Direct Selection for Mutations Affecting Specific Splice Sites in a Hamster Dihydrofolate Reductase Minigene

REFERENCES

• Adema, G. J., K. L. van Hulst, and P. D. Baas. 1990. Uridine branch acceptor is a cis-acting element involved in regulation of the alternative processing of calcitonin/CGRP-I pre-mRNA. Nucleic Acids Res. 18:5365–5373.
   PubMedGoogle Scholar
• Aebi, Μ., H. Hornig, R. A. Padgett, J. Reiser, and C. Weissmann. 1986. Sequence requirements for splicing of higher eukaryotic nuclear pre-mRNA. Cell 47:555–565.
   PubMed Web of Science ®Google Scholar
• Aebi, Μ., H. Hornig, and C. Weissmann. 1987. 5′ cleavage site in eukaryotic pre-mRNA splicing is determined by the overall 5′ splice region, not by the conserved 5′GU. Cell 50:237–246.
   PubMed Web of Science ®Google Scholar
• Aebi, Μ., and C. Weissmann. 1987. Precision and orderliness in splicing. Trends Genet. 3:102–107.
   Web of Science ®Google Scholar
• Archibald, A. L., N. A. Thompson, and S. Kvist. 1986. A single nucleotide difference at the 3′ end of an intron causes differential splicing of two histocompatibility genes. EMBO J. 5:957–965.
   PubMedGoogle Scholar
• Ashman, C. R., and R. L. Davidson. 1987. DNA base sequence changes induced by ethyl methanesulfonate in a Chromosomally integrated shuttle vector gene in mouse cells. Somatic Cell Mol. Genet. 13:563–568.
   PubMedGoogle Scholar
• Bigger, C., J. Strandberg, H. Yagi, D. Jerina, and A. Dippie. 1989. Mutagenic specificity of a potent carcinogen, ben- zo[c]phenanthrene (4R,3S)α-dihydrodiol (2S,1R)α-epoxide, which reacts with adenine and guanine in DNA. Proc. Natl. Acad. Sci. USA 86:2291–2295.
   PubMedGoogle Scholar
• Carothers, A. Μ., J. Mucha, and D. Grunberger. 1991. DNA strand-specific mutations induced by (±)-3α,4β-dihydroxy- la,2a-epoxy-l,2,3,4-tetrahydrobenzo[c]phenanthrene in the dihydrofolate reductase gene. Proc. Natl. Acad. Sci. USA 88:5749–5753.
   PubMedGoogle Scholar
• Carothers, A. Μ., G. Urlaub, N. Ellis, and L. A. Chasin. 1983. Structure of the dihydrofolate reductase gene in Chinese ham-ster ovary cells. Nucleic Acids Res. 11:1997–2012.
   PubMedGoogle Scholar
• Carothers, A. Μ., G. Urlaub, D. Grunberger, and L. A. Chasin. 1988. Mapping and characterization of mutations induced by benzo[a]pyrene diol epoxide at the dihydrofolate reductase locus in CHO cells. Somatic Cell Mol. Genet. 14:169–183.
   PubMedGoogle Scholar
• Carothers, A. Μ., G. Urlaub, D. Grunberger, and L. A. Chasin. 1992. Unpublished data.
   Google Scholar
• Carothers, A. Μ., G. Urlaub, D. Mucha, D. Grunberger, and L. A. Chasin. 1989. Point mutation analysis in a mammalian gene: rapid preparation of total RNA, PCR amplification of cDNA, and Taq sequencing by a novel method. BioTechniques 7:494–499.
   PubMed Web of Science ®Google Scholar
• Carothers, A. Μ., G. Urlaub, J. Mucha, R. Harvey, L. A. Chasin, and D. Grunberger. 1990. Splicing mutations in the CHO DHFR gene preferentially induced by (±)-3α,4β-dihy- droxy-1a,2a-epoxy-1,2,3,4,-tetrahydrobenzo[c]phenanthrene. Proc. Natl. Acad. Sci. USA 87:5464–5468.
   PubMed Web of Science ®Google Scholar
• Carstens, R. P., W. A. Fenton, and L. R. Rosenberg. 1991. Identification of RNA splicing errors resulting in human orni-thine transcarbamylase deficiency. Am. J. Hum. Genet. 48:1105–1114.
   PubMedGoogle Scholar
• Chen, I-T., and L. A. Chasin. 1992. Update on point mutation analysis in a mammalian gene, p. 60. In J. Ellingboe and U. B. Gyllensten (ed.), The PCR technique: DNA sequencing. Eaton Publishing Co., Natick, Mass.
   Google Scholar
• Chen, R. W., V. Μ. Maher, and J. J. McCormick. 1990. Effect of excision repair by diploid human fibroblasts on the kinds and locations of mutations induced by BPDE in the coding region of the HPRT gene. Proc. Natl. Acad. Sci. USA 87:8680–8684.
   PubMed Web of Science ®Google Scholar
• Chirgwin, J. Μ., A. E. Przybyla, R. J. MacDonald, and W. J. Rutter. 1979. Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease. Biochemistry 18:5294–5299.
   PubMed Web of Science ®Google Scholar
• Ciudad, C. J., G. Urlaub, and L. Chasin. 1988. Deletion analysis of the Chinese hamster dihydrofolate reductase gene promoter. J. Biol. Chem. 263:16274–16282.
   PubMed Web of Science ®Google Scholar
• Clouet-d’Orval, B., Y. d’Aubenton-Carafa, P. Sirand-Pugnet, Μ. Gallego, E. Brody, and J. Marie. 1991. RNA secondary structure repression of a muscle-specific exon in HeLa cell nuclear extracts. Science 252:1823–1828.
   PubMedGoogle Scholar
• Crouse, G. F., R. N. McEwan, and Μ. L. Pearson. 1983. Expression and amplification of engineered mouse dihydrofolate reductase minigenes. Mol. Cell. Biol. 3:257–266.
   PubMedGoogle Scholar
• Deshler, L. O., and J. J. Rossi. 1991. Unexpected point mutations activate cryptic 3′ splice sites by perturbing a natural secondary structure within a yeast intron. Genes Dev. 5:1252–1263.
   PubMedGoogle Scholar
• Dipple, A., Μ. A. Pigott, S. K. Agarwal, H. Yagi, J. Μ. Sayer, and D. Μ. Jerina. 1987. Optically active benzo[c]phenanthrene diol epoxides bind extensively to adenine in DNA. Nature (London) 327:535–536.
   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
• 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
• Freier, S., R. Kierzek, J. A. Jaeger, N. Sugimoto, Μ. Caruthers, T. Neilson, and D. H. Turner. 1986. Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl. Acad. Sci. USA 83:9373–9377.
   PubMed Web of Science ®Google Scholar
• Fu, X.-D., R. A. Katz, A. Μ. Skalka, and T. Maniatis. 1991. The role of branchpoint and 3′-exon sequences in the control of balanced splicing of avian retrovirus RNA. Genes Dev. 5:211–220.
   PubMedGoogle Scholar
• Fu, X.-D., and T. Maniatis. 1990. Factor required for mammalian Spliceosome assembly is localized to discrete regions in the nucleus. Nature (London) 343:437–441.
   PubMed Web of Science ®Google Scholar
• Fu, X.-Y., and J. L. Manley. 1987. Factors influencing alternative splice site utilization in vitro. Mol. Cell. Biol. 7:738–748.
   PubMed Web of Science ®Google Scholar
• Fuscoe, J. C., R. G. Fenwick, D. H. Ledbetter, and C. T. Caskey. 1983. Deletion and amplification of the HGPRT locus in Chinese hamster cells. Mol. Cell. Biol. 3:1086–1096.
   PubMed Web of Science ®Google Scholar
• Green, Μ. R. 1986. Pre-mRNA splicing. Annu. Rev. Genet. 20:671–708.
   PubMed Web of Science ®Google Scholar
• Green, Μ. R. 1991. Biochemical mechanisms of constitutive and regulated pre-mRNA splicing. Annu. Rev. Cell Biol. 7:559–599.
   PubMedGoogle Scholar
• Hampson, R., L. Follette, and F. Rottman. 1989. Alternative processing of bovine growth hormone mRNA is influenced by downstream exon sequences. Mol. Cell. Biol. 9:1604–1610.
   PubMedGoogle Scholar
• Hidaka, Y., T. D. Palella, T. E. O’Toole, S. A. Tarlé, and W. N. Kelley. 1987. Human adenine phosphoribosyltransferase: identification of allelic mutations at the nucleotide level as a cause of complete deficiency of the enzyme. J. Clin. Invest. 80:1409–1415.
   PubMed Web of Science ®Google Scholar
• Hornig, H., Μ. Aebi, and C. Weissmann. 1986. Effect of mutations at the lariat branch acceptor site on β-globin pre- mRNA splicing in vitro. Nature (London) 324:589–591.
   PubMedGoogle Scholar
• Huang, S., and D. L. Spector. 1991. Nascent pre-mRNA transcripts are associated with nuclear regions enriched in splicing factors. Genes Dev. 5:2288–2302.
   PubMedGoogle Scholar
• Ip, J., G. Landau, J. Schmidt, and L. A. Chasin. 1992. Unpublished data.
   Google Scholar
• Jackson, I. L. 1991. A reappraisal of non-consensus mRNA splice sites. Nucleic Acids Res. 19:3795–3798.
   PubMedGoogle Scholar
• Kedes, D. H., and J. A. Steitz. 1987. Accurate 5′ splice-site selection in mouse kappa-immunoglobin light chain premessenger RNAs is not cell-type specific. Proc. Natl. Acad. Sci. USA 84:7928–7932.
   PubMedGoogle Scholar
• Kedes, D. H., and J. A. Steitz. 1988. Correct in vivo splicing of the mouse immunoglobulin κ light-chain pre-mRNA is dependent on the 5′ splice-site position even in the absence of transcription. Genes Dev. 2:1448–59.
   PubMedGoogle Scholar
• Kuivaniemi, H., S. Kontusaari, G. Tromp, Μ. Zhao, C. Sabol, and D. J. Prockop. 1990. Identical G+1 to A mutations in three different introns of the type III procollagen gene (COL3A1) produce different patterns of RNA splicing in three variants of Ehlers-Danlos syndrome IV. J. Biol. Chem. 265:12067–12074.
   PubMed Web of Science ®Google Scholar
• Lawrence, J. B., R. H. Singer, and L. Μ. Marselle. 1989. Highly localized tracks of specific transcripts within interphase nuclei visualized by in situ hybridization. Cell 57:493–502.
   PubMed Web of Science ®Google Scholar
• Lebkowski, J., J. H. Miller, and Μ. P. Calos. 1986. Determination of DNA sequence changes induced by ethyl methanesulfonate in human cells using a shuttle vector system. Mol. Cell. Biol. 6:1838–1842.
   PubMed Web of Science ®Google Scholar
• Libri, D., A. Piseri, and Μ. Y. Fiszman. 1991. Tissue-specific splicing in vivo of the β-tropomyosin gene: dependence on an RNA secondary structure. Science 252:1842–1845.
   PubMed Web of Science ®Google Scholar
• Lossi, A.-M., and J.-L. Berge-Lefranc. 1989. The mRNA transcripts from a mutant β-globin gene derived from splicing at preferential cryptic sites. FEBS Lett. 256:163–166.
   PubMedGoogle Scholar
• Lowery, D., and B. Van Ness. 1987. In vitro splicing of kappa immunoglobulin precursor mRNA. Mol. Cell. Biol. 7:1346–1351.
   PubMedGoogle Scholar
• Lowy, L., A. Pellicer, J. F. Jackson, G.-K. Sim, S. Silverstein, and R. Axel. 1980. Isolation of transforming DNA: cloning the hamster aprt gene. Cell 22:817–823.
   PubMed Web of Science ®Google Scholar
• Mitchell, P., G. Urlaub, and L. A. Chasin. 1986. Spontaneous splicing mutations at the dihydrofolate reductase locus in CHO cells. Mol. Cell. Biol. 6:1926–1935.
   PubMedGoogle Scholar
• Mitchell, P. J., A. Μ. Carothers, J. H. Han, J. D. Harding, E. Kas, L. Venolia, and L. A. Chasin. 1986. Multiple transcription start sites, DNase I-hypersensitive sites, and an opposite strand exon in the 5′ region of the CHO dhfr gene. Mol. Cell. Biol. 6:425–440.
   PubMedGoogle Scholar
• Mount, S. Μ. 1982. A catalogue of splice junction sequences. Nucleic Acids Res. 10:459–472.
   PubMed Web of Science ®Google Scholar
• Mulligan, R. C., and P. Berg. 1980. Expression of a bacterial gene in mammalian cells. Science 209:1422–1427.
   PubMed Web of Science ®Google Scholar
• Nalbantoglu, J., D. Goncalves, and Μ. Meuth. 1985. Structure of mutant alleles at the APRT locus of CHO cells. J. Mol. Biol. 167:575–594.
   Google Scholar
• Nelson, K. K., and Μ. R. Green. 1988. Splice site selection and ribonucleoprotein complex assembly during in vitro pre-mRNA splicing. Genes Dev. 2:319–329.
   PubMedGoogle Scholar
• Nelson, K. K., and Μ. R. Green. 1989. Mammalian U2 snRNA has a sequence-specific RNA-binding activity. Genes Dev. 3:1562–1571.
   PubMedGoogle Scholar
• Noble, J. C., C. Prives, and J. Manley. 1988. Alternative splicing of SV40 early pre-mRNA is determined by branch site selection. Genes Dev. 2:1460–75.
   PubMedGoogle Scholar
• Orkin, S. H., and H. H. Kazazian, Jr. 1984. The mutation and polymorphism of the human β-globin gene and its surrounding DNA. Annu. Rev. Genet. 18:131–71.
   PubMed Web of Science ®Google Scholar
• Patterson, B., and C. Guthrie. 1991. A U-rich tract enhances usage of an alternative 3′ splice site in yeast. Cell 64:181–187.
   PubMedGoogle Scholar
• Penotti, F. E. 1991. Human pre-mRNA splicing signals. J. Theor. Biol. 150:385–420.
   PubMedGoogle Scholar
• Reed, R. 1989. The organization of 3′ splice-site sequences in mammalian introns. Genes Dev. 3:2113–2123.
   PubMedGoogle Scholar
• Reed, R., and T. Maniatis. 1986. A role for exon sequences and splice-site proximity in splice-site selection. Cell 46:681–690.
   PubMed Web of Science ®Google Scholar
• Reed, R., and T. Maniatis. 1988. The role of the mammalian branchpoint sequence in pre-mRNA splicing. Genes Dev. 2:1268–1276.
   PubMedGoogle Scholar
• Roberson, B., G. Cote, and S. Berget. 1990. Exon definition may facilitate splice site selection in RNAs with multiple exons. Mol. Cell. Biol. 10:84–94.
   PubMedGoogle Scholar
• Ruskin, B., J. Greene, and Μ. Green. 1985. Cryptic branch point activation allows accurate in vitro splicing of human β-globin intron mutants. Cell 41:833–44.
   PubMedGoogle Scholar
• Seetharam, S., and I. B. Dicker. 1991. A rapid and complete 4-step protocol for obtaining nucleotide sequence from E. coli genomic DNA from overnight cultures. BioTechniques 11:32–34.
   Google Scholar
• Senapathy, P., Μ. P. Shapiro, and N. Harris. 1990. Splice junctions, branch point sites, and exons: sequence statistics, identification, and applications to genome project. Methods Enzymol. 183:252–278.
   PubMed Web of Science ®Google Scholar
• Shapiro, Μ. P., and P. Senapathy. 1987. RNA splice junction of different classes of eukaryotes: sequence statistics and functional implications in gene expression. Nucleic Acids Res. 15:7155–7174.
   PubMed Web of Science ®Google Scholar
• Siliciano, P., and C. Guthrie. 1988. 5′ splice site selection in yeast: genetic alterations in base-pairing with U1 reveal additional requirements. Genes Dev. 2:1258–1267.
   PubMed Web of Science ®Google Scholar
• Singer, B., and D. Grunberger. 1983. Molecular biology of mutagens and carcinogens, p. 56–59. Plenum Press, New York.
   Google Scholar
• Smith, C. W. J., and B. Nadal-Ginard. 1989. Mutually exclusive splicing of α-tropomyosin exons enforced by an unusual lariat branch point location: implications for constitutive splicing. Cell 56:749–758.
   PubMed Web of Science ®Google Scholar
• Southern, E. Μ. 1975. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol. 98:503–517.
   PubMed Web of Science ®Google Scholar
• Steingrimsdottir, H., G. Rowley, G. Dorado, J. Cole, and A. R. Lehmann. 1992. Mutations which alter splicing in the human hypoxanthine guanine phosphoribosyltransferase gene. Nucleic Acids Res. 20:1201–1208.
   PubMedGoogle Scholar
• Streuli, Μ., and H. Saito. 1989. Regulation of tissue-specific alternative splicing: exon-specific cis-elements govern the splicing of leukocyte common antigen pre-mRNA. EMBO J. 8:787–796.
   PubMedGoogle Scholar
• Talerico, Μ., and S. 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
• Turnbull-Ross, A. D., A. J. Else, and I. C. Eperon. 1988. The dependence of splicing efficiency on the length of 3′ exon. Nucleic Acids Res. 16:395–411.
   PubMedGoogle Scholar
• Turner, D. H., N. Sugimoto, and S. Freier. 1988. RNA structure prediction. Annu. Rev. Biophys. Chem. 17:167–192.
   PubMedGoogle Scholar
• Urlaub, G., and L. A. Chasin. 1980. Isolation of Chinese hamster cell mutants deficient in dihydrofolate reductase activity. Proc. Natl. Acad. Sci. USA 77:4216–4220.
   PubMed Web of Science ®Google Scholar
• Urlaub, G., E. Kas, A. Μ. Carothers, and L. A. Chasin. 1983. Deletion of the diploid dihydrofolate reductase locus from cultured mammalian cells. Cell 33:405–412.
   PubMed Web of Science ®Google Scholar
• Urlaub, G., P. J. Mitchell, C. J. Ciudad, and L. A. Chasin. 1989. Nonsense mutations in the dihydrofolate reductase gene affect RNA processing. Mol. Cell. Biol. 9:2868–2880.
   PubMedGoogle Scholar
• Urlaub, G., P. J. Mitchell, E. Kas, L. A. Chasin, V. L. Funanage, T. T. Myoda, and J. L. Hamlin. 1986. The effect of gamma rays at the dihydrofolate reductase locus: deletions and inversions. Somatic Cell Mol. Genet. 12:555–566.
   PubMedGoogle Scholar
• Venolia, L., G. Urlaub, and L. A. Chasin. 1987. Polyadenylation of Chinese hamster dihydrofolate reductase genomic genes and minigenes after gene transfer. Somat. Cell Mol. Genet. 13:491–501.
   PubMedGoogle Scholar
• Vrieling, H., Μ. J. Niericker, J. W. I. Μ. Simons, and A. A. van Zeeland. 1988. Molecular analysis of mutations induced by N-ethyl-N-nitrosourea at the HPRT locus in mouse lymphoma cells. Mutat. Res. 198:99–106.
   PubMedGoogle Scholar
• Vrieling, H., Μ. L. Van Roouen, N. A. Groden, Μ. Z. Zdzienicka, J. W. I. Μ. Simons, P. H. Lohman, and A. A. van Zeeland. 1989. DNA strand specificity for UV-induced mutations in mammalian cells. Mol. Cell. Biol. 9:1277–1283.
   PubMedGoogle Scholar
• Weber, S., and Μ. Aebi. 1988. In vitro splicing of mRNA precursors: 5′ cleavage site can be predicted from the interaction between the 5′ splice region and the 5′ terminal of U1 snRNA. Nucleic Acids Res. 16:471–486.
   PubMed Web of Science ®Google Scholar
• Wieringa, B., F. Meyer, J. Reiser, and C. Weissmann. 1983. Unusual splice sites revealed by mutagenetic inactivation of an authentic splice site of the rabbit β-globin gene. Nature (London) 301:38–43.
   PubMed Web of Science ®Google Scholar
• Wigler, Μ., A. Pellicer, S. Silverstein, R. Axel, G. Urlaub, and L. A. Chasin. 1979. Transformation of the APRT locus in mammalian cells. Proc. Natl. Acad. Sci. USA 76:1373–1376.
   PubMed Web of Science ®Google Scholar
• Wu, J., and J. L. Manley. 1989. Mammalian pre-mRNA branch site selection by U2 snRNP involves base pairing. Genes Dev. 3:1553–1561.
   PubMed Web of Science ®Google Scholar
• Zhang, L.-H., H. Vrieling, A. A. van Zeeland, and D. Jenssen. 1992. Spectrum of spontaneously occurring mutations in the hprt gene of V7, Chinese hamster cells. J. Mol. Biol. 223:627–635.
   PubMedGoogle Scholar
• Zhuang, Y., and A. Weiner. 1986. A compensatory base change in U1 snRNA suppresses a 5′ splice site mutation. Cell 46:827–835.
   PubMed Web of Science ®Google Scholar
• Zhuang, Y., and A. Weiner. 1989. A compensatory base change in human U2 snRNA can suppress a branch site mutation. Genes Dev. 3:1545–1552.
   PubMed Web of Science ®Google Scholar
• Zuker, Μ. 1989. On finding all sub-optimal foldings of an RNA molecule. Science 244:48–52.
   PubMed Web of Science ®Google Scholar