMed Web of Science ®Google Scholar
• Krainer, A. R., A. Mayeda, D. Kozak, and G. Binns. 1991. Functional expression of cloned human splicing factor SF2: homology to RNA-binding proteins, U1 70K, and Drosophila splicing regulators. Cell 66:383–394.
   PubMed Web of Science ®Google Scholar
• Kraus, M. E. 1995. The Drosophila melanogaster RNA splicing factor B52: overexpression studies and mechanisms of recruitment to nuclear targets. Ph.D. thesis. Cornell University, Ithaca, N.Y.
   Google Scholar
• Kraus, M. E., and J. T. Lis. 1994. The concentration of B52, an essential splicing factor and regulator of splice site choice, is critical for Drosophila development. Mol. Cell. Biol. 14:5360–5370.
   PubMedGoogle Scholar
• Levine, T. D., F. Gao, P. H. King, L. G. Andrews, and J. D. Keene. 1993. Hel-N1: an autoimmune RNA-binding protein with specificity for 3′ uridy-late-rich untranslated regions of growth factor mRNAs. Mol. Cell. Biol. 13:3494–3504.
   PubMed Web of Science ®Google Scholar
• Manley, J. L., and R. Tacke. 1996. SR proteins and splicing control. Genes Dev. 10:1569–1579.
   PubMed Web of Science ®Google Scholar
• Mayeda, A., A. M. Zahler, A. Krainer, and M. Roth. 1992. Two members of a conserved family of nuclear phosphoproteins are involved in pre-mRNA splicing. Proc. Natl. Acad. Sci. USA 89:1301–1304.
   PubMedGoogle Scholar
• Moore, M. J., C. C. Query, and P. A. Sharp. 1993. Splicing of precursors to mRNAs by the spliceosome, p. 303–357. In R. F. Gesteland and J. F. Atkins (ed.), The RNA world. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
   Google Scholar
• Oubridge, C., N. Ito, P. R. Evans, C.-H. Teo, and K. Nagai. 1994. Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature 372:432–438.
   PubMed Web of Science ®Google Scholar
• Peng, X., and S. M. Mount. 1995. Genetic enhancement of RNA-processing defects by a dominant mutation in B52, the Drosophila gene for an SR protein splicing factor. Mol. Cell. Biol. 15:6273–6282.
   PubMedGoogle Scholar
• Ring, H. Z., and J. T. Lis. 1994. The SR protein B52/SRp55 is essential for Drosophila development. Mol. Cell. Biol. 14:7499–7506.
   PubMed Web of Science ®Google Scholar
• Roth, M. B., A. M. Zahler, and J. A. Stolk. 1991. A conserved family of nuclear phosphoproteins localized to sites of polymerase II transcription. J. Cell Biol. 115:587–596.
   PubMed Web of Science ®Google Scholar
• Schneider, D., C. Tuerk, and L. Gold. 1992. Selection of high affinity RNA ligands to the bacteriophage R17 coat protein. J. Mol. Biol. 228:862–869.
   PubMed Web of Science ®Google Scholar
• Screaton, G. R., J. F. Caceres, A. Mayeda, M. V. Bell, M. Plebanski, D. G. Jackson, J. I. Bell, and A. R. Krainer. 1995. Identification and characterization of three members of the human SR family of pre-mRNA splicing factors. EMBO J. 14:4336–4349.
   PubMed Web of Science ®Google Scholar
• Sharp, P. A. 1994. Split genes and RNA splicing. Cell 77:805–815.
   PubMed Web of Science ®Google Scholar
• Shi, H., and J. T. Lis. Unpublished results.
   Google Scholar
• Summers, M. D., and G. E. Smith. 1987. A manual of methods for baculo-virus vectors and insect cell culture procedures. Bulletin no. 1555. Texas Agricultural Experiment Station, College Station.
   Google Scholar
• Sun, Q., A. Mayeda, R. K. Hampson, A. R. Krainer, and F. M. Rottman. 1993. General splicing factor SF2/ASF promotes alternative splicing by binding to an exonic splicing enhancer. Genes Dev. 7:2598–2608.
   PubMed Web of Science ®Google Scholar
• Tacke, R., and J. L. Manley. 1995. The human splicing factors ASF/SF2 and SC35 possess distinct, functionally significant RNA binding specificities. EMBO J. 14:3540–3551.
   PubMed Web of Science ®Google Scholar
• Tian, Y., N. Adya, S. Wagner, C.-Z. Giam, M. R. Green, and A. D. Ellington. 1995. Dissecting protein:protein interactions between transcription factors with an RNA aptamer. RNA 1:317–326.
   PubMedGoogle Scholar
• Tsai, D. E., D. S. Harper, and J. D. Keene. 1991. U1-snRNP-A protein selects a ten nucleotide consensus sequence from a degenerate RNA pool presented in various structural contexts. Nucleic Acids Res. 19:4931–4936.
   PubMed Web of Science ®Google Scholar
• Tuerk, C., and L. Gold. 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505–510.
   PubMed Web of Science ®Google Scholar
• Ueda, A., S. Kawamoto, T. Igarashi, Y. Ishigatsubo, K. Tani, T. Okubo, and K. Okuda. 1994. Human monocyte chemoattractant protein-1 expressed in a baculovirus system. Gene 140:267–272.
   PubMedGoogle Scholar
• Wu, J. Y., and T. Maniatis. 1993. Specific interactions between proteins implicated in splice site selection and regulated alternative splicing. Cell 75:1061–1070.
   PubMed Web of Science ®Google Scholar
• Wyatt, J. R., and I. Tinoco, Jr. 1993. RNA structural elements and RNA function, p. 465–496. In R. F. Gesteland and J. F. Atkins (ed.), The RNA world. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
   Google Scholar
• Zahler, A. M., W. S. Lane, J. A. Stolk, and M. B. Roth. 1992. SR proteins: a conserved family of pre-mRNA splicing factors. Genes Dev. 6:837–847.
   PubMed Web of Science ®Google Scholar
• Zahler, A. M., K. M. Neugebauer, W. S. Lane, and M. B. Roth. 1993. Distinct functions of SR proteins in alternative pre-mRNA splicing. Science 260:219–222.
   PubMed Web of Science ®Google Scholar
• Zahler, A. M., and M. B. Roth. 1995. Distinct functions of SR proteins in recruitment of U1 small nuclear ribonucleoprotein to alternative 5′ splice sites. Proc. Natl. Acad. Sci. USA 92:2642–2646.
   PubMed Web of Science ®Google Scholar
• Zuker, M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244:48–52.
   PubMed Web of Science ®Google Scholar