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Finding Candidate Genes by Preparative in Situ Hybridization

  • Chapter
Identification of Transcribed Sequences

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Abstract

We have developed preparative in situ hybridization (Prep-I.S.H.) of complex DNA populations to mitotic chromosomes as a means of generating chromosome region-specific cDNA subpopulations. Prep-I.S.H. is a combination of two cytogenetic techniques: hybridization of DNA molecules to mitotic chromosomes, and chromosome microdissection. Here we provide technical details of the procedure and describe its application to the human chromosome 11q22–23 region containing the ataxia telangiectasia genes. Prep-I.S.H. has a number of applications in studies of gene expression and genome organization, including efficient cytogenetic sorting of tissue-specific cDNAs and in dramatically reducing the number of candidate genes to aid in gene discovery. Prep-I. S.H. provides a technical approach to a “positional candidate” strategy for gene discovery that differs from positional cloning by focusing on analysis of the genes in a chromosomal region of interest rather than on detailed analysis of physical and genetic maps.

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References

  1. F.S. Collins, Positional cloning: Let’s not call it reverse anymore, Nature Genetics 1:3 (1992).

    Article  PubMed  CAS  Google Scholar 

  2. A. Ballabio, The rise and fall of positional cloning?, Nature Genetics 3:277 (1993).

    Article  PubMed  CAS  Google Scholar 

  3. Human Genome, U.S. Department of Energy, Washington, D.C. (1992).

    Google Scholar 

  4. R.C. Levitt, Polymorphisms in the transcribed 3’ untranslated region of eukaryotic genes, Genomics 11:484 (1991).

    Article  PubMed  CAS  Google Scholar 

  5. M. Olson, L. Hood, C. Cantor and D. Botstein, A common language for physical mapping of the human genome, Science 245:1434 (1989).

    Article  PubMed  CAS  Google Scholar 

  6. M.D. Adams, J.M. Kelley, J.D. Gocayne, M. Dubnick, M.H. Polymeropoulos, H. Xiao, C.R. Merrill, A. Wu, B. Olde, R.F. Moreno, A.R. Kerlavage, W.R. Mc Combie and J.C. Venter, Complementary DNA sequencing: Expressed sequence tags and human genome project, Science 252:1651 (1991).

    Article  PubMed  CAS  Google Scholar 

  7. M.D. Adams, M. Dubnick, A.R. Kerlavage, R. Moreno, J.M. Kelley, T.R. Utterback, J.W. Nagle, C. Fields and J.C. Venter, Sequence identification of 2,375 human brain genes, Nature 355:632 (1992).

    Article  PubMed  CAS  Google Scholar 

  8. J.R. Sawyer and J.C. Hozier, High resolution of mouse chromosomes: Banding homology between man and mouse, Science 232:1632 (1986).

    Article  PubMed  CAS  Google Scholar 

  9. J.R. Sawyer, Highly conserved segments in mammalian chromosomes, J. Heredity 82:128 (1991).

    CAS  Google Scholar 

  10. J.C. Hozier and L.M. Davis, Cytogenetic approaches to genome mapping, Anal. Biochem. 200:205 (1992).

    Article  PubMed  CAS  Google Scholar 

  11. J.C. Hozier, R. Graham, T. Westfall, P. Siebert and L.M. Davis, Preparative in situ hybridization: Selection of chromosome region-specific libraries on mitotic chromosomes, In Press: Genomics (1994).

    Google Scholar 

  12. G. Ruano, W. Fenton and K.K. Kidd, Biphasic amplification of very dilute DNA samples via “booster” PCR., Nucl. Acids Res. 17:5407 (1989).

    Article  PubMed  CAS  Google Scholar 

  13. G. Ruano, D.E. Brash and K.K. Kidd, PCR: the first few cycles, Amplifications 7:1–4 (1991).

    Google Scholar 

  14. R.A. Gatti, E. Boder, H.V. Vinters, et al., Ataxia-telangiectasia: An interdisciplinary approach to pathogenesis, Medicine 70:99 (1991).

    Article  PubMed  CAS  Google Scholar 

  15. R.P. Sedgwick and E. Boder, Ataxia-telangiectasia, Elsevier Science Publ., pp. 347 (1991).

    Google Scholar 

  16. M.C. Paterson and P.J. Smith, Ataxia telangiectasia: An inherited human disorder involving hypersensitivity to ionizing radiation and related DNA-damaging chemicals, Ann. Rev. Genet. 13:291 (1979).

    Article  PubMed  CAS  Google Scholar 

  17. R.A. Gatti, Localizing the genes for ataxia-telangiectasia: a human model for inherited cancer susceptibility, Adv. Cancer Res. 56:77 (1991).

    Article  PubMed  CAS  Google Scholar 

  18. P.J. Mc Kinnon, Ataxia-telangiectasia: an inherited disorder of ionizing-radiation sensitivity in man, Hum. Genet. 75:197 (1987).

    Article  PubMed  CAS  Google Scholar 

  19. N.G.J. Jaspers, R.A. Gatti and C. Baan, et al., Genetic complementation analysis of ataxia-telangiectasia and Nijmegen breakage syndrome: a survey of 50 patients, Cytogenet. Cell Genet. 49:259 (1988).

    Article  PubMed  CAS  Google Scholar 

  20. R.A. Gatti, I. Berkel, and E. Boder, et al.,Localization of an ataxia-telangiectasia gene to chromosome 11q22–23, Nature 336:577 (1988).

    Article  PubMed  CAS  Google Scholar 

  21. C.M. Mc Conville, C.J. Formstone and D. Hernandez, et al., Fine mapping of the chromosome 11q2 2–23 region using PFGE, linkage and haplotype analysis: Localization of the gene for ataxia-telangiectasia to a 5 cM region flanked by NCAM/DRD2 and STMY/CJ52.75, ph2.22, Nucl. Acids Res. 18:4335 (1990).

    Article  PubMed  CAS  Google Scholar 

  22. T. Foround, S. Wei and Y. Ziv, et al., Localization of an ataxia-telangiectasia locus to a 3-cM interval on chromosome 11q23: linkage analysis of 111 families by an international consortium, Am. J. Hum. Genet. 49:1263 (1991).

    Google Scholar 

  23. Y. Ziv, G. Rotman and M. Frydman, et al., The ATC (ataxia-telangiectasia complementation group C) locus localizes to chromosome 11q22-q23, Genomics 9:373 (1991).

    Article  PubMed  CAS  Google Scholar 

  24. K. Komatsu, S. Kodama and Y. Okumura, et al., Restoration of radiation resistance in ataxia-telangiectasia cells by the introduction of normal human chromosome 11., Mutat. Res. 235:59 (1990).

    Article  PubMed  CAS  Google Scholar 

  25. E. Sobel, E. Lange and N.G.J. Jaspers, et al., Ataxia-telangiectasia: Linkage evidence for genetic heterogeneity, Am. J. Hum. Genet. 50:1343 (1992).

    PubMed  CAS  Google Scholar 

  26. F. Cornelis, D. Cherif and M. James, et al., Precise localization of a gene responsible for ataxia-telangiectasia on chromosome 11q., Cytogenet. Cell Genet. 58:111 (1991).

    Google Scholar 

  27. C. Lambert, R.A. Schultz and M. Smith, et al., Functional complementation of ataxia-telangiectasia group D (AT-D) cells by microcell-mediated chromosome transfer and mapping of the AT-D locus to the region 11q22–23, Proc. Natl. Acad. Sci. USA 88:5907 (1991).

    Article  PubMed  CAS  Google Scholar 

  28. L.N. Kapp, R.B. Painter and L.-C. Yu, et al., Cloning of a candidate gene for ataxia-telangiectasia group D, Amer. J. Hum. Genet. 51:45 (1992).

    PubMed  CAS  Google Scholar 

  29. NIH/CEPH Collaborative Mapping Group, A comprehensive genetic linkage map of the human genome, Science 258:67 (1992).

    Article  Google Scholar 

  30. M.W. Smith, S.P. Clark, J.S. Hutchinson, Y.H. Wei, A.C. Churukian, L.B. Daniels, K.L. Diggle, M.W. Gen, A. J. Romo, Y. Lin, L. Selleri, D. L. Mc Elligott and G.A. Evans, A sequence-tagged site map of human chromosome 11, Genomics 17:699 (1993).

    Article  PubMed  CAS  Google Scholar 

  31. A. Tunnacliffe, H. Perry, P. Radice, M. Budarf and B.S. Emanuel, A panel of sequence tagged sites for chromosome band 11q23, Genomics 17:744 (1993).

    Article  PubMed  CAS  Google Scholar 

  32. C.W. Richard III, D.R. Cox, L. Kapp, J. Mumane, F. Cornelis, C. Julier, G.M. Lathrop and M.A. James, A radiation hybrid map of human chromosome 11q22-q23 containing the ataxia-telangiectasia disease locus, Genomics 17:1 (1993).

    Article  PubMed  CAS  Google Scholar 

  33. E. Lange, P. Concannon, N. Uhrhammer, Y. Nakamura, R.A. Gatti, Localization of polymorphic probes in the region of ataxia-telangiectasia at chromosome 11q22, Am. J. Hum. Genet. 53:A1028 (1993).

    Google Scholar 

  34. R.A. Gatti, K. Peterson, J. Novak, X. Chen, L. Yang-Chen, T. Liang, E. Lange and K. Lange, Prenatal diagnosis of ataxia-telangiectasia by genotyping, Am. J. Hum. Genet. 53:A1409 (1993).

    Google Scholar 

  35. R. Oskato, A. Bar-Shira, L. Vanagaite, Y. Ziv, S. Ehrlich, G. Rotman, C.M. Mc Conville, A. Chakravartiz and Y. Shiloh, Ataxia-telangiectasia: Allelic association with 11q22–23 markers in Moroccan-Jewish patients, Am. J. Hum. Genet. 53:A1055 (1993).

    Google Scholar 

  36. C.M. Mc Conville, P.J. Byrd, H. Ambrose, T. Stankovic, Y. Shiloh, J.O. Mc Namara, T. Kuwahara and A.M.R. Taylor, Mapping of newly identified polymorphic loci together with genes for mitochondrial acetoacetyl-coenzyme A thiolase (ACAT), glutamate receptor 4 (GLUR4), and interleukin 113 converting enzyme (ILIBCE) close to the locus for ataxia telangiectasia on chromosome 11q22–23, Am J. Hum. Genet. 53:A1043 (1993).

    Google Scholar 

  37. K.E. Davies and A.P. Read, Molecular basis of inherited disease, IRL Press, Second Edition, p.37.

    Google Scholar 

  38. U. Hochgeschwender, J.G. Sutcliffe and M.B. Brennan, Construction and screening of a genomic library specific for mouse chromosome 16, Proc. Natl. Acad. Sci. USA 86:8482 (1989).

    Article  PubMed  CAS  Google Scholar 

  39. M.S.H. Ko, An ‘equalized cDNA library’ by the reassociation of short double-stranded cDNAs, Nucl. Acids Res. 18:5705 (1990)

    Article  PubMed  CAS  Google Scholar 

  40. S.R. Patanjali, S. Parimoo and S.M. Weissman, Construction of a uniform-abundance (normalized) cDNA library, Proc. Natl. Acad. Sci. USA 88:1943 (1991).

    Article  PubMed  CAS  Google Scholar 

  41. R.M. Myers, The pluses of subtraction, Science 259:942 (1993).

    Article  PubMed  CAS  Google Scholar 

  42. M. Orita, Y. Suzuki, T. Sekiya and T. Hayashi, Rapid and sensitive detection of point mutations and DNA polymorphisms using the polymerase chain reaction, Genomics 5:874 (1989).

    Article  PubMed  CAS  Google Scholar 

  43. S.E. Poduslo, M. Dean, U. Kolch and S.J. O’Brien, Detecting high-resolution polymorphisms in human coding loci by combining PCR and single-strand conformation polymorphism (SSCP) analysis, Am. J. Hum. Genet. 49:106 (1991).

    PubMed  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Applied Genetics Laboratories, Melbourne, Florida, USA

    J. C. Hozier & L. M. Davis

  2. Clontech Laboratories, Palo Alto, California, USA

    P. D. Siebert

  3. Cross Cancer Institute and University of Alberta, Edmonton, Alberta, Canada

    K. Dietrich & M. C. Paterson

Authors
  1. J. C. Hozier
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  2. L. M. Davis
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  3. P. D. Siebert
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  4. K. Dietrich
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  5. M. C. Paterson
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Editor information

Editors and Affiliations

  1. National Institute of Mental Health, Bethesda, Maryland, USA

    Ute Hochgeschwender

  2. Eleanor Roosevelt Institute for Cancer Research, Denver, Colorado, USA

    Katheleen Gardiner

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© 1994 Springer Science+Business Media New York

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Hozier, J.C., Davis, L.M., Siebert, P.D., Dietrich, K., Paterson, M.C. (1994). Finding Candidate Genes by Preparative in Situ Hybridization. In: Hochgeschwender, U., Gardiner, K. (eds) Identification of Transcribed Sequences. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-2562-2_13

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  • DOI: https://doi.org/10.1007/978-1-4615-2562-2_13

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4613-6094-0

  • Online ISBN: 978-1-4615-2562-2

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