Abstract
We have developed a new technique for the generation of YAC contigs in the mouse genome that is based on the ability to detect overlapping clones by hybridization of shared IRS-PCR products. As a demonstration of the technique, a 5-cM, >5 megabase contig was developed on the distal half of mouse Chromosome (Chr) 1, spanning the region from Lamb2 to At3. The contig covers roughly 5% of the genetic distance of the chromosome and is comprised of more than 80 clones; 71 probes were assigned physical order on the chromosome, of which 59 were new markers generated in this study. Eight of the new probes were shown to be polymorphic between C3H/HeJ-gld and M. spretus. Three probes were mapped on a [(C3H/HeJ-gld x M. spretus) x C3H/HeJ-gld] interspecific backcross to integrate the physical map with a high-resolution genetic map of the region.
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Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A., Struhl, K., eds. (1991), Current Protocols in Molecular Biology. (New York, N.Y.: Greene Publishing Associates, John Wiley and Sons).
Bennet, K.L., Hill, R.E., Pietras, D.F., Woodworth-Gutal, M., Kane-Haas, C., Houston, J.M., Heath, J.K., Hastie, N.D. (1984). Most highly repeated dispersed DNA families in the mouse genome. Mol. Cell. Biol. 4, 1561–1571.
Burke, D.T., Carle, G.T., Olson, M.V. (1987). Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. Science 236, 806–812.
Chapman, V.M., Copeland, N.G., Costantini, F.D., Dove, W.F., Nadeau, J.H., Reeves, R.H., Rossant, J., Smithies, O., Woychik, R.P. (1993). A plan for the mouse genome project. Mamm. Genome 4, 293–300.
Chartier, F.L., Keer, J.T., Sutcliffe, M.J., Henriques, D.A., Mileham, P., Brown, S.D.M. (1992). Construction of a mouse yeast artificial chromosome library in a recombination-deficient strain of yeast. Nature Genet. 1, 132–136.
Chumakov, I., Rigault, P., Guillou, S., Ougen, P., Billaut, A., Guasconi, G., Gervy, P., et al. (1992). Continuum of overlapping clones spanning the entire human chromosome 22q. Nature 359, 380–387.
Cohen, D., Chumakov, I., Weissenbach, J. (1993) A first-generation physical map of the human genome. Nature 366, 698–700
Collins, F., Galas, D. (1993). A new five year plan for the U.S. human genome project. Science 262, 43–46.
Copeland, N.G., Jenkins, N.A., Gilbert, D.J., Eppig, J.T., Maltais, J.C., Dietrich, W.F., Weaver, A., Lincoln, S.E., Steen, R.G., Stein, L.D., Nadeau, J.H., Lander, E.S. (1993). A genetic linkage map of the mouse: current applications and future prespects. Science 262, 57–66.
Cornall, R.C., Aitman, T.J., Hearne, C.M., Todd, J.A. (1991). The generation of a library of PCR-analyzed microsatellite variants for genetic mapping of the mouse genome. Genomics 10, 874–881.
Dietrich, W., Katz, H., Lincoln, S.E., Shin, H.-S., Friedman, J., Dracopoli, N., Lander, E.S. (1992). A genetic map of the mouse suitable for typing intraspecific crosses. Genetics 131, 423–447.
Dietrich, W., Miller, J., Katz, H., Joyce, D., Steen, R., Lincoln, S., Daly, M., Reeve, M.P., Weaver, A., Goodman, N., Dracopoli, N., Lander, E.S. (1993). SSLP genetic map of the mouse (Mus musculus) 2N=40. Genetic Maps, 6th ed., S. O'Brien, ed. (Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press).
Feinberg, A., Vogelstein, B. (1984). A technique for radiolabelling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 137, 266–267
Foote, S., Vollrath, D., Hilton, A., Page, D.C. (1992). The human Y chromosome: overlapping DNA clones spanning the euchromatic region. Science 258, 60–66.
Gordenin, D.A., Lobachev, K.S., Degtyareva, N.P., Malkova, A.L., Perkins, E., Resnick, M.A. (1993). Inverted DNA repeats: a source of eukaryotic genomic instability. Mol. Cell. Biol. 13, 5315–5322.
Hamvas, R.M.J., Larin, Z., Brockdorff, N., Rastan, S., Lehrach, H., Chartier, F.L., Brown, S.D.M. (1993). YAC clone contigs surrounding the Zfx and Pola loci on the mouse X chromosome. Genomics 17, 52–58.
Hastie, N.D. (1989). Highly repeated DNA families in the genome of Mus musculus. In Genetic Variants and Strains of the Laboratory Mouse, M.F. Lyons, A.G. Searle, eds. (New York: Oxford University Press), pp. 559–573.
Hunter, K., Housman, D., Hopkins, N. (1991). Isolation and characterization of irradiation fusion hybrids from mouse Chromosome 1 for mapping Rmc-1, a gene encoding a cellular receptor for MCF class murine retroviruses. Somat. Cell Mol. Genet. 2, 169–183.
Hunter, K.W., Watson, M.L., Rochelle, J., Ontiveros, S., Munroe, D., Seldin, M.F., Housman, D.E. (1993). Single-strand conformational polymorphism (SSCP) mapping of the mouse genome: integration of the SSCP, microsatellite, and gene maps of mouse Chromosome 1. Genomics 18, 510–519.
Kusumi, K., Smith, J.S., Segre, J.A., Koos, D.S., Lander, E.S. (1993). Construction of a large-insert yeast artificial chromosome library of the mouse genome. Mamm. Genome 4, 391–392.
Little, R.D., Pilia, G., Johnson, S., D'urso, M., Schlessinger, D. (1992). Yeast artificial chromosomes spanning 8 megabase and 10–15 centimorgans of human cytogenetic band Xq26. Proc. Natl. Acad. Sci. USA 89, 177–181.
Marchuk, D., Drumm, M., Saulino, A., Collins, F.S. (1991). Construction of T-vectors, a rapid and general system for direct cloning of unmodified PCR products. Nucleic Acids Res. 19, 1154.
Nelson, D.L., Ledbetter, S.A., Corbo, L., Victoria, M.F., Ramierz-Solis, R., Webster, T.D., Ledbetter, D.H., Caskey, C.T. (1989). Alu polymerase chain reaction: a method for rapid isolation of human-specific sequences from complex DNA sources. Proc. Natl. Acad. Sci. USA 86, 6686–6690.
Orita, M., Suzuki, Y., Sekiya, T., Hayashi, K. (1989a). Rapid and sensitive detection of point mutations and DNA polymorphisms using the polymerase chain reaction. Genomics 5, 874–879.
Orita, M., Iwahana, H., Kanazawa, H., Hayashi, K., Sekiya, T. (1989b). Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformational polymorphisms. Proc. Natl. Acad. Sci. USA 86, 2766–2770.
Riley, J., Butler, R., Ogilivie, D., Finniear, R., Jenner, D., Powell, S., Anand, R., Smith, J.C., Markham, A.F. (1990). A novel, rapid method for the isolation of terminal sequences from yeast artificial chromosome (YAC) clones. Nucleic Acids Res. 18, 2887–2890.
Sambrook, J., Fritsch, E.F., Maniatis, T. (1989). Molecular Cloning, A laboratory Manual, 2nd ed. (Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press).
Schlessinger, D., Little, R.D., Freije, D., Abidi, F., Zucchi, I., Porta, G., Pilia, G., Nagaraja, R., Johnson, S.K., Yoon, J.-Y., Srivastava, A., Kere, J., Palmieri, G., Ciccodicola, A., Montanaro, V., Romano, G., Casamassimi, A., D'Urso, M. (1991). Yeast artificial chromosome-based genome mapping: some lessons from Xq24–28. Genomics 11, 783–793.
Seldin, M.F., Morse, III, H.C., Reeves, J.P., Scribner, C.L., LeBoeuf, R.C., Steinberg, A.D. (1988). Genetic analysis of “autoimmune” gld mice. I. Identification of a restriction fragment length polymorphism closely linked to the gld mutation within a conserved linkage group. J. Exp. Med. 167, 688–693.
Simmler, M.-C., Cox, R.D., Avner, P. (1991). Adaptation of the interspersed repetitive sequence polymerase chain reaction to the isolation of mouse DNA probes from somatic cell hybrids on a hamster background. Genomics 10, 770–778
Spinardi, L., Mazars, R., Theillet, C. (1991). Protocols for an improved detection of point mutations by SSCP. Nucleic Acids Res. 19, 4009.
Vetrie, D., Kendall, E., Coffey, A., Hassock, S., Collins, J., Todd, C., Lehrach, H., Bobrow, M., Bentley, D.R., Harris, A. (1994). A 6.5 Mb yeast artificial chromosome contig incorporating 33 DNA markers of the human X chromosome at Xq22. Genomics 19, 42–47.
Watson, M.L., D'Eustachio, P., Mock, B.A., Steinberg, A.D., Morse, III, H.C., Oakey, R.J., Howard, T.A., Rochelle, J.M., Seldin, M.F. (1992). A linkage map of mouse Chromosome 1 using an interspecific cross segregating for the gld autoimmunity mutation. Mamm. Genome 2, 158–171.
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Hunter, K.W., Ontiveros, S.D., Watson, M.L. et al. Rapid and efficient construction of yeast artificial chromosome contigs in the mouse genome with interspersed repetitive sequence PCR (IRS-PCR): Generation of a 5-cM, >5 megabase contig on mouse Chromosome 1. Mammalian Genome 5, 597–607 (1994). https://doi.org/10.1007/BF00411453
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DOI: https://doi.org/10.1007/BF00411453