Evidence for Splice Site Pairing via Intron Definition in Schizosaccharomyces pombe

REFERENCES

• Abovich, N., Liao, X. C., and Rosbash, M.. 1994. The yeast MUD2 protein: an interaction with PRP11 defines a bridge between commitment complexes and U2 snRNP addition. Genes Dev. 8:843–854
   PubMed Web of Science ®Google Scholar
• Abovich, N., and Rosbash, M.. 1997. Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals. Cell 89:403–412
   PubMed Web of Science ®Google Scholar
• Aebi, M., Hornig, H., Padgett, R. A., Reiser, J., and Weissmann, C.. 1986. Sequence requirements for splicing of higher eukaryotic nuclear pre-mRNA. Cell 47:555–565
   PubMed Web of Science ®Google Scholar
• Alvarez, C. J., Romfo, C. M., VanHoy, R. W., Porter, G. L., and Wise, J. A.. 1996. Mutational analysis of U1 function in S. pombe: pre-mRNAs differ in the extent and nature of their requirements for this snRNA in vivo. RNA 2:404–418
   PubMedGoogle Scholar
• Amrein, H., Hedley, M. L., and Maniatis, T.. 1994. The role of specific protein-RNA and protein-protein interactions in positive and negative control of pre-mRNA splicing by transformer 2. Cell 76:735–746
   PubMed Web of Science ®Google Scholar
• Berget, S. M.. 1995. Exon recognition in vertebrate splicing. J. Biol. Chem. 270:2411–2414
   PubMed Web of Science ®Google Scholar
• Berglund, J. A., Chua, K., Abovich, N., Reed, R., and Rosbash, M.. 1997. The splicing factor BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC. Cell 89:781–787
   PubMed Web of Science ®Google Scholar
• Birney, E., Kumar, S., and Krainer, A. R.. 1993. Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors. Nucleic Acids Res. 21:5803–5816
   PubMed Web of Science ®Google Scholar
• Black, D. L.. 1991. Does steric interference between splice sites block the splicing of a short c-src neuron-specific exon in non-neuronal cells? Genes Dev. 5:389–402
   PubMedGoogle Scholar
• Black, D. L.. 1992. Activation of c-src neuron-specific splicing by an unusual RNA element in vivo and in vitro. Cell 69:795–807
   PubMedGoogle Scholar
• Black, D. L.. 1995. Finding splice sites within a wilderness of RNA. RNA 1:763–771
   PubMedGoogle Scholar
• Blumenthal, T., and Thomas, J.. 1988. Cis and trans splicing in C. elegans. Trends Genet. 4:305–308
   PubMedGoogle Scholar
• Carlo, T., Sterner, D. A., and Berget, S. M.. 1996. An intron splicing enhancer containing a G-rich repeat facilitates inclusion of a vertebrate micro-exon. RNA 2:342–343
   PubMed Web of Science ®Google Scholar
• Chou, M.-Y., Rooke, N., Turck, C. W., and Black, D. L.. 1999. hnRNP H is a component of a splicing enhancer complex that activates a c-src alternative exon in neuronal cells. Mol. Cell. Biol. 19:69–77
   PubMed Web of Science ®Google Scholar
• Csank, C. F., Taylor, M., and Martindale, D. W.. 1990. Nuclear pre-mRNA introns: analysis and comparison of intron sequences from Tetrahymena thermophila and other eukaryotes. Nucleic Acids Res. 18:5133–5141
   PubMed Web of Science ®Google Scholar
• Cunningham, S. A., Else, A. J., Potter, B. V. L., and Eperon, I. C.. 1991. Influences of separation and adjacent sequences on the use of alternative 5′ splice sites. J. Mol. Biol. 217:265–281
   PubMedGoogle Scholar
• DeVoti, J., Seydoux, G., Beach, D., and McLeod, M.. 1991. Interaction between ran1+ protein kinase and cAMP dependent protein kinase as negative regulators of fission yeast meiosis. EMBO J. 10:3759–3768
   PubMed Web of Science ®Google Scholar
• Dominski, Z., and Kole, R.. 1991. Selection of splice sites in pre-mRNAs with short internal exons. Mol. Cell. Biol. 11:6075–6083
   PubMed Web of Science ®Google Scholar
• Eng, F. J., and Warner, J. R.. 1991. Structural basis for the regulation of splicing of a yeast messenger RNA. Cell 65:797–804
   PubMed Web of Science ®Google Scholar
• Engebrecht, J., Voelkel-Meiman, K., and Roeder, G. S.. 1991. Meiosis-specific splicing in yeast. Cell 66:1257–1268
   PubMed Web of Science ®Google Scholar
• Eperon, I. C., Ireland, D. C., Smith, R. A., Mayeda, A., and Krainer, A. R.. 1993. Pathways for selection of 5′ splice sites by U1 snRNPs and SF2/ASF. EMBO J. 9:3607–3617
   Google Scholar
• Fields, C.. 1990. Information content of Caenorhabditis elegans splice site sequences varies with intron length. Nucleic Acids Res. 18:1509–1512
   PubMed Web of Science ®Google Scholar
• Fouser, L. A., and Friesen, J. D.. 1986. Mutations in a yeast intron demonstrate the importance of specific conserved nucleotides for the two stages of nuclear pre-mRNA splicing. Cell 45:81–93
   PubMedGoogle Scholar
• Gatermann, K. B., Hoffman, A., Rosenberg, G. H., and Käufer, N. F.. 1989. Introduction of functional artificial introns into the naturally intronless ura4 gene of Schizosaccharomyces pombe. Mol. Cell. Biol. 9:1526–1535
   PubMedGoogle Scholar
• Goguel, V., and Rosbash, M.. 1993. Splice site choice and splicing efficiency are positively influenced by pre-mRNA intramolecular base pairing in yeast. Cell 72:893–901
   PubMed Web of Science ®Google Scholar
• Gross, T., Richert, K., Mierke, C., Lützelberger, M., and Kaüfer, N. F.. 1998. Identification and characterization of srp1, a gene of fission yeast encoding a RNA binding domain and a RS domain typical of SR splicing factors. Nucleic Acids Res. 26:505–511
   PubMedGoogle Scholar
• Guo, M., Lo, P. C., and Mount, S. M.. 1993. Species-specific signals for the splicing of a short Drosophila intron in vitro. Mol. Cell. Biol. 13:1104–1118
   PubMedGoogle Scholar
• Guo, M., and Mount, S. M.. 1995. Localization of sequences required for size-specific splicing of a small Drosophila intron in vitro. J. Mol. Biol. 253:426–437
   PubMedGoogle Scholar
• Hawkins, J. D.. 1988. A survey on intron and exon lengths. Nucleic Acids Res. 16:9893–9908
   PubMed Web of Science ®Google Scholar
• Higuchi, R.. 1990. Recombinant PCR PCR protocols: a guide to methods and applications. Innis, M. A., Gelfand, D. M., Sinisky, J. J., and White, T. J. 177–183 Academic Press, Inc., San Diego, Calif
   Google Scholar
• Hindley, J., and Phear, G. A.. 1984. Sequence of the cell division gene CDC2 from Schizosaccharomyces pombe; patterns of splicing and homology to protein kinases. Gene 31:129–134
   PubMed Web of Science ®Google Scholar
• Hoffman, B. E., and Grabowski, P. J.. 1992. U1 snRNP targets an essential splicing factor, U2AF65, to the 3′ splice site by a network of interactions spanning the exon. Genes Dev. 6:2554–2568
   PubMed Web of Science ®Google Scholar
• Horowitz, D. S., and Krainer, A. R.. 1994. Mechanisms for selecting 5′ splice sites in mammalian pre-mRNA splicing. Trends Genet. 10:100–106
   PubMedGoogle Scholar
• Howe, K. J., Ares, M.Jr.. 1997. Intron self-complementarity enforces exon inclusion in a yeast pre-mRNA. Proc. Natl. Acad. Sci. USA 94:12467–12472
   PubMedGoogle Scholar
• Innis, M. A., and Gelfand, D. H.. 1990. Optimization of PCR PCR protocols: a guide to methods and applications. Innis, M. A., Gelfand, D. H., Sinisky, J. J., and White, T. J. 3–12 Academic Press, Inc., San Diego, Calif
   Google Scholar
• Kennedy, C. F., Krämer, A., and Berget, S. M.. 1998. A role for SRp54 during intron bridging of small introns with pyrimidine tracts upstream of the branchpoint. Mol. Cell. Biol. 18:5425–5434
   PubMedGoogle Scholar
• Kishida, M., Nagai, T., Nakaseko, Y., and Shimoda, C.. 1994. Meiosis-dependent mRNA splicing of the fission yeast Schizosaccharomyces pombe mes1+ gene. Curr. Genet. 25:497–503
   PubMedGoogle Scholar
• Kohtz, J. D., Jamison, S. F., Will, C. L., Zuo, P., Lührmann, R., Garcia-Blanco, M. A., and Manley, J. L.. 1994. Protein-protein interactions and 5′ splice site recognition in mammalian mRNA precursors. Nature 368:119–124
   PubMed Web of Science ®Google Scholar
• Kostrub, C. F., Al-Khodary, F., Ghazizadeh, H., Carr, A. M., and Enoch, T.. 1997. Molecular analysis of hus1+, a fission yeast gene required for S-M and DNA damage checkpoints. Mol. Gen. Genet. 254:389–399
   PubMedGoogle Scholar
• Kuo, H.-C., Nasim, F. H., and Grabowski, P. J.. 1991. Control of alternative splicing by the differential binding of U1 small nuclear ribonucleoprotein particle. Science 251:1045–1050
   PubMed Web of Science ®Google Scholar
• Lopez, A. J.. 1998. Alternative splicing of pre-mRNA: developmental consequences and mechanisms of regulation. Annu. Rev. Genet. 32:279–305
   PubMed Web of Science ®Google Scholar
• Lützelberger, M., Gross, T., and Kaüfer, N. F.. 1999. Srp2, an SR protein family member of fission yeast: in vivo characterization of its modular domains. Nucleic Acids Res. 27:2618–2626
   PubMedGoogle Scholar
• Maundrell, K.. 1990. nmt1 of fission yeast. J. Biol. Chem. 265:10857–10864
   PubMed Web of Science ®Google Scholar
• Min, H., Chan, R. C., and Black, D. L.. 1995. The generally expressed hnRNP F is involved in a neural-specific pre-mRNA splicing event. Genes Dev. 9:2659–2671
   PubMedGoogle Scholar
• Min, H., Turck, C. W., Nokolic, J. M., and Black, D. L.. 1997. A new regulatory protein, K-SRP, mediates exon inclusion through an intronic splicing enhancer. Genes Dev. 11:1023–1036
   PubMedGoogle Scholar
• Mount, S. M., Burks, C., Hertz, G., Stormo, G. D., White, O., and Fields, C.. 1992. Splicing signals in Drosophila: intron size, information content, and consensus sequences. Nucleic Acids Res. 10:4255–4262
   Google Scholar
• Peng, X., and Mount, S. M.. 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
• Pikielny, C. W., and Rosbash, M.. 1985. mRNA splicing efficiency in yeast and the contribution of nonconserved sequences. Cell 41:119–126
   PubMed Web of Science ®Google Scholar
• Potashkin, J., Naik, K., and Wentz-Hunter, K.. 1993. U2AF homolog required for splicing in vivo. Science 262:573–575
   PubMedGoogle Scholar
• Prabhala, G., Rosenberg, G. H., and Käufer, N. F.. 1992. Architectural features of pre-mRNA introns in the fission yeast Schizosaccharomyces pombe. Yeast 8:171–182
   PubMedGoogle Scholar
• Reed, R., and Maniatis, T.. 1986. A role for exon sequences and splice site proximity in splice site selection. Cell 46:681–690
   PubMed Web of Science ®Google Scholar
• Reich, C. I., VanHoy, R. W., Porter, G. L., and Wise, J. A.. 1992. Mutations at the 3′ splice site can be suppressed by compensatory base changes in U1 snRNA in fission yeast. Cell 69:1159–1169
   PubMedGoogle Scholar
• Robberson, B. L., Cote, G. J., and Berget, S. M.. 1990. Exon definition may facilitate splice site selection in RNAs with multiple exons. Mol. Cell. Biol. 10:84–94
   PubMed Web of Science ®Google Scholar
• Romfo, C. M., and Wise, J. A.. 1997. Both the polypyrimidine tract and the 3′ splice site function prior to the first step of splicing in fission yeast. Nucleic Acids Res. 25:4658–4665
   PubMedGoogle Scholar
• Romfo, C. M., Lakhe-Reddy, S., and Wise, J. A.. 1999. Molecular genetic analysis of U2AF59 in Schizosaccharomyces pombe: differential sensitivity of introns to mutational inactivation. RNA 5:49–65
   PubMedGoogle Scholar
• Rymond, B. C., and Rosbash, M.. 1992. Yeast pre-mRNA splicing The molecular and cellular biology of the yeast Saccharomyces: gene expression. Broach, J. R., Pringle, J. R., and Jones, E. W. 143–192 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y
   Google Scholar
• Shen, J., Zu, K., Cass, C. L., Beyer, A. L., and Hirsch, J.. 1995. Exon skipping by overexpression of a Drosophila heterogeneous nuclear ribonucleoprotein in vivo. Proc. Natl. Acad. Sci. USA 92:1822–1825
   PubMedGoogle Scholar
• Spingola, M., Grate, L., Haussler, D., Ares, M.Jr.. 1999. Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae. RNA 5:221–234
   PubMed Web of Science ®Google Scholar
• Sterner, D. A., and Berget, S. M.. 1993. In vivo recognition of a vertebrate micro-exon as an exon-intron-exon unit. Mol. Cell. Biol. 13:2677–2687
   PubMedGoogle Scholar
• Sterner, D. A., Carlo, T., and Berget, S. M.. 1996. Architectural limits on split genes. Proc. Natl. Acad. Sci. USA 93:15081–15085
   PubMed Web of Science ®Google Scholar
• Talerico, M., and Berget, S. M.. 1990. Effect of 5′ splice site mutations on splicing of the preceding intron. Mol. Cell. Biol. 10:6299–6305
   PubMed Web of Science ®Google Scholar
• Talerico, M., and Berget, S. M.. 1994. Intron definition in splicing of small Drosophila introns. Mol. Cell. Biol. 14:3434–3445
   PubMed Web of Science ®Google Scholar
• Treisman, R., Orkin, S. H., and Maniatis, T.. 1983. Specific transcription and RNA splicing defects in five cloned β-thalassemia genes. Nature 302:591–596
   PubMed Web of Science ®Google Scholar
• Vijayraghavan, U., Parker, R., Tamm, J., Iimura, Y., Rossi, J., Abelson, J., and Guthrie, C.. 1986. Mutations in conserved intron sequences affect multiple steps in the yeast splicing pathway, particularly assembly of the spliceosome. EMBO J. 5:1683–1695
   PubMed Web of Science ®Google Scholar
• Wang, A. M., and Mark, D. F.. 1990. Quantitative PCR PCR protocols: a guide to methods and applications. Innis, M. A., Gelfand, D. M., Sinisky, J. J., and White, T. J. 70–75 Academic Press Inc., San Diego, Calif
   Google Scholar
• Wei, N., Lin, C. Q., Modafferi, E. F., Gomes, W. A., and Black, D. L.. 1997. A unique intronic splicing enhancer controls the inclusion of the agrin Y exon. RNA 3:1275–1288
   PubMedGoogle Scholar
• Wentz-Hunter, K., and Potashkin, J.. 1996. The small subunit of the splicing factor U2AF is conserved in fission yeast. Nucleic Acids Res. 24:1849–1854
   PubMedGoogle Scholar
• Wieringa, B., Meyer, F., Reiser, J., and Weissman, C.. 1983. Unusual splice sites revealed by mutagenic inactivation of an authentic splice site of the rabbit β-globin gene. Nature 301:38–43
   PubMed Web of Science ®Google Scholar
• Wieringa, B., Hofer, E., and Weissman, C.. 1984. A minimal intron length but no specific internal sequence is required for splicing in the large rabbit β-globin intron. Cell 37:915–925
   PubMed Web of Science ®Google Scholar
• Wu, J. Y., and Maniatis, T.. 1993. Specific interactions between proteins implicated in splice site selection and regulated alternative splicing. Cell 75:1061–1070
   PubMed Web of Science ®Google Scholar
• Zhang, L., Ashiya, M., Sherman, T. G., and Grabowski, P. J.. 1996. Essential nucleotides direct neuron-specific splicing of γ2 pre-mRNA. RNA 2:682–698
   PubMedGoogle Scholar
• Zhang, M. Q., and Marr, T. G.. 1994. Fission yeast gene structure and recognition. Nucleic Acids Res. 22:1750–1759
   PubMedGoogle Scholar