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Gene Mapping, Discovery, and Expression pp 31–57Cite as

Quantitative DNA Fiber Mapping in Genome Research and Construction of Physical Maps

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 338))

Abstract

Efforts to prepare a first draft of the human DNA genomic sequence forced multidisciplinary teams of researchers to face unique challenges.At the same time,these unprecedented obstacles stimulated the development of many highly innovative approaches to biomedical problem solving,robotics,and bioinformatics.High-resolution physical maps are required for ordering individual segments of information for the construction of a comprehensive map of the entire genome.This chapter describes a novel way to identify,delineate,and characterize selected,often small DNA sequences along a larger piece of the human genome.The technology is based on immobilization of high molecular weight DNA molecules on a solid substrate (such as a glass slide)followed by uniform stretching of the DNA molecule by the force of a receding meniscus.The hydrodynamic force stretches the DNA molecules homogeneously to approximately 2.3 kb/μm,so that distances measured after probe binding in μm can be converted directly into kb distances.Out of a large number of applications,this article focuses on mapping of genomic sequences relative to one another,the assembly of physical maps with near kb resolution,and,finally,quality control during physical map assembly and sequencing.

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References

  1. Collins, F. and Galas, D.(1993) A new five-year plan for the U.S.human genome project.Science 262, 43–46.

    Article  PubMed  CAS  Google Scholar 

  2. Boguski, M., Chakravarti, A., Gibbs, R., Green, E., and Myers, R.M.(1996)The end of the beginning:the race to begin human genome sequencing.Genome Res. 6, 771–772.

    Article  PubMed  CAS  Google Scholar 

  3. Cheng, J.-F. and Weier H.-U.G.(1997)Approaches to high resolution physical mapping of the human genome,in Biotechnology International (Fox, C.F.and Connor, T.H., eds.), Universal Medical Press, San Francisco, pp. 149–157.

    Google Scholar 

  4. Martin, J., Han, C., Gordon, L.A., et al.(2004)The sequence and analysis of duplication-rich human chromosome 16.Nature 4, 988–994.

    Article  Google Scholar 

  5. Chumakov, I., Rigault, P., Guillou, S., et al. (1992)Continuum of overlapping clones spanning the entire human chromosome-21q.Nature 359, 380–387.

    Article  PubMed  CAS  Google Scholar 

  6. Cohen, D., Chumakov, I., and Weissenbach, J. (1993) A first-generation physical map of the human genome.Nature 366, 698–701.

    Article  PubMed  CAS  Google Scholar 

  7. Olson, M.V.(1993)The human genome project. Proc. Natl. Acad. Sci. USA 90, 4338–4344.

    Google Scholar 

  8. Selleri, L., Eubanks, J.H., Giovannini, M., et al. (1992) Detection and characterization of &quote;chimeric&quote; yeast artificial chromosome clones by fluorescent in situ suppression hybridization.Genomics 1, 536–541.

    Article  Google Scholar 

  9. Vetrie, D., Bobrow, M., and Harris, A.(1993)Construction of a 5.2-megabase physical map of the human X chromosome at Xq22 using pulsed-field gel electrophoresis and yeast artificial chromosomes.Genomics 15, 631–642.

    Article  PubMed  CAS  Google Scholar 

  10. Trask, B., Pinkel, D., and van den Engh, G. (1989) The proximity of DNA sequences in interphase cell nuclei is correlated to genomic distance and permits ordering of cosmids spanning 250 kilobase pairs.Genomics 5, 710–717.

    Article  PubMed  CAS  Google Scholar 

  11. Brandriff, B.F., Gordon, L.A., Tynan, K.T., et al. (1992) Order and genomic distances among members of the carcinoembryonic antigen (CEA)gene family determined by fluorescence in situ hybridization.Genomics 12, 773–779.

    Article  PubMed  CAS  Google Scholar 

  12. Warrington, J.A. and Bengtsson, U.(1994)High-resolution physical mapping of human 5q31-q33 using three methods:radiation hybrid mapping,interphase fluorescence in situ hybridization,and pulse field gel electrophoresis.Genomics 24, 395–398.

    Article  PubMed  CAS  Google Scholar 

  13. Lu-Kuo, J.M., Le Paslier, D., Weissenbach, J., Chumakov, I., Cohen, D., and Ward, D.C.(1994)Construction of a YAC contig and a STS map spanning at least seven megabasepairs in chromosome 5q34-35.Hum. Mol. Genet. 3, 99–106.

    Article  PubMed  CAS  Google Scholar 

  14. Green, E.D. and Olson, M.V.(1990)Systematic screening of yeast artificial-chromosome libraries by use of the polymerase chain reaction.Proc. Natl. Acad. Sci. USA 87, 1213–1217.

    Article  PubMed  CAS  Google Scholar 

  15. Coffey, A.J., Roberts, R.G., Green, E.D., et al. (1992) Construction of a 2.6-Mb contig in yeast artificial chromosomes spanning the human dystrophin gene using an STS-based approach.Genomics 12, 474–484.

    Article  PubMed  CAS  Google Scholar 

  16. Weissenbach, J., Gyapay, G., Dib, C., et al. (1992) A second-generation linkage map of the human genome.Nature 359, 794–801.

    Article  PubMed  CAS  Google Scholar 

  17. Locke, J., Rairdan, G., McDermid, H., et al. (1996) Cross-screening:a new method to assemble clones rapidly and unambiguously into contigs.Genome Res. 6, 155–165.

    Article  PubMed  CAS  Google Scholar 

  18. Cai, W., Aburatani, H., Stanton, V.P., Housman, D.E., Wang, Y.K., and Schwartz, D.C.(1995)Ordered restriction endonuclease maps of yeast artificial chromosomes created by optical mapping on surfaces.Proc. Natl. Acad. Sci. USA 92, 5164–5168.

    Article  PubMed  CAS  Google Scholar 

  19. Samad, A., Huff, E.J., Cai, W., and Schwartz, D.C.(1995)Optical mapping:a novel,single-molecule approach to genomic analysis.Genome Res. 5, 1–4.

    Article  PubMed  CAS  Google Scholar 

  20. Waterston, R. and Sulston, J.(1995)The genome of Caenorhabditis elegans Proc. Natl. Acad. Sci. USA 92, 10836–10840.

    Article  PubMed  CAS  Google Scholar 

  21. Bellanné-Chantelot, C., Lacroix, B., Ougen, P., et al. (1992) Mapping the whole human genome by fingerprinting yeast artificial chromosomes.Cell 70, 1059–1068.

    Article  PubMed  Google Scholar 

  22. Zucchi, I. and Schlessinger, D.(1992)Distribution of moderately repetitive sequences pTR5 and LF1 in Xq24-q28 human DNA and their use in assembling YAC con-tigs.Genomics 12, 264–275.

    Article  PubMed  CAS  Google Scholar 

  23. Porta, G., Zucchi, I., Hillier, L., et al. (1993) Alu and L1 sequence distributions in Xq24-q28 and their comparative utility in YAC contig assembly and verification. Genomics 16, 417–425.

    Article  PubMed  CAS  Google Scholar 

  24. Bell, C., Budarf, M.L., Nieuwenhuijsen, B.W., Barnoski, B.L., and Buetow, K.H. (1995)Integration of physical,breakpoint and genetic maps of chromosome 22. Localization of 587 yeast artificial chromosomes with 238 mapped markers.Hum. Mol. Genet. 4, 59–69.

    Article  PubMed  CAS  Google Scholar 

  25. Foote, S., Vollrath, D., Hilton, A., and Page, D.C. (1992) The human Y chromosome: overlapping DNA clones spanning the euchromatic region.Science 258, 60–66.

    Article  PubMed  CAS  Google Scholar 

  26. Stallings R.L., Doggett N.A., Callen D., et al. (1992) Evaluation of a cosmid contig physical map of human chromosome 16.Genomics 13, 1031–1039.

    Article  PubMed  CAS  Google Scholar 

  27. Tynan, K., Olsen, A., Trask, B., et al. (1992) Assembly and analysis of cosmid contigs in the CEA-gene family region of human chromosome 19.Nucleic Acids Res. 20, 1629–1636.

    Article  PubMed  CAS  Google Scholar 

  28. Nizetic, D., Gellen, L., Hamvas, R.M., et al. (1994) An integrated YAC-overlap and’ cosmid-pocket’ map of the human chromosome 21..Hum. Mol. Genet. 3, 759–770.

    Article  PubMed  CAS  Google Scholar 

  29. Patil, N., Peterson, A., Rothman, A., DeJong, P.J., Myers, R.M., and Cox, D.R. (1994)A high resolution physical map of 2.5 Mbp of the Down syndrome region on chromosome 21.Hum. Mol. Genet. 3, 1811–1817.

    Article  PubMed  CAS  Google Scholar 

  30. Cherry J.M., Ball C., Weng S., et al. (1997) Genetic and physical maps of Sac-charomyces cerevisiae Nature 387(Suppl), 67–73.

    PubMed  CAS  Google Scholar 

  31. Pierce J.C., Sauer B., and Sternberg N.(1992) A positive selection vector for cloning high molecular weight DNA by the bacteriophage-P1 system —improved cloning efficacy.Proc. Natl. Acad. Sci. USA 89, 2056–2060.

    Article  PubMed  CAS  Google Scholar 

  32. Ioannou P.A., Amemiya C.T., Garnes J., et al.(1994) A new bacteriophage P1-derived vector for the propagation of large human DNA fragments.Nat. Genet. 6, 84–89.

    Article  PubMed  CAS  Google Scholar 

  33. Shizuya H., Birren B., Kim U.J., et al. (1992) Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector.Proc. Natl. Acad. Sci. USA 89, 8794–8797.

    Article  PubMed  CAS  Google Scholar 

  34. Branscomb E., Slezak T., Pae R., Galas D., Carrano A.V., and Waterman M. (1990)Optimizing restriction fragment fingerprinting methods for ordering large genomic libraries.Genomics 8, 351–366.

    Article  PubMed  CAS  Google Scholar 

  35. Nelson D.L.(1991)Applications of polymerase chain reaction methods in genome mapping.Curr. Opin. Genet. Dev. 1, 62–68.

    Google Scholar 

  36. Chang E., Welch S., Luna J., Giacalone J., and Francke U.(1993)Generation of a human chromosome 18-specific YAC clone collection and mapping of 55 unique YACs by FISH and fingerprinting.Genomics 17, 393–402.

    Article  PubMed  CAS  Google Scholar 

  37. Riles L., Dutchik J.E., Baktha A., et al. (1993) Physical maps of the six smallest chromosomes of Saccharomyces cerevisiae at a resolution of 2.6-kilobase pairs. Genetics 134, 81–150.

    PubMed  CAS  Google Scholar 

  38. Gillett W., Hanks L., Wong G.K., Yu J., Lim R., and Olson M.(1996)Assembly of high-resolution restriction maps based on multiple complete digests of a redundant set of overlapping clones.Genomics 33, 389–408.

    Article  PubMed  CAS  Google Scholar 

  39. Hoheisel J.D. and Lehrach H.(1993)Use of reference libraries and hybridisation fingerprinting for relational genome analysis.FEBS Lett. 325, 118–122.

    Article  PubMed  CAS  Google Scholar 

  40. Locke J., Raidan G., McDermid H., et al. (1996) Cross-screening:a new method to assemble clones rapidely and unambiguously into contigs.Gen. Res. 6, 155–165.

    Article  CAS  Google Scholar 

  41. Sapolsky R.J. and Lipshutz R.J.(1996)Mapping genomic libray clones using oligonucleotide arrays.Genomics 33, 445–456.

    Article  PubMed  CAS  Google Scholar 

  42. Green E.D., Mohr R.M., Idol J.R., et al. (1991)Systematic generation of sequence-tagged sites for physical mapping of human chromosomes:application to the mapping of human chromosome 7 using yeast artificial chromosomes. Genomics 11, 548–564.

    Article  PubMed  CAS  Google Scholar 

  43. Arveiler B.(1994)Yeast artificial chromosome recombinants in a global strategy for chromosome mapping.Amplification of internal and terminal fragments by PCR,and generation of fingerprints.Methods Mol. Biol. 29, 403–423.

    Google Scholar 

  44. Aburatani H., Stanton V.P., and Housman D.E.(1996)High-resolution physical mapping by combined Alu-hybridization/PCR screening:contruction of a yeast artificial chromosome map covering 31 centimorgans in 3p21-p14.Proc. Natl. Acad. Sci. USA 93, 4474–4479.

    Article  PubMed  CAS  Google Scholar 

  45. Cox D.R., Burmeister M., Price E.R., Kim S., and Myers R.M.(1990)Radiation hybrid mapping:a somatic cell genetic method for constructing highresolution maps of mammalian chromosomes.Science 250, 245–250.

    Article  PubMed  CAS  Google Scholar 

  46. Mungall A.J., Edwards C.A., Ranby S.A., et al. (1996) Physical mapping of chromosome 6:a strategy for the rapid generation of sequence-ready contigs.DNA Sequence 7, 47–49.

    PubMed  CAS  Google Scholar 

  47. Haaf T. and Ward D.C. (1994)High resolution ordering of YAC contigs using extended chromatin and chromosomes.Hum. Mol. Genet. 3, 629–633.

    Article  PubMed  CAS  Google Scholar 

  48. Florijn R.J., Bonden L.A.J., Vrolijk H., et al. (1995)High-resolution DNA Fiber-FISH for genomic DNA mapping and colour bar-coding of large genes.Hum. Mol. Genet. 4, 831–836.

    Article  PubMed  CAS  Google Scholar 

  49. Heiskanen M., Karhu R., Hellsten E., Peltonen L., Kallioniemi O.P., and Palotie A.(1994)High resolution mapping using fluorescence in situ hybridization to extended DNA fibers prepared from agarose-embedded cells.Biotechniques 17, 928–933.

    PubMed  CAS  Google Scholar 

  50. Bensimon A., Simon A., Chiffaudel A., Croquette V., Heslot F., and Bensimon D.(1994)Alignment and sensitive detection of DNA by a moving interface.Science 265, 2096–2098.

    Article  PubMed  CAS  Google Scholar 

  51. Weier H.-U.G., Wang M., Mullikin J.C., et al. (1995)Quantitative DNA fiber mapping.Hum. Mol. Genet. 4, 1903–1910.

    Article  PubMed  CAS  Google Scholar 

  52. Wang M., Duell T., Gray J.W., and Weier H.-U.G. (1996) High sensitivity, high resolution physical mapping by fluorescence in situ hybridization on to individual straightened DNA molecules. Bioimaging 4, 1–11.

    Article  Google Scholar 

  53. Hu J., Wang M., Weier H.-U.G., et al.(1996)Imaging of single extended DNA molecules on flat (aminopropyl)triethoxysilane-mica by atomic force microscopy. Langmuir 12, 1697–1700.

    Article  CAS  Google Scholar 

  54. Weier H.-U.G.(2001)Quantitative DNA fiber mapping,in Methods in Cell Biology vol.64,part B,Cytometry 3rd ed.(Darzynkiewicz Z., Chrissman H.A., and Robinson J.P.,eds.),Academic Press, San Diego,pp.37–56.

    Google Scholar 

  55. Weier H.-U.G.(2001)DNA fiber mapping techniques for the assembly of highresolution physical maps.J. Histochem. Cytochem. 49, 939–948.

    Google Scholar 

  56. Duell T., Wang M., Wu J., Kim U.-J., and Weier H.-U.G.(1997)High resolution physical map of the immunoglobulin lambda variant gene cluster assembled by quantitative DNA fiber mapping.Genomics 45, 479–486.

    Article  PubMed  CAS  Google Scholar 

  57. Duell T., Nielsen L.B., Jones A., Young S.G., and Weier, H.-U.G.(1998) Con-struction of two near-kilobase resolution restriction maps of the 5’regulatory region of the human apolipoprotein B gene by quantitative DNA fiber mapping (QDFM).Cytogenet. Cell. Genet. 79, 64–70.

    Article  Google Scholar 

  58. Breier A.M., Weier H.-U.G., and Cozzarelli N.R.(2005)Independence of replisomes in Escherichia coli chromosomal replication.Proc. Natl. Acad. Sci. USA 102, 3942–3947.

    Article  PubMed  CAS  Google Scholar 

  59. Weier H.-U.G.(2002)Quantitative DNA fiber mapping,in FISH Technology (Rautenstrauss B. and Liehr T.,eds.),Springer Verlag, Heidelberg,pp.226–253.

    Google Scholar 

  60. Hsieh H.B., Wang M., Lersch R.A., Kim U.-J., and Weier H.-U.G.(2000) Rational design of landmark probes for quantitative DNA fiber mapping (QDFM). Nucleic Acids Res. 28, e30.

    Article  PubMed  CAS  Google Scholar 

  61. Cassel M.J., Munné S., Fung J., and Weier H.-U.G.(1997)Carrier-specific breakpoint-spanning DNA probes for pre-implantation genetic diagnosis (PGD) in interphase cells.Hum. Reprod. 12, 101–109.

    Article  Google Scholar 

  62. Fung J.L., Munné S., Garcia J., Kim U.-J., and Weier H.-U.G.(1999)Reciprocal translocations and infertility:molecular cloning of breakpoints in a case of constitutional translocation t(11;22)(q23;q11)and preparation of probes for preimplantation genetic diagnosis (PGD).Reprod. Fertil. Dev. 11, 17–23.

    Article  PubMed  CAS  Google Scholar 

  63. Collins C., Rommens J.M., Kowbel D., et al. (1998)Positional cloning of ZNF217 and NABC1:genes amplified at 20q13.2 and overexpressed in breast carcinoma. Proc. Natl. Acad. Sci. USA 95, 8703–8708.

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Genome Biology, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA

    Heinz-Ulrich G. Weier & Lisa W. Chu

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  1. Heinz-Ulrich G. Weier
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  2. Lisa W. Chu
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Editors and Affiliations

  1. Department of Chemistry, Purdue University, West Lafayette, IN, USA

    Minou Bina

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© 2006 Humana Press Inc.

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Weier, HU.G., Chu, L.W. (2006). Quantitative DNA Fiber Mapping in Genome Research and Construction of Physical Maps. In: Bina, M. (eds) Gene Mapping, Discovery, and Expression. Methods in Molecular Biology, vol 338. Humana Press. https://doi.org/10.1385/1-59745-097-9:31

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  • DOI: https://doi.org/10.1385/1-59745-097-9:31

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-575-0

  • Online ISBN: 978-1-59745-097-3

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