Summary
Reports of single base-pair substitutions that cause human genetic disease and that have been located and characterized in an unbiased fashion were collated; 32% of point mutations were CG → TG or CG → CA transitions consistent with a chemical model of mutation via methylation-mediated deamination. This represents a 12-fold higher frequency than that predicted from random expectation, confirming that CG dinucleotides are indeed hotspots of mutation causing human genetic disease. However, since CG also appears hypermutable irrespective of methylation-mediated deamination, a second mechanism may also be involved in generating CG mutations. The spectrum of point mutations occurring outwith CG dinucleotides is also non-random, at both the mono- and dinucleotide levels. An intrinsic bias in clinical detection was excluded since frequencies of specific amino acid substitutions did not correlate with the ‘chemical difference’ between the amino acids exchanged. Instead, a strong correlation was observed with the mutational spectrum predicted from the experimentally measured mispairing frequencies of vertebrate DNA polymerases α and β in vitro. This correlation appears to be independent of any difference in the efficiency of enzymatic proofreading/mismatch-repair mechanisms but is consistent with a physical model of mutation through nucleotide misincorporation as a result of transient misalignment of bases at the replication fork. This model is further supported by an observed correlation between dinucleotide mutability and stability, possibly because transient misalignment must be stabilized long enough for misincorporation to occur. Since point mutations in human genes causing genetic disease neither arise by random error nor are independent of their local sequence environment, predictive models may be considered. We present a computer model (MUTPRED) based upon empirical data; it is designed to predict the location of point mutations within gene coding regions causing human genetic disease. The mutational spectrum predicted for the human factor IX gene was shown to resemble closely the observed spectrum of point mutations causing haemophilia B. Further, the model was able to predict successfully the rank order of disease prevalence and/or mutation rates associated with various human autosomal dominant and sex-linked recessive conditions. Although still imperfect, this model nevertheless represents an initial attempt to relate the variable prevalence of human genetic disease to the mutability inherent in the nucleotide sequences of the underlying genes.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Alber T (1989) Mutational effects on protein stability. Annu Rev Biochem 58:765–789
Bains W, Bains J (1987) Rate of base substitution in mammalian nuclear DNA is dependent on local sequence context. Mutat Res 179:65–74
Barker D, Schaefer M, White R (1984) Restriction sites containing CpG show a higher frequency of polymorphism in human DNA. Cell 36:131–138
Bessman MJ, Reha-Krantz LJ (1977) Studies on the biochemical basis of spontaneous mutation. V. Effect of temperature on mutation frequency. J Mol Biol 116:115–123
Beutler E, Gelbart T, Han J, Koziol JA, Beutler B (1989) Evolution of the genome and the genetic code: selection at the dinucleotide level by methylation and polyribonucleotide cleavage. Proc Natl Acad Sci USA 86:192–196
Bialek G, Nasheuer H-P, Goetz H, Grosse F (1989) Exonucleotic proofreading increases the accuracy of DNA synthesis by human lymphocyte DNA polymerase αDNA primase. EMBO J 8:1833–1839
Bird AP (1986) CpG-rich islands and the function of DNA methylation. Nature 321:209–213
Boosalis MS, Mosbaugh DW, Hamatake R, Sugino A, Kunkel TA, Goodman MF (1989) Kinetic analysis of base substitution mutagenesis by transient misalignment of DNA and by miscoding. J Biol Chem 264:11360–11366
Brown TC, Jiricny J (1988) Different base/base mispairs are corrected with different efficiencies and specificities in monkey kidney cells. Cell 54:705–711
Castora FJ, Arnheim N, Simpson NN (1980) Mitochondrial DNA polymorphism: evidence that variants detected by restriction enzymes differ in nucleotide sequence rather than in methylation. Proc Natl Acad Sci USA 77:6415–6419
Conkling MA, Koch RE, Drake JW (1980) Determination of mutation rates in bacteriophage T4 by unneighborly base pairs: genetic analysis. J Mol Biol 143:303–315
Cooper DN (1983) Eukaryotic DNA methylation. Hum Genet 64:315–333
Cooper DN, Gerber-Huber S (1985) DNA methylation and CpG suppression. Cell Differ 17:199–205
Cooper DN, Krawczak M (1989) Cytosine methylation and the fate of CpG dinucleotides in vertebrate genomes. Hum Genet 83:181–189
Cooper DN, Schmidtke J (1984) DNA restriction fragment length polymorphisms and heterozygosity in the human genome. Hum Genet 66:1–16
Cooper DN, Schmidtke J (1989) Diagnosis of genetic disease using recombinant DNA. Second edition. Hum Genet 83:307–334
Cooper DN, Tuddenham EGD (1991) The molecular genetics of coagulation disorders. Oxford University Press, Oxford (in press)
Cooper DN, Youssoufian H (1988) The CpG dinucleotide and human genetic disease. Hum Genet 78:151–155
Cooper DN, Errington LH, Clayton RM (1983) Variation in the DNA methylation pattern of expressed and non-expressed genes in chicken. DNA 2:131–140
Cooper DN, Gerber-Huber S, Nardelli D, Schubiger JL, Wahli W (1987) The distribution of the dinucleotide CpG and cytosine methylation in the vitellogenin gene family. J Mol Evol 25:107–115
Coulondre C, Miller JH, Farabaugh PJ, Gilbert W (1978) Molecular basis of base substitution hotspots in Escherichia coli. Nature 274:775–780
Crow JF, Denniston C (1985) Mutation in human populations. Adv Hum Genet 14:59–123
De Jong PJ, Grosovsky AJ, Glickman BW (1988) Spectrum of spontaneous mutation at the APRT locus of Chinese hamster ovary cells: an analysis at the DNA sequence level. Proc Natl Acad Sci USA 85:3499–3503
Drake JW (1970) The molecular basis of mutation. Holden Day, San Francisco
Duncan BK, Miller JH (1980) Mutagenic deamination of cytosine residues in DNA. Nature 287:560–561
Ehrlich M, Norris KF, Wand RYH, Kuo KC, Gehrke CW (1986) DNA cytosine methylation and heat-induced deamination. Biosci Rep 6:387–393
Epstein CJ (1967) Non-randomness of amino-acid changes in the evolution of homologous proteins. Nature 215:355–359
Fersht AR (1979) Fidelity of replication of phage Phi-X174 DNA by DNA polymerase-III holoenzyme: spontaneous mutation by misincorporation. Proc Natl Acad Sci USA 76:4946–4950
Fitch WM (1980) Estimating the total number of nucleotide substitutions since the common ancestor of a pair of homologous genes: comparison of several methods and three beta hemoglobin messenger RNAs. J Mol Evol 16:153–209
Gardiner-Garden M, Frommer M (1987) CpG islands in vertebrate genomes. J Mol Biol 196:261–282
Giroux CN, Mis JRA, Pierce MK, Kohalmi SE, Kunz BA (1988) DNA sequence analysis of spontaneous mutations in the SUP4-o gene of Saccharomyces cerevisiae. Mol Cell Biol 8:978–981
Gojobori TZ, Li W-H, Graur D (1982) Patterns of nucleotide substitution in pseudogenes and functional genes. J Mol Evol 18:360–369
Golding GB, Glickman BW (1985) Sequence-directed mutagenesis: evidence from a phylogenetic history of human α-interferon genes. Proc Natl Acad Sci USA 82:8577–8581
Golding GB, Glickman B W (1986) Evidence for local DNA influences on patterns of substitution in the human α-interferon gene family. Can J Genet Cytol 28:483–496
Grantham R (1974) Amino acid difference formula to help explain protein evolution. Science 185:862–864
Groot GSP, Kroon AM (1979) Mitochondrial DNA from various organisms does not contain internally methylated cytosine in-CCGG-sequences. Biochem Biophys Acta 564:355–357
Hsie AW, Recio L, Katz DS, Lee CQ, Wagner M, Shenley RL (1986) Evidence for reactive oxygen species inducing mutations in mammalian cells. Proc Natl Acad Sci USA 83:9616–9620
Hubrich-Kühner K, Buhk H-J, Wagner H, Kröger H, Simon D (1989) Non-CG recognition sequences of DNA cytosine-5-methyltransferase from rat liver. Biochem Biophys Res Commun 160:1175–1182
Jones M, Wagner R, Radman M (1987) Repair of a mismatch is influenced by the base composition of the surrounding nucleotide sequence. Genetics 115:605–610
Kunkel TA (1984) Mutational specificity of depurination. Proc Natl Acad Sci USA 81:1494–1498
Kunkel TA (1985a) The mutational specificity of DNA polymerase-β during in vitro DNA synthesis. J Biol Chem 260:5787–5796
Kunkel TA (1985b) The mutational specificity of DNA polyemerases -α and -γ during in vitro DNA synthesis. J Biol Chem 260:12866–12874
Kunkel TA (1988) Exonucleolytic proofreading. Cell 53:837–840
Kunkel TA, Alexander PS (1986) The base substitution fidelity of eukaryotic DNA polymerases. J Biol Chem 261:160–166
Kunkel TA, Bebenek K (1988) Recent studies of the fidelity of DNA synthesis. Biochem Biophys Acta 951:1–15
Kunkel TA, Soni A (1988) Mutagenesis by transient misalignment. J Biol Chem 263:14784–14789
Kunkel TA, Schaaper RM, Beckmann RA, Loeb LA (1981) On the fidelity of DNA replication. J Biol Chem 256:9883–9889
Kunkel TA, Schaaper RM, Loeb LA (1983) Depurinationinduced infidelity of DNA synthesis with purified DNA replication proteins in vitro. Biochemistry 22:2378–2384
Kunkel TA, Sabatino RD, Bambara RA (1987) Exonucleolytic proofreading by calf thymus DNA polymerase δ. Proc Natl Acad Sci USA 84:4865–4869
Landis CA, Masters SB, Spada A, Pace AM, Bourne HR, Vallar L (1989) GTPase inhibiting mutations activate the α chain of Gs and stimulate adenylyl cyclase in human pituitary tumours. Nature 340:692–696
Li W-H, Wu C-I, Luo C-C (1984) Non-randomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications. J Mol Evol 21:58–71
Lindahl T (1982) DNA repair enzymes. Annu Rev Biochem 51:61–87
Lindahl T, Nyberg B (1972) Rate of depurination of native deoxyribonucleic acid. Biochemistry 11:3610–3618
Loeb LA (1985) Apurinic sites as mutagenic intermediates. Cell 40:483–484
Loeb LA, Kunkel TA (1982) Fidelity of DNA synthesis. Annu Rev Biochem 52:429–457
Loeb LA, Preston BD (1986) Mutagenesis by apurinic/apyrimidinic sites. Annu Rev Genet 20:201–230
Maeda N, Wu C-I, Bliska J, Reneke J (1988) Molecular evolution of intergenic DNA in higher primates: pattern of DNA changes, molecular clock, and evolution of repetitive sequences. Mol Biol Evol 5:1–20
Maruyama R, Gojobori T, Aota S, Ikemura T (1986) Codon usage tabulated from the GenBank genetic sequence data. Nucleic Acids Res 14 [Suppl]:r151-r197
McMahon JE, Tinoco I (1978) Sequences and efficiencies of proposed mRNA terminators. Nature 271:275–277
Mendelman LV, Boosalis MS, Petruska J, Goodman MF (1989) Nearest neighbour influences on DNA polymerase insertion fidelity. J Biol Chem 264:14415–14423
Meuth M (1989) The molecular basis of mutations induced by deoxynucleoside triphosphate pool imbalances in mammalian cells. Exp Cell Res 181:305–316
Modrich P (1987) DNA mismatch correction. Annu Rev Biochem 56:435–466
Nalbantoglu J, Goncalves O, Meuth M (1983) Structure of mutant alleles of the aprt locus in Chinese hamster ovary cells. J Mol Biol 167:575–594
Nalbantoglu J, Phear G, Meuth M (1987) DNA sequence analysis of spontaneous mutations at the aprt locus of hamster cells. Mol Cell Biol 7:1445–1449
Nussinov R (1981) Nearest neighbour nucleotide patterns; structural and biological implications. J Biol Chem 256:8458–8462
Ohno S (1988) Universal rule for coding sequence construction: TA/CG deficiency TG/CT excess. Pro Natl Acad Sci USA 85:9630–9634
Pattinson JK, Millar DS, Grundy CB, Wieland K, Mibashan RS, Martinowitz U, McVey J, Tan-Un K, Vidaud M, Goossens M, Sampietro M, Krawczak M, Reiss J, Zoll B, Whitmore D, Bradshaw A, Wensley R, Ajani A, Mitchell V, Rizza C, Maia R, Winter P, Mayne EE, Schwartz M, Green PJ, Kakkar VV, Tuddenham EGD, Cooper DN (1990) The molecular genetic analysis of haemophilia A; a directed-search strategy for the detection of point mutations in the human factor VIII gene. Blood (in press)
Petruska J, Goodman MF (1985) Influence of neighbouring bases on DNA polymerase insertion and proofreading fidelity. J Biol Chem 260:7533–7539
Phear G, Nalbantoglu J, Meuth M (1987) Next-nucleotide effects in mutations driven by DNA precursor pool imbalances at the aprt locus of Chinese hamster ovary cells. Proc Natl Acad Sci USA 84:4450–4454
Phear G, Armstrong W, Meuth M (1989) Molecular basis of spontaneous mutation at the aprt locus of hamster cells. J Mol Biol 209:577–582
Reyland ME, Lehman IR, Loeb LA (1988) Specificity of proofreading by the 3′ → 5′ exonuclease of the DNA polymeraseprimase of Drosophila melanogaster. J Biol Chem 263:6518–6524
Richter C, Park J-W, Ames BN (1988) Normal oxidative damage to mitochondrial and nuclear DNA is extensive. Proc Natl Acad Sci USA 85:6465–6467
Roberts JD, Kunkel TA (1986) Mutational specificity of animal cell DNA polymerases. Environ Mol Mutagen 8:769–789
Rodeghiero F, Castaman G, Dini E (1987) Epidemiological investigation of the prevalence of von Willebrand's disease. Blood 69:454–459
Sagher D, Strauss B (1983) Insertion of nucleotides opposite apurinic/apyrimidinic sites in deoxyribonucleic acid during in vitro synthesis: uniqueness of adenine nucleotides. Biochemistry 22:4518–4526
Salser W (1978) Globin mRNA sequences: analysis of base pairing and evolutionary implications. Cold Spring Harb Symp Quant Biol 42:985–1002
Saluz HP, Jost JP (1989) A simple high-resolution procedure to study DNA methylation and in vivo DNA-protein interactions on a single-copy gene level in higher eukaryotes. Proc Natl Acad Sci USA 86:2602–2606
Savatier P, Trabuchet G, Fauré C, Cheblouré Y, Gouy M, Verdier G, Nigon VM (1985) Evolution of the primate beta-globin gene region. High rate of variation in CpG dinucleotides and in short repeated sequences between man and chimpanzee. J Mol Biol 182:21–29
Schaaper RM, Kunkel TA, Loeb LA (1983) Infidelity of DNA synthesis associated with bypass of apurinic sites. Proc Natl Acad Sci USA 80:487–491
Setlow P (1976) Nearest neighbour frequencies in deoxyribonucleic acids. In: Fasman GD (ed) Handbook of biochemistry and molecular biology, vol 2: Nucleic acids, 3rd edn. CRC Press, Cleveland, pp 312–318
Shearman CW, Loeb LA (1979) The effects of depurination on the fidelity of DNA synthesis. J Mol Biol 128:197–218
Stout JT, Caskey CT (1985) HPRT: gene structure, expression and mutation. Annu Rev Genet 19:127–148
Takeshita M, Chang C-N, Johnson F, Will S, Grollman A (1987) Oligodeoxynucleotides containing synthetic abasic sites. J Biol Chem 262:10171–10179
Thacker J (1985) The molecular nature of mutations in cultured mammalian cells: a review. Mutat Res 150:431–442
Topal MD, Fresco JR (1976) Complementary base pairing and the origin of substitution mutations. Nature 263:285–289
Vogel F (1972) Non-randomness of base replacement in point mutation. J Mol Evol 1:334–367
Vogel F, Kopun M (1977) Higher frequencies of transitions among point mutations. J Mol Evol 9:159–180
Vogel F, Motulsky AG (1986) Human genetics ⇆roblems and approaches, 2nd edn. Springer, Berlin Heidelberg New York
Vogel F, Kopun M, Rathenburg R (1976) Mutation and molecular evolution. In: Goodman M, Tashian RE, Tashian JH (eds) Molecular anthropology. Plenum Press, New York, pp 13–33
Woodcock DM, Crowther PJ, Diver WP (1987) The majority of methylated deoxycytidines in human DNA are not in the CpG dinucleotide. Biochem Biophys Res Commun 145:888–894
Woodcock DM, Crowther PJ, Jefferson S, Diver WP (1988) Methylation at dinucleotides other than CpG: implications for human maintenance methylation. Gene 74:151–152
Wu C-I, Maeda N (1987) Inequality in mutation rates of the two strands of DNA. Nature 327:169–170
Youssoufian H, Antonarakis SE, Bell W, Griffin AM, Kazazian HH (1988) Nonsense and missense mutations in hemophilia A: estimate of the relative mutation rate at CG dinucleotides. Am J Hum Genet 42:718–725
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Cooper, D.N., Krawczak, M. The mutational spectrum of single base-pair substitutions causing human genetic disease: patterns and predictions. Hum Genet 85, 55–74 (1990). https://doi.org/10.1007/BF00276326
Received:
Revised:
Issue Date:
DOI: https://doi.org/10.1007/BF00276326