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Analysis of Yeast Artificial Chromosome Clones

  • Protocol
Pulsed-Field Gel Electrophoresis

Abstract

The technology of cloning large fragments of DNA in yeast as yeast artificial chromosomes (YACs) (1), combined with that of electro-phoretic separation of large fragments by pulsed-field gel electrophoresis (PFGE), has revolutionized research in molecular genetics. In addition to the large insert size, the YAC cloning system offers relatively unbiased genome representation compared to the conventional bacterial cloning systems based on plasmids or bacteriophages (2,3). The enormous impact of YAC cloning and PFGE techniques on physical mapping is being realized with the building of multimegabase contigs (contiguous cloned stretches of DNA). Some examples include mapping and cloning of a large gene like cystic fibrosis (CF) (4), of a chromosomal band like that of 18q21.3 (5), of a substantial portion of an entire human chromosome, Xq24–28 (3), and even an entire organism, C. eI.egum (2). Similarly, the use of YAC clones in the identification of disease-related genes like neurofibromatosis (NFl) is well documented (6). PFGE techniques play a major and critical role in the construction (see Chapter 16) and characterization (later in this chapter) of YAC clones.

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References

  1. Burke, D. T., Carle, G. F., and Olson, M. V. (1987) Clonmg of large segments of exogenous DNA into yeast by means of arhficial chromosome vectors. Science 236, 806–812.

    Article  PubMed  CAS  Google Scholar 

  2. Coulson, A., Kozono, Y., Lutterbach, B., Shownkeen, R., Sulston, J., and Waterson, R. (1991) YACs and the C.elegans genome. BioEssays 13, 413–417.

    Article  PubMed  CAS  Google Scholar 

  3. Schlessmger, D., Little, R. D., Freue, D., Abidi, F., Zucchi, I., Porta, G., Piha, G., Nagaraja, R., Johnson, S. K., Yoon, J-Y., Snvastava, A., Kere, J., Palmien, G., Gccodicola, A., Montanaro, V., Romano, G., Casamassimi, A., and D’Urso, M. (1991) Yeast artificial chromosome-based genome mapping: Some lessons form Xq24-q28. Genomics 11, 783–793.

    Article  Google Scholar 

  4. Green, E. D. and Olson, M. V. (1990) Chromosomal region of the cystic fibrosis gene in yeast artificial chromosomes: A model for human genome mapping. Science 250, 94–98.

    Article  PubMed  CAS  Google Scholar 

  5. Silverman, G. A., Jockel, J. I., Domer, P. H., Mohr, R. M., Tadlon-Miller, P., and Korsmeyer, S. J.(1991) Yeast artdicial chromosome cloning of a two megabase-size contig within a chromosomal band 18q21 establishes physical linkage between BCL2 and plasminogen activator inhibitor type-2. Genomics 9, 219–228.

    Article  PubMed  CAS  Google Scholar 

  6. Wallace, M. R., Marchuk, D. A., Andersen, L. B., Letcher, R., Odeh, H. M., Saulino, A. M., Fountain, J. W., Brereton, A., Nicholson, J., Mitchell, A. L., Brownstem, B. H., and Collms, F. S. (1990) Type 1 neurofibromatosis gene: Idenutication of a large transcript disrupted m three NFl patients. Science 249, 181–186.

    Article  PubMed  CAS  Google Scholar 

  7. Burke, D. T. and Olson, M. V. (1991) Preparation of clone libraries in yeast artificial chromosome vectors. Methods Enzymol. 194, 251–270.

    Article  PubMed  CAS  Google Scholar 

  8. Mamaus, T., Fritsch, E. F., and Sambrook, J. (1982) Molecular clonzng: A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Sprmgs Harbor, NY.

    Google Scholar 

  9. Olson, M. V., Loughney, K., and Hall, B. D. (1979) Idennfication of the yeast DNA sequences that correspond to specific tyrosme-insertmg nonsense suppressor loci.J, Mol. Bzol. 132, 387–410.

    Article  CAS  Google Scholar 

  10. Carle, G. F. and Olson, M. V. (1984) Separation of chromosomal DNA molecules from yeast by orthogonal-field-alternation gel electrophoresis. Nucleic Acids Res. 12, 5647–5664.

    Article  PubMed  CAS  Google Scholar 

  11. Brownstein, B. H., Silverman, G. A., Little, R. D., Burke, D. T., Korsmeyer, S. J., Schlessmger, D., and Olson, M. V. (1989) Isolation of single-copy human genes from a library of yeast artificial chromosome clones. Science 244, 1348–1351.

    Article  PubMed  CAS  Google Scholar 

  12. Little, R. D., Porta, G., Carle, G., Schlessmger, D., and D’Urso, M. (1989) Yeast arnficial chromosomes with 200-to 800-kilobase inserts of human DNA contammg HLA, V,k 5S, and Xq24-28 sequences. Proc. Natl. Acad. Soi. USA 86, 1598–1602.

    Article  CAS  Google Scholar 

  13. Wada, M., Little, R. D., Abide, F., Porta, G., Labella, T., Cooper, T., Della Valle, G., D’Urso, M., and Schlessmger, D. (1990) Human Xq24Xq28: Approaches to mappmg with yeast aruficlal chromosomes. Am.J Hum. Genet 46, 95–106.

    PubMed  CAS  Google Scholar 

  14. Gaensler, K. M. L., Burmeister, M., Brownstem, B. H., Talllon-Miller, P., and Myers, R. M. (1991) Physical mapping of yeast artificial chromosomes containing sequences from the human beta globm gene region. Genomics 10, 976–984.

    Article  PubMed  CAS  Google Scholar 

  15. Neil, D. L., Vdlasante, A., Fisher, R. B., Vetne, D., Cox, B., and Tyler-Smith, C. (1990) Structural instability of human tandemly repeated DNA sequences cloned in yeast arulicial chromosome vectors. Nudeic Acids Res. 18, 1421–1428.

    Article  CAS  Google Scholar 

  16. Smith, H. 0. and Bimstiel, M. L. (1976) A simple method for DNA restriction site mapping. Nucleic Acids Res. 3, 2387–2398.

    PubMed  CAS  Google Scholar 

  17. Bronson, S. K., Pei, J., Talllon-Miller, P., Chomey, M. J., Geraghty, D. E., and Chaplin, D. D. (1991) Isolation and characterization of yeast arhficial chromosome clones linking the HLA-B and HLA-C loci. Proc. Natl. Acad. Sci. USA 88, 1676–1680.

    Article  PubMed  CAS  Google Scholar 

  18. Green, E. D., Riethman, H. C., Dutchik, J. E., and Olson, M. V. (1991) Detection and characterization of yeast artificial chromosome clones. Genomics 11, 658–669.

    Article  PubMed  CAS  Google Scholar 

  19. Rowley, J. D., Diaz, M. O., Espinosa III, R., Patel, Y. D., van Melle, E., Zlemin, S., Taillon-Miller, P., Lichter, P., Evans, G. A., Kersey, J. H., Ward, D. C., Domer, P. H., and LeBeau, M. M. (1990) Mapping chromosome band 1lq23 in human acute leukemia with biotinylated probes: Identification of 1lq23 translocation breakpoints with a yeast artificial chromosome. Proc. Natl. Acad. Sci. USA 87, 9358–9362.

    Article  PubMed  CAS  Google Scholar 

  20. Chandrasekharappa, S. C., Stock., W., Neuman, W. L., LeBeau, M. M., Brownstein, B., and Westbrook, C. A. Characterization of yeast artificial chromosomes containing interleukin genes on human chromosome 5. (manuscript in preparation).

    Google Scholar 

  21. Hermanson, G.G., Hoekstra, M.F., McElligot, D.L.,and Evans, G.A. (1991) Rescue of end fragments of yeast arnficial chromosomes by homologous recombmation in yeast. Nucic Acids Res. 19, 4943–4948.

    Article  CAS  Google Scholar 

  22. Marchuk, D. A., Tavakkol, R., Wallace, M., Brownstein, B., Taillon-Miller, P., Fong, C., Legius, E., Andersen, L., Clover, T., and Collins, F. S. A yeast artificial chromosome contig encompassing the type 1 neurofibromatosis (NFl) gene. (subrmtted).

    Google Scholar 

  23. Nelson, D. (1990) Current methods for YAC clone characterization. Gene Anal. Tech. Appl. 7, 100–106.

    Article  CAS  Google Scholar 

  24. Riley, J., Ogilvie, D., Finnier, R., Jenner, D., Powell, S., Anand, R., Smith, J. C., and Markham, A. F. (1990). A novel, rapid method for the isolation of termmal sequences from yeast arnficial chromosome (YAC) clones. Nucleic Acids Res. 18, 2887–2890.

    Article  PubMed  CAS  Google Scholar 

  25. Lagerstrom, M., Pank, J., Malmgrem, H., Stewart, J., Patterson, U., and Landegren, U. (1991) Capture PCR: Efficient amplification of DNA fragments adjacent to a known sequence in human and YAC DNA. PCR Methods and Applications 1, 11l–l19.

    Google Scholar 

  26. Silverman, G. A., Ye, R. D., Pollock, K. M., Sadler, J. E., and Korsmeyer, S. J.(1989) Use of yeast Arnficial chromosome clones for mapping and walking within human chromosome segment 18q21.3. Proc. Natl. Acad. Sci. USA 86, 7485–7489.

    Article  PubMed  CAS  Google Scholar 

  27. Grootscholten, P M., Den Dunnen, J. T., Monaco, A. P., Anand, R., and Van Ommen, G-J. B. (1991) YAC mapping strategies applied to the DMD-gene. Technique 3, 41–50

    CAS  Google Scholar 

  28. Albertsen, H. M., Le Paslier, D., Abderrahim, H., Dausset, J., Cann, H., and Cohen, D. (1989) Improved control of partial DNA restriction enzyme digest in agarose using limiting concentrations of Mg. Nucleic Acids Res. 12, 808.

    Article  Google Scholar 

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© 1992 The Humana Press Inc.

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Chandrasekharappa, S.C., Marchuk, D.A., Collins, F.S. (1992). Analysis of Yeast Artificial Chromosome Clones. In: Burmeister, M., Ulanovsky, L. (eds) Pulsed-Field Gel Electrophoresis. Methods in Molecular Biology™, vol 12. Humana Press. https://doi.org/10.1385/0-89603-229-9:235

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  • DOI: https://doi.org/10.1385/0-89603-229-9:235

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-229-3

  • Online ISBN: 978-1-59259-499-3

  • eBook Packages: Springer Protocols

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