Skip to main content
SpringerLink
Log in

Variation in genomic alu repeat density as a basis for rapid construction of low resolution physical maps of human chromosomes

  • Original Articles
  • Published:
Chromosoma Aims and scope Submit manuscript

Abstract

Human DNA restriction fragments containing high numbers of Alu repeat sequences can be preferentially detected in the presence of other human DNA restriction fragments in DNA from human:rodent somatic cell hybrids when the DNA is fragmented with enzymes that cleave mammalian DNA infrequently. This ability to lower the observed human DNA complexity allowed us to develop an approach to order rapidly somatic hybrid cell lines retaining overlapping human genomic domains. The ordering process also generates a relative physical map of the human fragments detected with Alu probe DNA. This process can generate physical mapping information for human genomic domains as large as an entire chromosome (100,000 kb). The strategy is demonstrated by ordering Alu-detected NotI fragments in a panel of mouse:human hybrid cells that span the entire long arm of human chromosome 17.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Bernardi G (1989) The ischochore organization of the human genome. Annu rev Genet 23: 637–661

    Google Scholar 

  • Brownstein BH, Silverman GA, Little RD, Burke DT, Korsmeyer SJ, Schlessinger D, Olson MV (1989) Isolation of single copy human genes from a library of yeast artificial chromosome clones. Science 244: 1348–1351

    Google Scholar 

  • Cepko CL, Roberts BE, Mulligan RC (1984) Construction and applications of a highly transmissible murine retrovirus shuttle vector. Cell 37: 1053–1062

    Google Scholar 

  • Chen TC, Manuelidis L (1989) SINEs and LiNEs cluster in distinct DNA fragments of Giemsa band size. Chromosoma 98: 309–316

    Google Scholar 

  • Chu G, Vollrath D, Davis RW (1986) Separation of large DNA molecules by contour-clamped homogeneous electric fields. Science 234: 1582–1585

    Google Scholar 

  • Church GM, Gilbert W (1984) Genomic sequencing. Proc Natl Acad Sci USA 81: 1991–1995

    Google Scholar 

  • Coulson A, Sulston J, Brenner S, Karn J (1986) Proc Natl Acad Sci USA 83: 7821–7825

    Google Scholar 

  • Fan YS, Davis LM, Shows TB (1990) Mapping small DNA sequences by fluorescence in situ hybridization directly on banded chromosomes. Proc Natl Acad Sci USA 87: 6223–6227

    Google Scholar 

  • Feinberg AP, Vogelstein B (1983) A technique for radiolabelling DNA restriction endonuclease fragments to high specific activity. Anal Biochem 132: 6–13

    Google Scholar 

  • Gardiner K, Watkins P, Munke M, Drabkin H, Jones C, Patterson D (1988) Partial physical map of human chromosome 21. Somatic Cell Mol Genet 14: 623–637

    Google Scholar 

  • Gardiner K, Housberger M, Kraus J, Tautravaki V, Korenberg J, Rao V, Reddy S, Patterson D (1990) Analysis of human chromosome 21: correlation of physical and cytogenetic maps; gene and CpG island distribution. EMBO J 9: 25–34

    Google Scholar 

  • Glaser T, Rose E, Morse H, Housman D, Jones C (1990) A panel of irradiation reduced hybrids selectively retaining human chromosome 11p13: Their structure and use to purify the WAGR complex. Genomics 6: 48–64

    Google Scholar 

  • Graw S, Davidson J, Gusella J, Watkins P, Tanzi R, Neve R, Patterson D (1988) Irradiation-reduced human chromosome 21 hybrids. Somatic Cell Mol Genet 14: 233–242

    Google Scholar 

  • Haines JL, Ozelius LJ, McFarlane H, Menon A, Tzall S, Martiniuc F, Hirschhorn R, Gusella JF (1990) A genetic linkage map of chromosome 17. Genomics 8: 1–6

    Google Scholar 

  • Holmquist G (1988) DNA sequences in G bands and R bands. In: Adolph KW (ed) Chromosomes and chromatin. CRC Press, Boca Raton, Fla, pp 76–121

    Google Scholar 

  • Hwu HR, Roberts JW, Davidson EH, Britten RJ (1986) Insertion and/or deletion of many repeated DNA sequences in human and higher ape evolution. Proc Natl Acad Sci USA 83: 3875–3879

    Google Scholar 

  • Kievits T, Devilee P, Weigant J, Wapenaar MC, Cornelisse CJ, van Ommen G (1990) Direct non-radioactive in situ hybridization of somatic cell hybrid DNA to human lymphocyte chromosomes. Cytometry 11: 105–109

    Google Scholar 

  • Korenberg JR, Rykowski MC (1988) Human genome organization: Alu, lines and the molecular structure of metaphase chromosome bands. Cell 53: 391–400

    Google Scholar 

  • Labuda D, Striker G (1989) Sequence conservation in Alu evolution. Nucleic Acids Res 17: 2477–2491

    Google Scholar 

  • Lander ES, Waterman MS (1988) Genomic mapping by finger-printing random clones: a mathematical analysis. Genomics 2: 231–237

    Google Scholar 

  • Leach RJ, Thayer MJ, Schafer AJ, Fournier REK (1989) Physical mapping of human chromosome 17 using fragment-containing microcell hybrids. Genomics 5: 167–176

    Google Scholar 

  • Ledbetter SA, Nelson DL, Warren ST, Ledbetter DH (1990) Rapid isolation of DNA probes within specific chromosome regions by interspersed repetitive sequence polymerase chain reaction. Genomics 6: 475–481

    Google Scholar 

  • Lichter P, Cremer T, Borden J, Manuelidis L, Ward DC (1988) Delineation of individual human chromosomes in metaphase and interphase cells by in situ suppression hybridization using recombinant DNA libraries. Hum Genet 80: 224–234

    Google Scholar 

  • Lichter P, Tang CJ, Call K, Hermanson G, Evans GA, Housman D, Ward DC (1990) High resolution mapping of human chromosome 11 by in situ hybridization with cosmid clones. Science 247: 64–69

    Google Scholar 

  • Lugo TG, Handelin B, Killary AM, Housman DE, Fournier REK (1987) Isolation of microcell hybrid clones containing retroviral vector insertion into specific human chromosomes. Mol Cell Biol 7: 3814–3820

    Google Scholar 

  • Maniatis T, Fritsch EF, Sambrook J (1982) Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

    Google Scholar 

  • Manuelidis L (1982) Nucleotide sequence definition of a major human repeated DNA, the Hind III 1.9-kb family. Nucleic Acids Res 10: 3211–3219

    Google Scholar 

  • Manuelidis L (1990) A view of interphase chromosomes. Science 250: 1533–1540

    Google Scholar 

  • Manuelidis L, Ward DC (1984) Chromosomal and nuclear distribution of the Hind III 1.9-kb human DNA repeat segment. Chromosoma 91: 28–38

    Google Scholar 

  • Miller AD, Buttimore C (1986) Redesign of retrovirus packaging cell lines to avoid recombination leading to helper virus production. Mol Cell Biol 6: 2895–2902

    Google Scholar 

  • Minoshima S, Kawasaki K, Fukuyama R, Malkawa M, Kudoh J, Shimusjo N (1990) Isolation of giant DNA fragments from flow-sorted human chromosomes. Cytometry 11: 539–541

    Google Scholar 

  • Moyzis RK, Torney DC, Meyne J, Buckingham JM, Wu J-R, Burks C, Sirotkin KM, Goad WB (1989) The distribution of interspersed repetitive DNA sequences in the human genome. Genomics 4: 273–289

    Google Scholar 

  • Nakamura Y, Lathrop M, O'Connell P, Leppert M, Barker D, Wright E, Skolnick M, Kondoleon S, Litt M, Lalouel JM (1988) A mapped set of DNA markers for human chromosome 17. Genomics 2: 302–309

    Google Scholar 

  • Nelson DL, Ledbetter SA, Corbo L, Victoria MF, Ramirez-Solis R, Webster TD, Ledbetter DH, Cashey CT (1989) Alu polymerase chain reaction: a method for rapid isolation of human specific sequences from complex DNA sources. Proc Natl Acad Sci USA 86: 6686–6690

    Google Scholar 

  • Olson MV, Dutchik JE, Graham MY, Brodeur GM, Helms C, Frank M, MacCollin M, Scheinman R, Frank T (1986) Random-clone strategy for genomic restriction mapping in yeast. Proc Natl Acad Sci USA 83: 7826–7830

    Google Scholar 

  • Rinehart FP, Ritch TG, Deininger PL, Schmid CW (1981) Renaturation rate studies of a single family of interspersed repeated sequences in human deoxyribonucleic acid. Biochemistry 20: 3003–3010

    Google Scholar 

  • Rose EA, Glaser T, Jones C, Smith CL, Lewis WH, Call KM, Minden M, Champagne E, Boretta L, Ager H, Housemen DE (1990) Complete physical map of the WAGR region of 11p13 localizes a candidate Wilms tumor gene. Cell 60: 495–508

    Google Scholar 

  • Ryan SC, Dugaiczyk A (1989) Newly arisen DNA repeats in primate phylogeny. Proc Natl Acad Sci USA 86: 9360–9364

    Google Scholar 

  • Sanford JA, Stubblefield E (1987) General protocol for microcell-mediated chromosome transfer. Somatic Cell Mol Genet 13: 279–284

    Google Scholar 

  • Schwartz DC, Cantor CR (1984) Separation of yeast chromosome sized DNAs by pulsed-field gradient electrophoresis. Cell 37: 67–75

    Google Scholar 

  • Staden R (1980) A new computer method for the storage and manipulation of DNA gel reading data. Nucleic Acids Res 8: 3673–3694

    Google Scholar 

  • Stallings RL, Torney DC, Hildebrand CE, Longmire JL, Deavan LL, Jett JH, Doggett NA, Moyzis RK (1990) Physical mapping of human chromosomes by repetitive sequence fingerprinting. Proc Natl Acad Sci USA 87: 6218–6222

    Google Scholar 

  • Waterbury PG, Lane MJ (1987) Generation of lambda phage concatamers for use as pulsed-field gel electrophoresis size markers. Nucleic Acids Res 15: 3930

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Medicine, State University of New York, Health Science Center at Syracuse, 50 E. Adams Street, 13210, Syracuse, NY, USA

    Michael J. Lane, Anne M. Smardon, Seth Mante & Douglas J. Hanlon

  2. Department of Microbiology, State University of New York, Health Science Center at Syracuse, 50 E. Adams Street, 13210, Syracuse, NY, USA

    Michael J. Lane, Anne M. Smardon, Seth Mante & Douglas J. Hanlon

  3. Genmap, Inc., 291 Whitney Avenue, 06511, New Haven, CT, USA

    Michael J. Lane, P. Greg Waterbury, William T. Carroll, Brian D. Faldasz, Scott M. Peshick, Clark S. Huckaby & Richar E. Kouri

  4. Department of Radiology, State University of New York, Health Science Center at Syracuse, 13210, Syracuse, NY, USA

    Peter J. Hahn

  5. Department of Medical Genetics, Florida Institute of Technology, 32901, Melbourne, FL, USA

    Jane M. Scalzi & John C. Hozier

Authors
  1. Michael J. Lane
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. P. Greg Waterbury
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. William T. Carroll
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Anne M. Smardon
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Brian D. Faldasz
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Scott M. Peshick
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Seth Mante
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Clark S. Huckaby
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Richar E. Kouri
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Douglas J. Hanlon
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Peter J. Hahn
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Jane M. Scalzi
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. John C. Hozier
    View author publications

    You can also search for this author in PubMed Google Scholar

Additional information

by L. Manuelidis

Rights and permissions

Reprints and permissions

About this article

Cite this article

Lane, M.J., Waterbury, P.G., Carroll, W.T. et al. Variation in genomic alu repeat density as a basis for rapid construction of low resolution physical maps of human chromosomes. Chromosoma 101, 349–357 (1992). https://doi.org/10.1007/BF00346014

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00346014

Keywords

Search

Navigation