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. 1996 May 15;24(10):1802–1808. doi: 10.1093/nar/24.10.1802

Random-breakage mapping method applied to human DNA sequences.

M Löbrich 1, B Rydberg 1, P K Cooper 1
PMCID: PMC145864  PMID: 8657558

Abstract

The random-breakage mapping method [Game et al. (1990) Nucleic Acids Res., 18, 4453-4461] was applied to DNA sequences in human fibroblasts. The methodology involves NotI restriction endonuclease digestion of DNA from irradiated calls, followed by pulsed-field gel electrophoresis, Southern blotting and hybridization with DNA probes recognizing the single copy sequences of interest. The Southern blots show a band for the unbroken restriction fragments and a smear below this band due to radiation induced random breaks. This smear pattern contains two discontinuities in intensity at positions that correspond to the distance of the hybridization site to each end of the restriction fragment. By analyzing the positions of those discontinuities we confirmed the previously mapped position of the probe DXS1327 within a NotI fragment on the X chromosome, thus demonstrating the validity of the technique. We were also able to position the probes D21S1 and D21S15 with respect to the ends of their corresponding NotI fragments on chromosome 21. A third chromosome 21 probe, D21S11, has previously been reported to be close to D21S1, although an uncertainty about a second possible location existed. Since both probes D21S1 and D21S11 hybridized to a single NotI fragment and yielded a similar smear pattern, this uncertainty is removed by the random-breakage mapping method.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Borrow J., Goddard A. D., Sheer D., Solomon E. Molecular analysis of acute promyelocytic leukemia breakpoint cluster region on chromosome 17. Science. 1990 Sep 28;249(4976):1577–1580. doi: 10.1126/science.2218500. [DOI] [PubMed] [Google Scholar]
  2. Burmeister M., Kim S., Price E. R., de Lange T., Tantravahi U., Myers R. M., Cox D. R. A map of the distal region of the long arm of human chromosome 21 constructed by radiation hybrid mapping and pulsed-field gel electrophoresis. Genomics. 1991 Jan;9(1):19–30. doi: 10.1016/0888-7543(91)90216-2. [DOI] [PubMed] [Google Scholar]
  3. Chu G. Bag model for DNA migration during pulsed-field electrophoresis. Proc Natl Acad Sci U S A. 1991 Dec 15;88(24):11071–11075. doi: 10.1073/pnas.88.24.11071. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Chumakov I., Rigault P., Guillou S., Ougen P., Billaut A., Guasconi G., Gervy P., LeGall I., Soularue P., Grinas L. Continuum of overlapping clones spanning the entire human chromosome 21q. Nature. 1992 Oct 1;359(6394):380–387. doi: 10.1038/359380a0. [DOI] [PubMed] [Google Scholar]
  5. Cook V. E., Mortimer R. K. A quantitative model of DNA fragments generated by ionizing radiation, and possible experimental applications. Radiat Res. 1991 Jan;125(1):102–106. [PubMed] [Google Scholar]
  6. Cox D. R., Burmeister M., Price E. R., Kim S., Myers R. M. Radiation hybrid mapping: a somatic cell genetic method for constructing high-resolution maps of mammalian chromosomes. Science. 1990 Oct 12;250(4978):245–250. doi: 10.1126/science.2218528. [DOI] [PubMed] [Google Scholar]
  7. Craig A. G., Nizetic D., Hoheisel J. D., Zehetner G., Lehrach H. Ordering of cosmid clones covering the herpes simplex virus type I (HSV-I) genome: a test case for fingerprinting by hybridisation. Nucleic Acids Res. 1990 May 11;18(9):2653–2660. doi: 10.1093/nar/18.9.2653. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Daniels D. L., Olson C. H., Brumley R., Blattner F. R. Field inversion gel electrophoresis applied to the rapid, multi-enzyme restriction mapping of phage lambda clones. Nucleic Acids Res. 1990 Mar 11;18(5):1312–1312. doi: 10.1093/nar/18.5.1312. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Doggett N. A., Smith C. L., Cantor C. R. The effect of DNA concentration on mobility in pulsed field gel electrophoresis. Nucleic Acids Res. 1992 Feb 25;20(4):859–864. doi: 10.1093/nar/20.4.859. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Fan Y. S., Davis L. M., Shows T. B. Mapping small DNA sequences by fluorescence in situ hybridization directly on banded metaphase chromosomes. Proc Natl Acad Sci U S A. 1990 Aug;87(16):6223–6227. doi: 10.1073/pnas.87.16.6223. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Ferrin L. J., Camerini-Otero R. D. Selective cleavage of human DNA: RecA-assisted restriction endonuclease (RARE) cleavage. Science. 1991 Dec 6;254(5037):1494–1497. doi: 10.1126/science.1962209. [DOI] [PubMed] [Google Scholar]
  12. Fountain J. W., Wallace M. R., Bruce M. A., Seizinger B. R., Menon A. G., Gusella J. F., Michels V. V., Schmidt M. A., Dewald G. W., Collins F. S. Physical mapping of a translocation breakpoint in neurofibromatosis. Science. 1989 Jun 2;244(4908):1085–1087. doi: 10.1126/science.2543076. [DOI] [PubMed] [Google Scholar]
  13. Game J. C., Bell M., King J. S., Mortimer R. K. Random-breakage mapping, a rapid method for physically locating an internal sequence with respect to the ends of a DNA molecule. Nucleic Acids Res. 1990 Aug 11;18(15):4453–4461. doi: 10.1093/nar/18.15.4453. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Gardiner K., Horisberger M., Kraus J., Tantravahi U., Korenberg J., Rao V., Reddy S., Patterson D. Analysis of human chromosome 21: correlation of physical and cytogenetic maps; gene and CpG island distributions. EMBO J. 1990 Jan;9(1):25–34. doi: 10.1002/j.1460-2075.1990.tb08076.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Goate A., Chartier-Harlin M. C., Mullan M., Brown J., Crawford F., Fidani L., Giuffra L., Haynes A., Irving N., James L. Segregation of a missense mutation in the amyloid precursor protein gene with familial Alzheimer's disease. Nature. 1991 Feb 21;349(6311):704–706. doi: 10.1038/349704a0. [DOI] [PubMed] [Google Scholar]
  16. Ichikawa H., Hosoda F., Arai Y., Shimizu K., Ohira M., Ohki M. A NotI restriction map of the entire long arm of human chromosome 21. Nat Genet. 1993 Aug;4(4):361–366. doi: 10.1038/ng0893-361. [DOI] [PubMed] [Google Scholar]
  17. Ichikawa H., Shimizu K., Saito A., Wang D. N., Oliva R., Kobayashi H., Kaneko Y., Miyoshi H., Smith C. L., Cantor C. R. Long-distance restriction mapping of the proximal long arm of human chromosome 21 with Not I linking clones. Proc Natl Acad Sci U S A. 1992 Jan 1;89(1):23–27. doi: 10.1073/pnas.89.1.23. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Kohara Y., Akiyama K., Isono K. The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell. 1987 Jul 31;50(3):495–508. doi: 10.1016/0092-8674(87)90503-4. [DOI] [PubMed] [Google Scholar]
  19. Korenberg J. R., Engels W. R. Base ratio, DNA content, and quinacrine-brightness of human chromosomes. Proc Natl Acad Sci U S A. 1978 Jul;75(7):3382–3386. doi: 10.1073/pnas.75.7.3382. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Lawrence S., Collins A., Keats B. J., Hulten M., Morton N. E. Integration of gene maps: chromosome 21. Proc Natl Acad Sci U S A. 1993 Aug 1;90(15):7210–7214. doi: 10.1073/pnas.90.15.7210. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Lehesjoki A. E., Koskiniemi M., Sistonen P., Miao J., Hästbacka J., Norio R., de la Chapelle A. Localization of a gene for progressive myoclonus epilepsy to chromosome 21q22. Proc Natl Acad Sci U S A. 1991 May 1;88(9):3696–3699. doi: 10.1073/pnas.88.9.3696. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Lippert M. J., Albertini R. J., Nicklas J. A. Physical mapping of the human hprt chromosomal region (Xq26). Mutat Res. 1995 Jan;326(1):39–49. doi: 10.1016/0027-5107(94)00147-w. [DOI] [PubMed] [Google Scholar]
  23. Löbrich M., Ikpeme S., Kiefer J. Analysis of the inversion effect in pulsed field gel electrophoresis by a two-dimensional contour-clamped homogeneous electric field system. Anal Biochem. 1993 Jan;208(1):65–73. doi: 10.1006/abio.1993.1009. [DOI] [PubMed] [Google Scholar]
  24. Löbrich M., Rydberg B., Cooper P. K. DNA double-strand breaks induced by high-energy neon and iron ions in human fibroblasts. II. Probing individual notI fragments by hybridization. Radiat Res. 1994 Aug;139(2):142–151. [PubMed] [Google Scholar]
  25. Olson M. V., Dutchik J. E., Graham M. Y., Brodeur G. M., Helms C., Frank M., MacCollin M., Scheinman R., Frank T. Random-clone strategy for genomic restriction mapping in yeast. Proc Natl Acad Sci U S A. 1986 Oct;83(20):7826–7830. doi: 10.1073/pnas.83.20.7826. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Pavan W. J., Hieter P., Reeves R. H. Generation of deletion derivatives by targeted transformation of human-derived yeast artificial chromosomes. Proc Natl Acad Sci U S A. 1990 Feb;87(4):1300–1304. doi: 10.1073/pnas.87.4.1300. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Petersen M. B., Slaugenhaupt S. A., Lewis J. G., Warren A. C., Chakravarti A., Antonarakis S. E. A genetic linkage map of 27 markers on human chromosome 21. Genomics. 1991 Mar;9(3):407–419. doi: 10.1016/0888-7543(91)90406-5. [DOI] [PubMed] [Google Scholar]
  28. Rydberg B., Löbrich M., Cooper P. K. DNA double-strand breaks induced by high-energy neon and iron ions in human fibroblasts. I. Pulsed-field gel electrophoresis method. Radiat Res. 1994 Aug;139(2):133–141. [PubMed] [Google Scholar]
  29. Smith C. L., Condemine G. New approaches for physical mapping of small genomes. J Bacteriol. 1990 Mar;172(3):1167–1172. doi: 10.1128/jb.172.3.1167-1172.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Stallings R. L., Torney D. C., Hildebrand C. E., Longmire J. L., Deaven L. L., Jett J. H., Doggett N. A., Moyzis R. K. Physical mapping of human chromosomes by repetitive sequence fingerprinting. Proc Natl Acad Sci U S A. 1990 Aug;87(16):6218–6222. doi: 10.1073/pnas.87.16.6218. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Tanzi R. E., Haines J. L., Watkins P. C., Stewart G. D., Wallace M. R., Hallewell R., Wong C., Wexler N. S., Conneally P. M., Gusella J. F. Genetic linkage map of human chromosome 21. Genomics. 1988 Aug;3(2):129–136. doi: 10.1016/0888-7543(88)90143-7. [DOI] [PubMed] [Google Scholar]
  32. Tassone F., Cheng S., Gardiner K. Analysis of chromosome 21 yeast artificial chromosome (YAC) clones. Am J Hum Genet. 1992 Dec;51(6):1251–1264. [PMC free article] [PubMed] [Google Scholar]
  33. Wang D., Fang H., Cantor C. R., Smith C. L. A contiguous Not I restriction map of band q22.3 of human chromosome 21. Proc Natl Acad Sci U S A. 1992 Apr 15;89(8):3222–3226. doi: 10.1073/pnas.89.8.3222. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Wang D., Smith C. L. Large-scale structure conservation along the entire long arm of human chromosome 21. Genomics. 1994 Apr;20(3):441–451. doi: 10.1006/geno.1994.1199. [DOI] [PubMed] [Google Scholar]
  35. Watkins P. C., Tanzi R. E., Gibbons K. T., Tricoli J. V., Landes G., Eddy R., Shows T. B., Gusella J. F. Isolation of polymorphic DNA segments from human chromosome 21. Nucleic Acids Res. 1985 Sep 11;13(17):6075–6088. doi: 10.1093/nar/13.17.6075. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. van den Engh G., Sachs R., Trask B. J. Estimating genomic distance from DNA sequence location in cell nuclei by a random walk model. Science. 1992 Sep 4;257(5075):1410–1412. doi: 10.1126/science.1388286. [DOI] [PubMed] [Google Scholar]

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