Abstract
Minisatellites, microsatellites, and short random oligonucleotides all uncover highly polymorphic DNA fingerprint patterns in Southern analysis of genomic DNA that has been digested with a restriction enzyme having a 4-bp specificity. The polymorphic nature of the fragments is attributed to tandem repeat number variation of embedded minisatellite sequences. This explains why DNA fingerprint fragments are uncovered by minisatellite probes, but does not explain how it is that they are also uncovered by microsatellite and random oligonucleotide probes. To clarify this phenomenon, we sequenced a large bovine genomic BamHI restriction fragment hybridizing to the Jeffreys 33.6 minisatellite probe and consisting of small and large Sau3A-resistant subfragments. The large Sau3A subfragment was found to have a complex architecture, consisting of two different minisatellites, flanked and separated by stretches of unique DNA. The three unique sequences were characterized by sequence simplicity, that is, a higher than chance occurrence of tandem or dispersed repetition of simple sequence motifs. This complex repetitive structure explains the absence of Sau3A restriction sites in the large Sau3A subfragment, yet provides this subfragment with the ability to hybridize to a variety of probe sequences. It is proposed that a large class of interspered tracts sharing this complex yet simplified sequence structure is found in the genome. Each such tract would have a broad ability to hybridize to a variety of probes, yet would exhibit a dearth of restriction sites. For each restriction enzyme having 4-bp specificity, a subclass of such tracts, completely lacking the corresponding restriction sites, will be present. On digestion with the given restriction enzyme, each such tract would form a large fragment. The largest fragments would be those that contained one or more long minisatellite tracts. Some of these large fragments would be highly polymorphic by virtue of the included minisatellite sequences; by virtue of their complex structure, all would be capable of hybridizing to a wide variety of probes, uncovering a DNA fingerprint pattern.
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References
Ali, S., Wallace, B. (1988). Intrinsic polymorphism of variable number tandem repeat loci in the human genome. Nucleic Acids Res. 16, 8487–8496.
Armour, J.A.I., Wang, Z., Wilson, V., Royle, N.J., Jeffreys, A.J. (1989). Sequence flanking the repeat arrays of human minisatellites: association with tandem and dispersed repeat elements. Nucleic Acids Res. 17, 4925–4935.
Bell, G.I., Selby, M.J., Rutter, W.J. (1982). The highly polymorphic region near the human insulin gene is composed of simple tandemly repeating units. Nature 295, 31–35.
Capon, D.I., Chen, E.Y., Levinson, A.D., Seeburn, P.H., Goeddel, C.V. (1983). Complete nucleotide sequences of the T24 human bladder carcinoma oncogene and its normal homologue. Nature 302, 33–37.
Feinberg, A.P., Vogelstein, B. (1983). A technique for radiolabelling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 132, 6–13.
Fischauf, A.M., Lehrbach, H., Poustka, A., Murray, N., (1983) Lambda replacement vectors carrying polylinker sequences. J. Mol. Biol. 170, 827–842.
Goodbourn, S.E.Y., Higgs, D.R., Cleggs, J.B., Weatherall D.J. (1983). Molecular basis of length polymorphism in the human zeta-globin gene complex. Proc. Natl. Acad Sci. USA, 80, 5022–5026.
Jeffreys, A.J., Wilson, B., Thein, S.L. (1985). Hypervariable ‘minisatellite’ regions in human DNA. Nature 314, 67–73.
Kashi, Y., Iraqi, F., Tikoschinsky, Y., Rudinsky, B., Nave, A., Beckmann, J.S., Friedman, A., Soller, M., Gruenbaum, Y. (1990a). Poly(TG) uncovers a Y-specific fragment in bovine. Genomics 7, 31–36.
Kashi, Y., Tikoschinsky, Y., Genislav, E., Iraqi, F., Nave, A., Beckmann, J.S., Gruenbaum, Y., Soller, M. (1990b). Poly(TG) uncovers highly polymorphic fingerprints in a number of vertebrates. Nucleic Acids Res. 18, 1129–1132.
Kashi, Y., Nave, A., Gruenbaum, Y., Soller, M., Beckmann, J.S. (1992). A minisatellite probe from bovine uncovers highly polymorphic DNA fingerprint patterns in mammals and chickens. Anim. Genet. 23: 570.
Kirschoff, C. (1988) GATA tandem repeats detect minisatellite regions in blowfly DNA (Diptera: Calliphoridae). Chromosoma 96, 107–111.
Litt, M., Luty, J.A. (1989) A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am. J. Hum. Genet. 44, 397–401.
Nakamura, Y., Leppert, M., O'Connell, P., Wolff, R., Holm, T., Culver, M., Martin, C., Fujimoto, E., Hoff, M., Kumlin, E., White, R. (1987). Variable number of tandem repeats (VNTR) markers for human gene mapping. Science 235, 1616–1622.
Nakamura, Y., Carlson, M., Krapcho, K., Kanamori, M., White, R. (1988) New approach for isolation of VNTR markers. Am. J. Hum. Genet. 43, 854–859.
Nurnberg, P., Roewer, L., Neitzel, H., Sperling, K., Popperl, A., Hundrieser, J., Poche, H., Epplen, C., Zischler, H., Epplen, J.T. (1989). DNA fingerprinting with the oligonucleotide probe (CAC)5/(GTG)5: somatic stability and germline mutations. Hum. Genet. 284, 75–84.
Royle, N.J., Clarkson, R.E., Wang, Z., Jeffreys, A.J. (1988) Clustering of hypervariable minisatellites in the proterminal regions of human autosomes. Genomics 3, 352–360.
Sanger, F., Nicklen, S., Coulson, A.R. (1977) DNA sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci. USA 74, 5463–5467.
Schafer, R., Ali, S., Epplen, J.T. (1986) The organization of the evolutionarily conserved GATA/GACA repeats in the mouse genome. Chromosoma 93, 502–510.
Tautz, D. (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res. 17, 6463–6471.
Tautz, D., Renz, M. (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12, 4127–4137.
Tautz, D., Trick, M., Dover, G.A. (1986) Cryptic simplicity in DNA is a major source of DNA variation. Nature 322, 652–656.
Vergnaud, G. (1989) Polymers of random short oligonucleotides detect polymorphic loci in the human genome. Nucleic Acids Res. 17, 7623–7630.
Walpole, R.E., Myers, R.H. (1978) Probability and Statistics for Engineers and Scientists, 2nd ed. (New York: Macmillan Publ. Co.).
Weber, J.L., May, P.E. (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am. J. Hum. Genet. 44, 388–396.
Zischler, H., Schafer, R., Epplen, J.T. (1989) Non-radioactive oligonucleotide fingerprinting in the gel. Nucleic Acids Res. 17, 4411.
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Kashi, Y., Nave, A., Darvasi, A. et al. How is it that microsatellites and random oligonucleotides uncover DNA fingerprint patterns?. Mammalian Genome 5, 525–530 (1994). https://doi.org/10.1007/BF00354924
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DOI: https://doi.org/10.1007/BF00354924