U1 Small Nuclear RNA-Promoted Exon Selection Requires a Minimal Distance between the Position of U1 Binding and the 3′ Splice Site across the Exon

References

• Berget, S. M. 1995. Exon recognition in vertebrate splicing. J. Biol. Chem. 270:2411–2414.
   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
• Black, D. L., B. Chabot, and J. A. Steitz. 1985. U2 as well as U1 small nuclear ribonucleoproteins are involved in premessenger RNA splicing. Cell 42:737–750.
   PubMed Web of Science ®Google Scholar
• Carlo, T., D. A. Sterner, and S. M. Berget. 1996. An intron splicing enhancer containing a G-rich repeat facilitates inclusion of a vertebrate micro-exon. RNA 2:342–353.
   PubMed Web of Science ®Google Scholar
• Chabot, B. 1996. Directing alternative splicing: cast and scenarios. Trends Genet. 12:472–478.
   PubMedGoogle Scholar
• Cohen, J. B., S. D. Broz, and A. D. Levinson. 1993. U1 small nuclear RNAs with altered specificity can be stably expressed in mammalian cells and promote permanent changes in pre-mRNA splicing. Mol. Cell. Biol. 13:2666–2676.
   PubMed Web of Science ®Google Scholar
• Cohen, J. B., J. E. Snow, S. D. Spencer, and A. D. Levinson. 1994. Suppression of mammalian 5′ splice-site defects by U1 small nuclear RNAs from a distance. Proc. Natl. Acad. Sci. USA 91:10470–10474.
   PubMed Web of Science ®Google Scholar
• Dominski, Z., and R. Kole. 1991. Selection of splice sites in pre-mRNAs with short internal exons. Mol. Cell. Biol. 11:6075–6083.
   PubMed Web of Science ®Google Scholar
• Dominski, Z., and R. Kole. 1992. Cooperation of pre-mRNA sequence elements in splice site selection. Mol. Cell. Biol. 12:2108–2114.
   PubMed Web of Science ®Google Scholar
• Dominski, Z., and R. Kole. 1994. Identification and characterization by antisense oligonucleotides of exon and intron sequences required for splicing. Mol. Cell. Biol. 14:7445–7454.
   PubMed Web of Science ®Google Scholar
• Eng, F. J., and J. R. Warner. 1991. Structural basis for the regulation of splicing of a yeast messenger RNA. Cell 65:797–804.
   PubMed Web of Science ®Google Scholar
• Eperon, I. C., D. C. Ireland, R. A. Smith, A. Mayeda, and A. R. Krainer. 1993. Pathways for selection of 5′ splice sites by U1 snRNPs and SF2/ASF. EMBO J. 12:3607–3617.
   PubMedGoogle Scholar
• Eperon, L. P., I. R. Graham, A. D. Griffiths, and I. C. Eperon. 1988. Effects of RNA secondary structure on alternative splicing of pre-mRNA: is folding limited to a region behind the transcribing RNA polymerase? Cell 54:393–401.
   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
• 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
• Grabowski, P. J., F. U. Nasim, H. C. Kuo, and R. Burch. 1991. Combinatorial splicing of exon pairs by two-site binding of U1 small nuclear ribonucleoprotein particle. Mol. Cell. Biol. 11:5919–5928.
   PubMedGoogle Scholar
• Green, M. R. 1991. Biochemical mechanisms of constitutive and regulated pre-mRNA splicing. Annu. Rev. Cell Biol. 7:559–599.
   PubMedGoogle Scholar
• Hampson, R. K., L. La Follette, and F. M. Rottman. 1989. Alternative processing of bovine growth hormone mRNA is influenced by downstream exon sequences. Mol. Cell. Biol. 9:1604–1610.
   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
• 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 P. J. Grabowski. 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
• Hwang, D. Y., and J. B. Cohen. 1996. Base pairing at the 5′ splice site with U1 small nuclear RNA promotes splicing of the upstream intron but may be dispensable for splicing of the downstream intron. Mol. Cell. Biol. 16:3012–3022.
   PubMedGoogle Scholar
• Hwang, D. Y., and J. B. Cohen. 1996. U1 snRNA promotes the selection of nearby 5′ splice sites by U6 snRNA in mammalian cells. Genes Dev. 10:338–350.
   PubMedGoogle Scholar
• Kohtz, J. D., S. F. Jamison, C. L. Will, P. Zuo, R. Luhrmann, M. A. Garcia-Blanco, and J. L. Manley. 1994. Protein-protein interactions and 5′-splicesite recognition in mammalian mRNA precursors. Nature 368:119–124.
   PubMed Web of Science ®Google Scholar
• Krainer, A. R., G. C. Conway, and D. Kozak. 1990. The essential pre-mRNA splicing factor SF2 influences 5′ splice site selection by activating proximal sites. Cell 62:35–42.
   PubMed Web of Science ®Google Scholar
• Krämer, A. 1987. Analysis of RNase-A-resistant regions of adenovirus 2 major late precursor-mRNA in splicing extracts reveals an ordered interaction of nuclear components with the substrate RNA. J. Mol. Biol. 196:559–573.
   PubMed Web of Science ®Google Scholar
• Krämer, A. 1996. The structure and function of proteins involved in mammalian pre-mRNA splicing. Annu. Rev. Biochem. 65:367–409.
   PubMed Web of Science ®Google Scholar
• Krawczak, M., J. Reiss, and D. N. Cooper. 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
• Kuo, H. C., F. H. Nasim, and P. J. Grabowski. 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
• Lavigueur, A., H. La Branche, A. R. Kornblihtt, and B. Chabot. 1993. A splicing enhancer in the human fibronectin alternate ED1 exon interacts with SR proteins and stimulates U2 snRNP binding. Genes Dev. 7:2405–2417.
   PubMed Web of Science ®Google Scholar
• Madhani, H. D., and C. Guthrie. 1994. Dynamic RNA-RNA interactions in the spliceosome. Annu. Rev. Genet. 28:1–26.
   PubMedGoogle Scholar
• Manley, J. L., and R. Tacke. 1996. SR proteins and splicing control. Genes Dev. 10:1569–1579.
   PubMed Web of Science ®Google Scholar
• Marvit, J., A. G. DiLella, K. Brayton, F. D. Ledley, K. J. H. Robson, and S. L. C. Woo. 1987. GT to AT transition at a splice donor site causes skipping of the preceding exon in phenylketonuria. Nucleic Acids Res. 15:5613–5628.
   PubMed Web of Science ®Google Scholar
• Min, H., R. C. Chan, and D. L. Black. 1995. The generally expressed hnRNP F is involved in a neural-specific pre-mRNA splicing event. Genes Dev. 9:2659–2671.
   PubMedGoogle Scholar
• Mitchell, P. J., G. Urlaub, and L. Chasin. 1986. Spontaneous splicing mutations at the dihydrofolate reductase locus in Chinese hamster ovary cells. Mol. Cell. Biol. 6:1926–1935.
   PubMedGoogle Scholar
• Moore, M. J., C. C. Query, and P. A. Sharp. 1993. Splicing of precursors to mRNA by the spliceosome, p. 303–357. In R. F. Gesteland and J. F. Atkins (ed.), The RNA world. Cold Spring Harbor Laboratory Press, Plainview, N.Y.
   Google Scholar
• Nagoshi, R. N., and B. S. Baker. 1990. Regulation of sex-specific RNA splicing at the Drosophila doublesex gene: cis-acting mutations in exon sequences alter sex-specific RNA splicing patterns. Genes Dev. 4:89–97.
   PubMedGoogle Scholar
• Nakai, K., and H. Sakamoto. 1994. Construction of a novel database containing aberrant splicing mutations of mammalian genes. Gene 141:171–177.
   PubMed Web of Science ®Google Scholar
• Nasim, F. H., P. A. Spears, H. M. Hoffmann, H. C. Kuo, and P. J. Grabowski. 1990. A sequential splicing mechanism promotes selection of an optimal exon by repositioning a downstream 5′ splice site in preprotachykinin pre- mRNA. Genes Dev. 4:1172–1184.
   PubMedGoogle Scholar
• Nelson, K. K., and M. R. Green. 1988. Splice site selection and ribonucleoprotein complex assembly during in vitro pre-mRNA splicing. Genes Dev. 2:319–329.
   PubMedGoogle Scholar
• Ramchatesingh, J., A. M. Zahler, K. M. Neugebauer, M. B. Roth, and T. A. Cooper. 1995. A subset of SR proteins activates splicing of the cardiac troponin T alternative exon by direct interactions with an exonic enhancer. Mol. Cell. Biol. 15:4898–4907.
   PubMed Web of Science ®Google Scholar
• Reed, R. 1996. Initial splice-site recognition and pairing during pre-mRNA splicing. Curr. Opin. Genet. Dev. 6:215–220.
   PubMed Web of Science ®Google Scholar
• Reyes, J. L., P. Kois, B. B. Konforti, and M. M. Konarska. 1996. The canonical GU dinucleotide at the 5′ splice site is recognized by p220 of the U5 snRNP within the spliceosome. RNA 2:213–225.
   PubMedGoogle Scholar
• Robberson, B. L., G. J. Cote, and S. M. Berget. 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
• Rosbash, M., and B. Séraphin. 1991. Who’s on first? The U1 snRNP-59 splice site interaction and splicing. Trends Biochem. Sci. 16:187–190.
   PubMedGoogle Scholar
• Ruskin, B., and M. R. Green. 1985. Specific and stable intron-factor interactions are established early during in vitro pre-mRNA splicing. Cell 43:131–142.
   PubMed Web of Science ®Google Scholar
• Ruskin, B., P. D. Zamore, and M. R. Green. 1988. A factor, U2AF, is required for U2 snRNP binding and splicing complex assembly. Cell 52:207–219.
   PubMed Web of Science ®Google Scholar
• Siebel, C. W., L. D. Fresco, and D. C. Rio. 1992. The mechanism of somatic inhibition of Drosophila P-element pre-mRNA splicing: multiprotein complexes at an exon pseudo-5′ splice site control U1 snRNP binding. Genes Dev. 6:1386–1401.
   PubMedGoogle Scholar
• Staknis, D., and R. Reed. 1994. SR proteins promote the first specific recognition of pre-mRNA and are present together with the U1 small nuclear ribonucleoprotein particle in a general splicing enhancer complex. Mol. Cell. Biol. 14:7670–7682.
   PubMed Web of Science ®Google Scholar
• Sterner, D. A., and S. M. Berget. 1993. In vivo recognition of a vertebrate mini-exon as an exon-intron-exon unit. Mol. Cell. Biol. 13:2677–2687.
   PubMedGoogle 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
• Talerico, M., and S. M. Berget. 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 S. M. Berget. 1994. Intron definition in splicing of small Drosophila introns. Mol. Cell. Biol. 14:3434–3445.
   PubMed Web of Science ®Google Scholar
• Tian, M., and T. Maniatis. 1993. A splicing enhancer complex controls alternative splicing of doublesex pre-mRNA. Cell 74:105–114.
   PubMedGoogle Scholar
• Treisman, R., S. H. Orkin, and T. Maniatis. 1983. Specific transcription and RNA splicing defects in five cloned β-thalassaemia genes. Nature 302:591–596.
   PubMed Web of Science ®Google Scholar
• Treisman, R., N. J. Proudfoot, M. Shander, and T. Maniatis. 1982. A singlebase change at a splice site in a β0-thalassemic gene causes abnormal RNA splicing. Cell 29:903–911.
   PubMed Web of Science ®Google Scholar
• Umen, J. G., and C. Guthrie. 1995. The second catalytic step of pre-mRNA splicing. RNA 1:869–885.
   PubMed Web of Science ®Google Scholar
• Wang, Z., H. M. Hoffmann, and P. J. Grabowski. 1995. Intrinsic U2AF binding is modulated by exon enhancer signals in parallel with changes in splicing activity. RNA 1:21–35.
   PubMed Web of Science ®Google Scholar
• Watakabe, A., K. Tanaka, and Y. Shimura. 1993. The role of exon sequences in splice site selection. Genes Dev. 7:407–418.
   PubMed Web of Science ®Google 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., E. J. Sontheimer, and J. A. Steitz. 1992. Site-specific crosslinking of mammalian U5 snRNP to the 5′ splice site before the first step of pre-mRNA splicing. Genes. Dev. 6:2542–2553.
   PubMed Web of Science ®Google Scholar
• Xu, R., J. Teng, and T. A. Cooper. 1993. The cardiac troponin T alternative exon contains a novel purine-rich positive splicing element. Mol. Cell. Biol. 13:3660–3674.
   PubMedGoogle 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
• Zhang, L., M. Ashiya, T. G. Sherman, and P. J. Grabowski. 1996. Essential nucleotides direct neuron-specific splicing of γ2 pre-mRNA. RNA 2:682–698.
   PubMedGoogle Scholar
• Zuo, P., and T. Maniatis. 1996. The splicing factor U2AF35 mediates critical protein-protein interactions in constitutive and enhancer-dependent splicing. Genes Dev. 10:1356–1368.
   PubMedGoogle Scholar
• Zuo, P., and J. L. Manley. 1994. The human splicing factor ASF/SF2 can specifically recognize pre-mRNA 5′ splice sites. Proc. Natl. Acad. Sci. USA 91:3363–3367.
   PubMedGoogle Scholar