In Situ Hybridization to Polytene Chromosomes

  • Robert D. C. Saunders
Part of the Methods in Molecular Biology™ book series (MIMB, volume 123)


Since its development by Pardue et al. (1), the technique of in situ hybridization to polytene chromosomes has played a central role in the molecular genetic analysis of Drosophila melanogaster. The power of in situ hybridization is due largely to the scale of polytene chromosomes and consequently the high degree of resolution they offer the researcher. The use of radiolabeled probes has now been largely superseded by nonradioactive signal detection systems, generally using biotin- or digoxygenin-substituted probes, which offer still greater resolution because there is less scatter of signal with immunochemical and immunofluorescent detection than with silver grains. The utilization of in situ hybridization technology is of particular interest to those engaged in chromosome walking or genome mapping projects, in which it is essential to check all clones along a chromosome walk by in situ hybridization to identify clones containing repetitive DNA, and to avoid the isolation of clones derived from regions outside that of interest. It is also useful when orienting a chromosome walk, and when determining if a particular clone is derived from DNA uncovered by a deficiency. At least one Drosophila genome mapping project (2) relied on in situ hybridization to accurately map sets of overlapping cosmids (contigs) to the polytene chromosome map, while another (3) used in situ hybridization as the sole means of ordering yeast artificial chromosome (YAC) clones along the genome.


Propionic Acid Polytene Chromosome Yeast Artificial Chromosome Saline Sodium Citrate Chromosome Walk 
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  1. 1.
    Pardue, M.-L., Gerbi, S. A., Eckhardt, R. A., and Gall, J. G. (1969) Cytological localization of DNA complementary to ribosomal RNA in polytene chromosomes of Diptera. Chromosoma 29, 268–290.CrossRefGoogle Scholar
  2. 2.
    Siden-Kiamos, I., Saunders, R. D. C., Spanos, L., Majerus, T., Trenear, J., Savakis, C., Louis, C., Glover, D. M., Ashburner, M., and Kafatos, F. C. (1990) Towards a physical map of the Drosophila melanogaster genome: mapping of cosmid clones within defined genomic divisions. Nucleic Acids Res. 18, 6261–6270.PubMedCrossRefGoogle Scholar
  3. 3.
    Ajioka, J. W., Smoller, D. A., Jones, R. W., Carulli, J. P., Vellek, A. E. C., Garza, D., Link, A. J., Duncan, I. W., and Hartl, D. L. (1991) Drosophila genome project: one-hit coverage in yeast artificial chromosomes. Chromosoma 100, 495–509.PubMedCrossRefGoogle Scholar
  4. 4.
    {mndella Torre}, A. (1997) Polytene chromosome preparation from anopheline mosquitos, in The Molecular Biology of Insect Disease Vectors (Crampton, J. M., Beard, C. B., and Louis, C., eds.), Chapman and Hall, London, pp. 329–336.Google Scholar
  5. 5.
    Feinberg, A. P. and Vogelstein, B. (1983) A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem., 132, 6–13.PubMedCrossRefGoogle Scholar
  6. 6.
    Feinberg, A. P. and Vogelstein, B. (1984) Addendum to Feinberg and Vogelstein (1983) Anal. Biochem. 137, 266–267.PubMedCrossRefGoogle Scholar
  7. 7.
    Wiegant, J., Ried, T., Nederlof, P. M., vander Ploeg, M., Tanke, H. J., and Raap, A. K. (1991) In situ hybridization with fluoresceinated DNA. Nucleic Acids Res. 19, 3237–3241.PubMedCrossRefGoogle Scholar
  8. 8.
    Sorsa, V. (1988) Chromosome maps of Drosophila. 2 vols., CRC Press, Boca Raton, FL.Google Scholar
  9. 9.
    Bridges, C. B. (1935) Salivary chromosome maps with a key to the banding of the chromosomes of Drosophila melanogaster. J. Hered. 26, 60–64.Google Scholar
  10. 10.
    Lefevre, G. (1976) A photographic representation and interpretation of the polytene chromosomes of Drosophila melanogaster salivary glands, in The Genetics and Biology of Drosophila, vol. 1a (Ashburner, M. and Novitski, E., eds.), Academic Press, New York, pp. 31–66.Google Scholar

Copyright information

© Humana Press Inc. 2000

Authors and Affiliations

  • Robert D. C. Saunders
    • 1
  1. 1.Department of Anatomy and Physiology, Old Medical SchoolUniversity of DundeeDundeeScotland

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