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Molecular Dissection of Heteromorphic Regions

  • Brynn Levy
  • Peter E. Warburton
Chapter

Abstract

The human genome project has provided detailed knowledge of the human DNA sequence and revealed its complexity. Genes and gene-related sequences (pro-motors, introns, etc.) account for about 25% of the 3300 Mb of DNA and only about 3% of the genome represents coding sequence. Repetitive sequences form a large part of our genome and are the basis of the polymorphisms detected at the molecular level and of the heteromorphisms observed at the chromosomal level. Repetitive DNA sequences are found either as individual repeat units interspersed throughout the genome, or as tandemly repeated units or motifs in various chromosomal locations. Three main types of tandemly repeated DNA sequences, classified by the length of the individual repeated motif and by the total size of the repeated units, are satellite,minisatellite and microsatellite. This chapter describes only tandemly repeated sequences, as these play a more significant role in chromosomal heteromorphisms.

Keywords

Pericentromeric Region Acrocentric Chromosome Centromere Function Human Artificial Chromosome rDNA Array 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    Waye JS, Creeper LA, Willard HF (1987). Organization and evolution of alpha satellite DNA from human chromosome 11. Chromosoma. 95: 182–8.PubMedCrossRefGoogle Scholar
  2. 2.
    Choo KHA, Vissel B, Earle E (1989). Evolution of alpha satellite DNA on human acrocentric chromosomes. Genomics. 5: 332–44.PubMedCrossRefGoogle Scholar
  3. 3.
    Prosser J, Frommer M, Paul C, Vincent PC (1986). Sequence relationships of three human satellite DNAs. J Mol Biol. 187: 145–55.PubMedCrossRefGoogle Scholar
  4. 4.
    Tagarro I, Wiegant J, Raap AK, Gonzalez-Aguilera JJ, Fernandez-Peralta AM (1994). Assignment of human satellite 1 DNA as revealed by fluorescent in situ hybridization with oligonucleotides. Hum Genet. 93: 125–8.PubMedGoogle Scholar
  5. 5.
    Jeanpierre M (1994). Human satellites 2 and 3. Ann Genet. 37: 63–71.Google Scholar
  6. 6.
    Waye JS, Willard HF (1989). Human beta satellite DNA: genomic organization and sequence definition of a class of highly repetitive tandem DNA. Proc Natl Acad Sci USA. 86: 6250–4.PubMedCrossRefGoogle Scholar
  7. 7.
    Vissel B, Choo KH (1989). Mouse major (gamma) satellite DNA is highly conserved and organized into extremely long tandem arrays: implications for recombination between non-homologous chromosomes. Genomics. 5: 407–14.PubMedCrossRefGoogle Scholar
  8. 8.
    Wier HU, Zitzelsberger HF, Gray JW (1992). Differential staining of human and murine chromatin in situ by hybridization with species-specific satellite DNA probes. Biochem Biophys Res Commun. 182: 1313–19.CrossRefGoogle Scholar
  9. 9.
    Sawyer JR, Swanson CM, Wheeler G, Cunniff C (1995). Chromosome instability in ICF syndrome: formation of micronuclei from multibranched chromosomes 1 demonstrated by fluorescence in situ hybridization. Am J Med Genet. 56: 203–9.PubMedCrossRefGoogle Scholar
  10. 10.
    Barbosa AC, Otto PA, Vanna-Morgante AM (2000). Replication timing of homologous alpha satelllite DNA in Roberts syndrome. Chromosome Res. 8: 645–50.PubMedCrossRefGoogle Scholar
  11. 11.
    Schildkraut CL, Marmur J, Doty P (1962). Determination of the base composition of deoxyribonucleic acid from its buoyant density in CsCl. J Mol Biol. 4: 430–43.PubMedCrossRefGoogle Scholar
  12. 12.
    Corneo G, Ginelli E, Polli E (1968). Isolation of the complementary strands of human satellite DNA. J Mol Biol. 33: 331–5.PubMedCrossRefGoogle Scholar
  13. 13.
    Corneo G, Ginelli E, Polli E (1970). Repeated sequences in human DNA. J Mol Biol. 48: 319–27.PubMedCrossRefGoogle Scholar
  14. 14.
    Ginelli E, Corneo G (1976). The organization of repeated DNA sequences in the human genome. Chromosoma. 56: 55–68.PubMedCrossRefGoogle Scholar
  15. 15.
    Jones KW, Prosser J, Corneo G, Ginnelli E, Bobrow M (1973). Satellite DNA, constitutive heterochromatin and human evolution. In: Pfeiffer RA, editor. Modern Aspects of Cytogenetics: Constitutive Heterochromatin in Man. Stuttgart: F.K. Schattauer Verlag, pp. 54–61.Google Scholar
  16. 16.
    Miklos GLB, John B (1979). Heterochromatin and satellite DNA in man: properties and progress. Am J Hum Genet. 31: 264–80.PubMedGoogle Scholar
  17. 17.
    Jones KW, Prosser J, Corneo G, Ginelli E (1973). The chromosomal location of human satellite DNA III. Chromosoma. 42: 445–51.PubMedCrossRefGoogle Scholar
  18. 18.
    Jones KW, Purdom LF, Prosser J, Corneo G (1974). The chromosomal location of human satellite DNA I. Chromosoma. 49: 161–71.PubMedCrossRefGoogle Scholar
  19. 19.
    Gosden JR, Mitchell AR, Buckland RA, Clayton RP, Evans HJ (1975). The location of four human satellite DNAs on human chromosomes. Exp Cell Res. 92: 148–58.PubMedCrossRefGoogle Scholar
  20. 20.
    Jackson MS, Mole SE, Ponder BA (1992). Characterization of a boundary between satellite III and alphoid sequences on human chromosome 10. Nucl Acids Res. 20: 4781–7.PubMedCrossRefGoogle Scholar
  21. 21.
    Madhani HD, Leadon SA, Smith CA, Hanawalt PC (1986). Alpha DNA in African green monkey cells organized into extremely long tandem arrays. J Biol Chem. 261: 2314–18.PubMedGoogle Scholar
  22. 22.
    Wu JC, Manuelidis L (1980). Sequence definition and organization of a human repeated DNA. J Mol Biol. 142: 363–8.PubMedCrossRefGoogle Scholar
  23. 23.
    Willard HF (1991). Evolution of alpha satellite DNA. Curr Opin Genet Devel. 1: 509–14.CrossRefGoogle Scholar
  24. 24.
    Sullivan KF, Glass CA (1991). CENP-B is a highly conserved mammalian centromere protein with homology to the helix–loop–helix family of proteins. Chromosoma. 100: 360–70.PubMedCrossRefGoogle Scholar
  25. 25.
    Lee C, Li X, Jabs EW, Court D, Lin CC (1995). Human gamma X satellite DNA: an X chromosome specific centromeric DNA sequences. Chromosoma. 104: 103–12.PubMedCrossRefGoogle Scholar
  26. 26.
    Johnson DH, Kroisel PM, Klapper HJ, Rosenkranz W (1992). Microdissection of a human marker chromosome reveals its origin and a new family of centromeric repetitive DNA. Hum Mol Genet. 1: 741–7.PubMedCrossRefGoogle Scholar
  27. 27.
    Harrington JJ, Bokkelen GV, Mays RW, Gustashaw K, Willard HF (1997). Formation of de novo centromeres and construction of first-generation human artificial microchromosomes. Nat Genet. 15: 345–55.PubMedCrossRefGoogle Scholar
  28. 28.
    Henning KA, Novotny EA, Compton ST, Guan XY, Liu PP, Ashlock MA (1999). Human artificial chromosomes generated by modification of a yeast artificial chromosome containing both human alpha satellite DNA and single-copy DNA sequences. Proc Natl Acad Sci USA. 96: 592–7.PubMedCrossRefGoogle Scholar
  29. 29.
    Warburton PE, Cooke CA, Bourassa S et al. (1997). Immunolocalization of CENP-A suggests a distinct nucleosome structure at the inner kinetophore plate of active centromeres. Curr Biol. 7: 901–4.PubMedCrossRefGoogle Scholar
  30. 30.
    Sullivan BA, Schwartz S (1995). Identification of centromeric antigens in dicentric Robertsonian translocations: CENP-C and CENP-E are necessary components of functional centromeres. Hum Mol Genet. 4: 2189–97.Google Scholar
  31. 31.
    Kipling D, Warburton PE (1997). Centromeres, CENP-B and Tigger too. Trends Genet. 13: 141–5.Google Scholar
  32. 32.
    Choo KHA (1997). Centromere DNA dynamics: latent centromeres and neocentromere formation. Am J Hum Genet. 61: 1225–33.PubMedCrossRefGoogle Scholar
  33. 33.
    Depinet TW, Zackowski JL, Earnshaw WC et al. (1997). Characterization of neo-centromere in marker chromosomes lacking detectable alpha-satellite DNA. Hum Mol Genet. 6: 1195–204.PubMedCrossRefGoogle Scholar
  34. 34.
    Warburton PE, Dolled M, Mahmood R et al. (2000). Molecular cytogenetic analysis of eight inversion duplications of human chromosome 13q that each contain a neocentromere. Am J Hum Genet. 66: 1794–806.PubMedCrossRefGoogle Scholar
  35. 35.
    Amar DJ, Choo KH (2002). Neocentromeres: role in human disease, evolution and centromere study. Am J Hum Genet. 7: 695–714.CrossRefGoogle Scholar
  36. 36.
    Bosi PR, Grant GR, Jeffreys AJ (2002). Minisatellites show rare and simple intra-allelic instability in the mouse germ line. Genomics. 80: 2–4.CrossRefGoogle Scholar
  37. 37.
    Nakamura Y, Leppert M, O’Connell P et al. (1987). Variable number of tandem repeat ( VNTR) markers for human gene mapping. Science. 235: 1616–22.Google Scholar
  38. 38.
    Desmarais E, Vigneron S, Buresi C, Cambien F, Cambou JP, Roizes G (1993). Variant mapping of the Apo(B) AT rich minisatellite. Dependence on nucleotide sequence of the copy number variations. Instability of the non-canonical alleles. Nucl Acids Res. 21: 2179–84.Google Scholar
  39. 39.
    Buresi C, Desmarais E, Vigneron S et al. (1996). Structural analysis of the minisatellite present at the 3’ end of the human apolipoprotein B gene: new definition of the alleles and evolutionary implications. Hum Mol Genet. 5: 61–8.PubMedCrossRefGoogle Scholar
  40. 40.
    Berg K (1986). DNA polymorphism at the apolipoprotein B locus is associated with lipoprotein level. Clin Genet. 30: 515–20.PubMedCrossRefGoogle Scholar
  41. 41.
    Yu S, Mangelsdorf M, Hewett D et al. (1997). Human chromosomal fragile site FRA16B is an amplified AT-rich minisatellite repeat. Cell. 88: 367–74.PubMedCrossRefGoogle Scholar
  42. 42.
    Hewett DR, Handt O, Hobson L et al. (1998). FRA10B structure reveals common elements in repeat expansion and chromosomal fragile site genesis. Mol Cell. 1: 773–81.PubMedCrossRefGoogle Scholar
  43. 43.
    Jobling MA, Bouzekri N, Taylor PG (1998). Hypervariable digital DNA codes for human paternal lineages: MVR-PCR at the Y-specific minisatellite, MSY1(DYF155S1). Hum Mol Genet. 7: 643–53.PubMedCrossRefGoogle Scholar
  44. 44.
    Bennett ST, Lucassen AM, Gough SC et al. (1995). Susceptibility to human type 1 diabetes at IDDM2 is determined by tandem repeat variation at the insulin gene minisatellite locus. Nat Genet. 9: 284–92.PubMedCrossRefGoogle Scholar
  45. 45.
    Bell GI, Karam JH, Rutter WJ (1981). Polymorphic DNA region adjacent to the 5’ end of the human insulin gene. Proc Natl Acad Sci USA. 78: 5759–63.PubMedCrossRefGoogle Scholar
  46. 46.
    Bell GI, Selby MJ, Rutter WJ (1982). The highly polymorphic region near the human insulin gene is composed of simple tandemly repeating elements. Nature. 295: 31–5.PubMedCrossRefGoogle Scholar
  47. 47.
    Lew A, Rutter WJ, Kenedy GC (2000). Unusual DNA structure of the diabetes susceptibility locus IDDM2 and its effect on transcription by the insulin promoter factor Pur-1/MAZ. Proc Natl Acad Sci USA. 97: 12508–12.PubMedCrossRefGoogle Scholar
  48. 48.
    Van Tol HH, Wu CM, Guan HC et al. (1992). Multiple dopamine D4 receptor variants in the human population. Nature. 358: 149–52.PubMedCrossRefGoogle Scholar
  49. 49.
    Lichter JB, Barr CL, Kennedy JL, Van Tol HH, Kidd KK, Livak KJ (1993). A hypervariable segment in the human dopamine receptor D4 (DRD4) gene. Hum Mol Genet. 2: 767–73.PubMedCrossRefGoogle Scholar
  50. 50.
    Benjamin J, Li L, Patterson C, Greenberg BD, Murphy DL, Hamer DH (1996). Population and familial association between the D4 dopamine receptor gene and measures of novelty seeking. Nat GenetGoogle Scholar
  51. 51.
    Ebstein RP, Segman R, Benjamin J, Osher Y, Nemanov L, Belmaker RH (1997). 5-HT2C (HTR2C) serotonin receptor gene polymorphism associated with the human personality trait of reward dependence: interaction with dopamine D4 receptor (D4DR) and dopamine D3 receptor ( D3DR) polymorphisms. Am J Med Genet. 74: 65–72.Google Scholar
  52. 52.
    Benjamin J, Ebstein RP, Belmaker RH (1997). Personality genetics. Isr J Psychiatry Relat Sci. 34: 270–80.PubMedGoogle Scholar
  53. 53.
    Turri MG, Cuin KA, Porter AC (1995). Characteristics of a novel minisatellite that provides multiple splice donor sites in an interferon-induced transcript. Nucl Acids Res. 23: 1854–6.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2004

Authors and Affiliations

  • Brynn Levy
  • Peter E. Warburton

There are no affiliations available

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