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. 1992 Jul 25;20(14):3665–3669. doi: 10.1093/nar/20.14.3665

A new strategy useful for rapid identification of microsatellites from DNA libraries with large size inserts.

B Baron 1, C Poirier 1, D Simon-Chazottes 1, C Barnier 1, J L Guénet 1
PMCID: PMC334016  PMID: 1386425

Abstract

Microsatellites are new powerful polymorphic markers used for gene mapping. Their characterization requires that all the sequence surrounding the repeat be known in order to be able to design primers for PCR amplification. However, when using DNA libraries with large cloned inserts, this sequence characterization is not immediately practicable. In this paper, we describe a new strategy, based both on the use of a microsatellite specific probing and on the creation of nested deleted clones with the Exonuclease III, in order to position microsatellites in a range allowing direct sequencing. This method was applied to the screening of a mouse chromosome 19 DNA specific library. In this way, thirteen clones were identified by specific probing and seven were submitted to the nested deletion strategy. Five of them presented microsatellite sequences in specific deleted subclones which were selected and sequenced. Primers were designed for each of them and polymorphism between the genomes of several inbred strain of mouse have been determined. These microsatellites were mapped, three of them to chromosome 19 and two to chromosome 11.

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Selected References

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  1. Baron B., Métézeau P., Hatat D., Roberts C., Goldberg M. E., Bishop C. Cloning of DNA libraries from mouse Y chromosomes purified by flow cytometry. Somat Cell Mol Genet. 1986 May;12(3):289–295. doi: 10.1007/BF01570788. [DOI] [PubMed] [Google Scholar]
  2. Baron B., Métézeau P., Kiefer-Gachelin H., Goldberg M. E. Construction and characterization of a DNA library from mouse chromosomes 19 purified by flow cytometry. Biol Cell. 1990;69(1):1–8. doi: 10.1016/0248-4900(90)90322-t. [DOI] [PubMed] [Google Scholar]
  3. Benton W. D., Davis R. W. Screening lambdagt recombinant clones by hybridization to single plaques in situ. Science. 1977 Apr 8;196(4286):180–182. doi: 10.1126/science.322279. [DOI] [PubMed] [Google Scholar]
  4. Blondel A., Thillet J. A fast and convenient way to produce single stranded DNA from a phagemid. Nucleic Acids Res. 1991 Jan 11;19(1):181–181. doi: 10.1093/nar/19.1.181. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Church G. M., Gilbert W. Genomic sequencing. Proc Natl Acad Sci U S A. 1984 Apr;81(7):1991–1995. doi: 10.1073/pnas.81.7.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Cornall R. J., Aitman T. J., Hearne C. M., Todd J. A. The generation of a library of PCR-analyzed microsatellite variants for genetic mapping of the mouse genome. Genomics. 1991 Aug;10(4):874–881. doi: 10.1016/0888-7543(91)90175-e. [DOI] [PubMed] [Google Scholar]
  7. Guénet J. L. Mouse chromosome 19. Mamm Genome. 1991;1(Spec No):S306–S317. doi: 10.1007/BF00656500. [DOI] [PubMed] [Google Scholar]
  8. Guénet J. L. The contribution of wild derived mouse inbred strains to gene mapping methodology. Curr Top Microbiol Immunol. 1986;127:109–113. doi: 10.1007/978-3-642-71304-0_13. [DOI] [PubMed] [Google Scholar]
  9. Hamada H., Petrino M. G., Kakunaga T. A novel repeated element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes. Proc Natl Acad Sci U S A. 1982 Nov;79(21):6465–6469. doi: 10.1073/pnas.79.21.6465. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hamada H., Petrino M. G., Kakunaga T., Seidman M., Stollar B. D. Characterization of genomic poly(dT-dG).poly(dC-dA) sequences: structure, organization, and conformation. Mol Cell Biol. 1984 Dec;4(12):2610–2621. doi: 10.1128/mcb.4.12.2610. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hearne C. M., McAleer M. A., Love J. M., Aitman T. J., Cornall R. J., Ghosh S., Knight A. M., Prins J. B., Todd J. A. Additional microsatellite markers for mouse genome mapping. Mamm Genome. 1991;1(4):273–282. doi: 10.1007/BF00352339. [DOI] [PubMed] [Google Scholar]
  12. Henikoff S. Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene. 1984 Jun;28(3):351–359. doi: 10.1016/0378-1119(84)90153-7. [DOI] [PubMed] [Google Scholar]
  13. Litt M., Luty J. A. A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet. 1989 Mar;44(3):397–401. [PMC free article] [PubMed] [Google Scholar]
  14. Love J. M., Knight A. M., McAleer M. A., Todd J. A. Towards construction of a high resolution map of the mouse genome using PCR-analysed microsatellites. Nucleic Acids Res. 1990 Jul 25;18(14):4123–4130. doi: 10.1093/nar/18.14.4123. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Manly K. F., Elliott R. W. RI Manager, a microcomputer program for analysis of data from recombinant inbred strains. Mamm Genome. 1991;1(2):123–126. doi: 10.1007/BF02443789. [DOI] [PubMed] [Google Scholar]
  16. Montagutelli X. GENE-LINK: a program in PASCAL for backcross genetic analysis. J Hered. 1990 Nov-Dec;81(6):490–491. doi: 10.1093/oxfordjournals.jhered.a111033. [DOI] [PubMed] [Google Scholar]
  17. Van Dilla M. A., Deaven L. L. Construction of gene libraries for each human chromosome. Cytometry. 1990;11(1):208–218. doi: 10.1002/cyto.990110124. [DOI] [PubMed] [Google Scholar]
  18. Weber J. L. Informativeness of human (dC-dA)n.(dG-dT)n polymorphisms. Genomics. 1990 Aug;7(4):524–530. doi: 10.1016/0888-7543(90)90195-z. [DOI] [PubMed] [Google Scholar]
  19. Weber J. L., May P. E. Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet. 1989 Mar;44(3):388–396. [PMC free article] [PubMed] [Google Scholar]

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