Summary
A cloned cDNA for α-1-antitrypsin (α-1-AT) was selected from a human liver cDNA library. The identity of the clone was established by hybrid-selected translation and partial DNA sequencing. The cDNA was used as a probe to search for restriction site polymorphisms (RSPs) near the α-1-AT gene. Only two RSPs were found using 29 different restriction enzymes. Each of these polymorphisms resulted from the loss of a restriction site, one for EcoRI and the other for Taq I. The frequency of polymorphic restriction was calculated to be 1.1% to 2.6% of all sites tested, a figure lower than the 9.3% value observed for 12 RSPs in the human β-globin gene cluster. Since the corresponding figure for detectable polymorphisms at the α-1-AT locus at the protein level is 12%, restriction enzymes are comparatively inefficient in detecting genetic variability. The basis of this inefficiency was studied by computing the nucleotide diversity from the RSP data. On the average, one in 500 to 1000 bases is polymorphic around the α-1-At locus. This value is comparable to that which we have calculated for the human β-globin gene cluster and the human growth hormone gene cluster (both one in 500). These data demonstrate the limited usefulness of linked RSPs for genetic linkage studies at the α-1-AT locus.
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Beaudet AL, Su T-S, O'Brien WE, D'Eustachio P, Barker PE, Ruddle FH (1982) Dispersion of arginosuccinate synthetase-like human genes to multiple autosomes and the X chromosome. Cell 30:287–293
Bell GI, Karam JH, Rutter WJ (1982) Polymorphic DNA region adjacent to the 5′ of the human insulin gene. Proc Natl Acad Sci USA 78:5759–5763
Botstein D, White RC, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331
Carrell RW, Jeppson J-O, Laurell CB, Brennan SO, Owen MC, Vaughn L, Boswell DR (1982) Structure and variation of human α-1-antitrypsin. Nature 298:329–334
Chakravarti A, Buetow KH, Antonarakis SE, Boehm CD, Kazazian HH (1981) Nonrandom association and evolution in the β-globin gene cluster. Am J Hum Genet 33:134a
Chakravarti A, Phillips JA, Mellits KH, Buetow KH, Seeburg PH (1984) Patterns of polymorphism and linkage disequilibrium in the human growth hormone cluster suggests multiple duplication events. Proc Natl Acad Sci USA 81:6085–6089
Chirgwin JM, Przybyla AE, MacDonald RJ, Rutter WJ (1979) Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease. Biochemistry 18:5295–5299
Daiger SP, Wilden RS, Su T-S (1982a) Sequences on the human Y chromosome homologous to the autosomal gene for argininosuccinate synthetase. Nature 298:682–684
Daiger SP, Wilden RS, Hoffman N, Su T-S (1982b) Restriction fragment length polymorphisms detected with a cDNA probe to argininosuccinate synthetase. Am J Hum Genet 34:180
Davis KE (1981) The application of DNA recombinant technology to the analysis of the human genome and genetic disease. Hum Genet 58:351–357
Ewens WJ, Spielman RS, Harris HH (1981) Estimation of genetic variation at the DNA level from restriction endonuclease data. Proc Natl Acad Sci USA 78:3748–3750
Gadek JE, Crystal RG (1983) α-Antitrypsin deficiency. In: Stanbury JB, Wyngaarden JB, Fredrickson DS (ed) The metabolic basis of inherited disease, 5th edn. McGraw-Hill, New York, pp 1456–1467
Gianelli F, Choo KH, Rees DJG, Boyd Y, Rizza CR, Brownlee GG (1983) Gene deletions in patients with hemophilia B and anti-factor IX antibodies. Nature 303:181–182
Gusella JF, Wexler NS, Conneally PM, Naylor SL, Anderson MA, Tanzi RE, Watkins PC, Ottina K, Wallace MR, Sakaguchi AY, Young AB, Shoulson I, Bonilla E, Martin JB (1983) A polymorphic DNA marker genetically linked to Huntington's disease. Nature 306:234–238
harris H, Hopkinson DA (1972) Average heterozygosity per locus in man: an estimate based on the incidence of enzyme polymorphisms. Ann Hum Genet 36:9–20
Jeffreys AJ (1979) DNA sequence variants in the Gγ-,Aγ-, δ-and β-globin genes of man. Cell 18:1–10
Jeppson JO (1976) Amino acid substitution Glu→lys in α-1-antitrypsin Pi Z. FEBS Lett 65:195–197
Kazazian HH, Chakravarti A, Orkin SH, Antonarakis SE (1983) DNA polymorphisms in the human β-globin gene cluster. In: Nei M, Kochn RK (eds) Evolution of genes and proteins. Sinauer, Sunderland, pp 137–146
Kidd V, Wallace RB, Itaruka K, Woo SLC (1983) ⇓-1-Antitrypsin deficiency detection by direct analysis of the mutation in the gene. Nature 304:230–234
Kunkel LM, Smith KD, Boyer SH, Borgaonkar DS, Wachtel SS, Miller OJ, Breg WR, Jones HW Jr, Rary JM (1977) Analysis of human Y-chromosome-specific reiterated DNA in chromosome variants. Proc Natl Acad Sci USA 74:1245–1249
Kurachi K, Chandra T, Friezner Degen SJ, White TT, Marchioto TL, Woo SLC, Davie EW (1981) Cloning and sequence of cDNA coding for α1-antitrypsin. Proc Natl Acad Sci USA 78:6826–6830
Leicht M, Long GL, Chandra T, Kurachi K, Kidd VJ, Mace M Jr, Davie EW, Woo SLC (1982) Sequence homology and structural comparison between the chromosomal human α-antitrypsin and chicken ovalbumin genes. Nature 297:655–659
Maxam AM, Gilbert W (1977) A new method for sequencing DNA. Proc Natl Acad Sci USA 74:560–564
Nei M (1975) Molecular population genetics and evolution. North Holland/Elsevier, Amsterdam New York
Nei M, Li W-H (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76:5269–5273
Nei M, Tajima F (1981) DNA polymorphism detectable by restriction endonucleases. Genetics 97:145–163
Norgard MV, Tocci MJ, Monahan JJ (1980) On the cloning of eukaryotic total poly(A)+-RNA populations in Escherichi coli. J Biol Chem 255:7665–7672
Orkin SH, Kazazian HH, Antonarakis SE, Goff SC, Boehm CD, Sexton JP, Waber PG, Giardina PJV (1982) Linkage of β-thalassemia mutations and β-globin gene polymorphisms with DNA polymorphisms in human β-globin gene cluster. Nature 296:627–631
Owen MC, Carrell RW (1976) Alpha-1-antitrypsin: molecular abnormality of S variant. Br Med J I:130–131
Page D, DeMartinville B, Barker D, Wyman A, White R, Franke U, Botstein D (1982) Single copy sequence hybridizes to polymorphic and homologous loci on human X and Y chromosomes. Proc Natl Acad Sci USA 79:5352–5356
Parnes JR, Baruch V, Felsenfeld A, Ramanathan L, Ferrini U, Appella E, Seidman JG (1981) Mouse β3 microglobulin cDNA clones: a screening procedure for cDNA clones corresponding to rare mRNAs. Proc Natl Acad Sci USA 78:2253–2257
Pelham HR, Jackson RJ (1976) An efficient mRNA-dependent translation system from reticulocyte lysates. Eur J Biochem 67:247–256
Phillips JA, Hjelle BL, Seeburg BL, Zachman M (1981) Molecular basis for familial isolated growth hormone deficiency. Proc Natl Acad Sci USA 78:6372–6375
Phillips JA, Parks JS, Hjelle BL, Herd JE, Plotnick LP (1982) Genetic analysis of familial isolated growth hormone deficiency, Type I. J Clin Invest 70:489–495
Prochownik EV, Antonarakis S, Bauer KA, Rosenberg RD, Feron ER, Orkin SH (1983) Molecular heterogeneity of inherited antithrombin III deficiency. N Engl J Med 308:1549–1552
Riccardi RP, Miller JS, Roberts BE (1979) Purification and mapping of specific mRNAs by hybridization, selection and cell-free translation. Proc Natl Acad Sci USA 76:4927–4931
Rigby DWJ, Dieckmann M, Rhodes C Berg P (1977) Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. J Mol Biol 113:237–251
Rotwein P, Chyn R, Chirgwin J, Cordell B, Goodman HM, Permutt MA (1981) Polymorphism in the 5′ flanking region of human insulin dependent diabetes and its possible relation to Type 2 diabetes. Science 213:1117–1120
Rotwein PS, Chirgwin J, Province MA, Knowler WC, Pettitt DJ, Cordell B, Goodman HM, Permutt MA (1983) Polymorphism in the 5′-flanking region of the human insulin gene: a genetic marker for non-insulin-dependent diabetes. N Engl J Med 308:54–71
Smith DF, Searles PF, Williams JG (1979) Characterization of bacterial clones containing DNA sequences derived from Xenopus laevis vitellogenin mRNA. Nucleic Acids Res 6:487–506
Southern EM (1975) Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98:503–517
Steffen D, Weinberg RA (1978) The integrated genome of murine leukemia virus. Cell 15:1003–1010
Su T-S, Bock H-GO, O'Brien WE, Beaudet AL (1981) Cloning of cDNA for argininosuccinate synthetase mRNA and study of overproduction in a human cell line. J Biol Chem 256:11826–11831
Su T-S, Bock H-GO, Beaudet AL, O'Brien WE (1982) Molecular analysis of argininosuccinate synthetase deficiency in human fibroblasts. J Clin Invest 70:1334–1339
Wahl GM, Padgett RA, Stark GR (1979) Gene amplification causes overproduction at the first three enzymes of UMP synthesis in N-(phosphonacetyl-(l))-l-aspartate resistant hamster cells. J Biol Chem 254:8679–8689
Woo SLC, Lidsky AS, Güttler F, Chandra T, Robson KJH (1983) Cloned human phenylalanine hydroxylase gene allows prenatal diagnosis and carrier detection of classical phenylketonuria. Nature 306:151–155
Wyman AR, White R (1980) A highly polymorphic locus in human DNA. Proc Natl Acad Sci USA 77:6754–6758
Yoshida A, Lieberman J, Gaidulis L, Ewing C (1976) Molecular abnormality of human alpha1-antitrypsin variant (Pi ZZ) associated with plasma activity deficiency. Proc Natl Acad Sci USA 73:1324–1328
Yoshida A, Ewing C, Wessels M, Lieberman J, Gaidulis L (1977) Molecular abnormality of Pi S variant of human alpha-a-antitrypsin. Am J Hum Genet 29:233–239
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Matteson, K.J., Ostrer, H., Chakravarti, A. et al. A study of restriction fragment length polymorphisms at the human alpha-1-antitrypsin locus. Hum Genet 69, 263–267 (1985). https://doi.org/10.1007/BF00293037
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DOI: https://doi.org/10.1007/BF00293037