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Selective Isolation of Large Chromosomal Regions by Transformation-Associated Recombination Cloning for Structural and Functional Analysis of Mammalian Genomes

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YAC Protocols

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 349))

Abstract

Transformation-associated recombination (TAR) cloning allows selective isolation of full-size genes and genomic loci as circular yeast artificial chromosomes in yeast. The method has a broad application for structural and functional genomics, long-range haplotyping, characterization of chromosomal rearrangements, and evolutionary studies. This chapter describes a basic protocol of gene isolation by TAR, as well as a method of conversion of TAR isolates into bacterial artificial chromosomes.

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References

  1. Larionov, V., Kouprina, N., Graves, J., Chen, X.-N., Korenberg, J., and Resnick, M. A. (1996) Specific cloning of human DNA as YACs by transformation-associated recombination. Proc. Nat. Acad. Sci. USA 93, 491–496.

    Article  CAS  PubMed  Google Scholar 

  2. Larionov, V., Kouprina, N., Graves, J., and Resnick, M. A. (1996) Highly selective isolation of human DNAs from rodent-human hybrid cells as circular YACs by TAR cloning. Proc. Nat. Acad. Sci. USA 93, 13,925–13,930.

    Article  CAS  PubMed  Google Scholar 

  3. Larionov, V. (1998) Direct isolation of specific chromosomal regions and entire genes by TAR cloning. In: Genetic Engineering: Principles and Methods, vol. 21 (Setlow, J. K., ed.), Kluwer Academic, New York, 141–159.

    Google Scholar 

  4. Resnick, M. A., Kouprina N., and Larionov V. (1998) TARgeting the human genome to make gene isolation easy. Gene Therapy Mol. Biol. 1, 609–612.

    Google Scholar 

  5. Kouprina, N. and Larionov, V. (2003) Exploiting the yeast Saccharomyces cerevisiae for the study of the organization of complex genomes. FEMS Microbiol. Rev. 27, 629–649.

    Article  CAS  PubMed  Google Scholar 

  6. Noskov, V., Koriabine, M., Solomon, G., et al. (2001) Defining the minimal length of sequence homology required for selective gene isolation by TAR cloning. Nucl. Acids Res. 29, E62.

    Article  Google Scholar 

  7. Stinchomb, D. T., Thomas, M., Kelly, I., Selker, E., and Davis, R. W. (1980) Eukaryotic DNA segments capable of autonomous replication in yeast. Proc. Natl. Acad. Sci. USA 77, 4559–4563.

    Article  Google Scholar 

  8. Noskov, V., Kouprina, N., Leem, S.-H., Koriabine, M., Barrett, J. C., and Larionov, V. (2002) A genetic system for direct selection of gene-positive clones during recombinational cloning in yeast. Nucl. Acid Res. 30, E8.

    Article  Google Scholar 

  9. Raymond, C. K., Sims, E. H., Kas, A., et al. (2002) Genetic variation at the O-antigen biosynthetic locus in Pseudomonas aeruginosa. J. Bacteriol. 184, 3614–3622.

    Article  CAS  PubMed  Google Scholar 

  10. Noskov, V., Kouprina, N., Leem, S.-H., Ouspenski, I., Barrett, J. C., and Larionov, V. (2003) A general transformation-associated recombination cloning system to selectively isolate any eukaryotic or prokaryotic genomic region. BMC Genomics 4, 16.

    Article  PubMed  Google Scholar 

  11. Kouprina, N., Annab, L., Graves, J., et al. (1998) Functional copies of a human gene can be directly isolated by TAR cloning with a small 3′ end target sequence. Proc. Nat. Acad. Sci. USA 95, 4469–4474.

    Article  CAS  PubMed  Google Scholar 

  12. Kouprina, N., Graves, J., Resnick, M. A., and Larionov, V. (1997) Specific isolation of human rDNA genes by TAR cloning. Gene 197, 269–276.

    Article  CAS  PubMed  Google Scholar 

  13. Cancilla, M., Tainton, K., Barry, A., et al. (1998) Direct cloning of human 10q25 neocentromere DNA transformation-associated recombination (TAR) in yeast. Genomics 47, 399–404.

    Article  CAS  PubMed  Google Scholar 

  14. Humble, M., Kouprina, N., Noskov, V., et al. (2000) Radial TAR cloning from the TgAC mouse. Genomics 70, 292–299.

    Article  CAS  PubMed  Google Scholar 

  15. Kim, J., Noskov, V., Lu, X., et al. (2000) Discovery of a novel, paternally expressed ubiquitin-specific processing protease gene through comparative analysis of an imprinted region of mouse chromosome 7 and human chromosome 19q13.4. Genome Res. 10, 1138–1147.

    Article  CAS  PubMed  Google Scholar 

  16. Kouprina, N, Noskov, V., Koriabine, M., Leem, S.-H., and Larionov, V. (2004) Exploring transformation-associated recombination cloning for selective isolation of genomic regions. Methods Mol. Biol. 255, 69–90.

    CAS  PubMed  Google Scholar 

  17. Kouprina, N., Campbell, M., Graves, J., et al. (1998) Construction of human chromosome 16-and 5-specific YAC/BAC libraries by in vivo recombination in yeast (TAR cloning). Genomics 53, 21–28.

    Article  CAS  PubMed  Google Scholar 

  18. Cancilla, M., Graves, J., Matesic, L., et al. (1998) Rapid cloning of mouse DNA as yeast artificial chromosomes by transformation-associated recombination (TAR). Mamm. Genome 9, 157–159.

    Article  CAS  PubMed  Google Scholar 

  19. Zeng, C., Kouprina, N., Zhu, B., et al. (2001) New BAC/YAC libraries allowing to selectively re-isolate a desired genomic region by in vivo recombination in yeast. Genomics 77, 27–34.

    Article  CAS  PubMed  Google Scholar 

  20. Nihei, N., Kouprina, N., Larionov, V., et al. (2002) Functional evidence for a metastasis suppressor gene for rat prostate cancer within a 60 kb region on human chromosome 8p21-p12. Cancer Res. 62, 367–370.

    CAS  PubMed  Google Scholar 

  21. Annab, L., Kouprina, N., Solomon, G., et al. (2000) Isolation of functional copy of the human BRCA1 gene by TAR cloning in yeast. Gene 250, 201–208.

    Article  CAS  PubMed  Google Scholar 

  22. Larionov, V., Kouprina, N., Solomon, G., Barrett, J. C., and Resnick, M. A. (1997) Direct isolation of human BRCA2 gene by transformation-associated recombination in yeast. Proc. Nat. Acad. Sci. USA 94, 7384–7387.

    Article  CAS  PubMed  Google Scholar 

  23. Leem, S.-H., Londono-Vallejo, J. A., Kim, J.-H., et al. Cloning of the human telomerase gene: complete genomic sequence and analysis of tandem repearts polymorphismjs in intronic regions. Oncogene 21, 769–777.

    Google Scholar 

  24. Kouprina, N., Ebersole, T., Koriabine, M., et al. (2003) Cloning of human centromeres by transformation-associated recombination in yeast and generation of functional human artificial chromosomes. Nucl. Acids Res. 31, 922–934.

    Article  CAS  PubMed  Google Scholar 

  25. Kim, J.-H., Leem, S.-H., Sunwoo, Y., and Kouprina, N. (2003) Separation of long-range human TERT gene haplotypes by transformation-associated recombination cloning in yeast. Oncogene 22, 2452–2456.

    Article  CAS  PubMed  Google Scholar 

  26. Noskov, V., Leem, S.-H., Solomon, G., et al. (2003) A novel strategy for analysis of gene homologs and segmental genome duplications. J. Mol. Evo. 56, 702–710.

    Article  CAS  Google Scholar 

  27. Kouprina, N., Mullokandov, M., Rogozin, I., et al. (2004) The SPANX gene family of cancer-testis specific antigens: rapid evolution, an unusual case of positive selection and amplification in African great apes and hominids. Proc. Natl. Acad. Sci. USA 101, 3077–3082.

    Article  CAS  PubMed  Google Scholar 

  28. Kouprina, N., Pavlicek, A., Mochida, G. H., et al. (2004) Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion. PLoS Biol. 2, 653–663.

    Article  CAS  Google Scholar 

  29. Pavlicek, A., Noskov, N., Kouprina, N., Barrett, J. C., Jurka, J., and Larionov, V. (2004) Evolution of the tumor suppressor BRCA1 locus in primates: implications for cancer predisposition. Hum. Mol. Genet. 13, 1–15.

    Article  Google Scholar 

  30. Theis, J. F. and Newlon, C. S. (1997) The ARS309 chromosomal replicator of Saccharomyces cerevisiae depends on an exceptional ARS consensus sequence. Proc. Natl. Acad. Sci. USA 94, 10,786–10,791.

    Article  CAS  PubMed  Google Scholar 

  31. Leem, S.-H., Kouprina, N., Grimwood, J., et al. (2004) Closing the gaps on human chromosome 19 revealed genes with a high density of repetitive tandemly arrayed elements. Genome Res. 14, 239–246.

    Article  CAS  PubMed  Google Scholar 

  32. Kouprina, N., Leem, S.-H., Solomon, G., et al. (2003) Segments missing from the draft human genome sequence can be isolated by TAR cloning in yeas. EMBO Report 4, 257–262.

    Article  CAS  Google Scholar 

  33. Sikorski, R. S. and Hieter, P. (1989) A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122, 19–27.

    CAS  PubMed  Google Scholar 

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Author information

Authors and Affiliations

  1. Laboratory of Biosystems and Cancer, National Cancer Institute (NCI, NIH), Bethesda, MD

    Natalay Kouprina, Vladimir N. Noskov & Vladimir Larionov

Authors
  1. Natalay Kouprina
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  2. Vladimir N. Noskov
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  3. Vladimir Larionov
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Editor information

Editors and Affiliations

  1. School of Medical Sciences, College of Life Sciences and Medicine, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, Scotland

    Alasdair MacKenzie

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© 2006 Humana Press Inc., Totowa NJ

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Kouprina, N., Noskov, V.N., Larionov, V. (2006). Selective Isolation of Large Chromosomal Regions by Transformation-Associated Recombination Cloning for Structural and Functional Analysis of Mammalian Genomes. In: MacKenzie, A. (eds) YAC Protocols. Methods in Molecular Biology™, vol 349. Humana Press. https://doi.org/10.1385/1-59745-158-4:85

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  • DOI: https://doi.org/10.1385/1-59745-158-4:85

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-612-2

  • Online ISBN: 978-1-59745-158-1

  • eBook Packages: Springer Protocols

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