Abstract
Pulsed-field gel electrophoresis (PFGE) has been used successfully to generate physical maps of a large region from many genomes. In addition, PFGE is useful for determining the order of genes or markers more precisely than is possible with genetic linkage analysis. Since a book in the Methods in Molecular Biology series (1) has already been devoted to this subject, the aim of this chapter is to give protocols that were successfully used in our laboratory for the human mucin genes. Whenever possible, we refer to the relevant chapters of this book or other references in which strat-egies or techniques are discussed in detail.
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Burmeister M. (1992) Strategies for mapping large regions of mammalian genomes, in Pulsed-Field Gel Electrophoresis: Protocols, Methods and Theories, Methods in Molecular Biology, vol. 12 (Burmeister M., and Vlanovsky L., eds.), Humana, Totowa, NJ pp. 259–284.
Chu G., Vollrath D., and Davis R. W. (1986) Separation of large DNA molecules by coutour clamped homogeneous electric fields. Science 234, 1582–1585.
Vollrath D. (1992) Resolving multimegabase DNA molecules using contour-clamped homogeneous electric fields (CHEF), in Pulsed-Field Gel Electrophoresis, Methods in Molecular Biology, vol. 12 (Burmeister M., and Vlanovsky L., eds.), Humana, Totowa, NJ, pp. 19–30.
Galiègue-Zouitina S., Collyn-d’Hooghe M., Denis C., Mainardi À., Hildebrand M. P., Tilly H., Bastard C., and Kerckaert J. P. (1994) Molecular cloning of at(11;14)(q13;q32) translocation breakpoint centromeric to the BCL1-MTC. Genes, Chromosomes Cancer 11, 246–255.
Pigny P., Guyonnet-Dupérat V., Hill A. S., Pratt W. S., Galiègue-Zouitina S., Collynd’Hooghe M., Laine A., Van Seuningen I., Degand P., Gum J. R., Kim Y. S., Swallow D. M., Aubert J. P., and Porchet N. (1996) Human mucin genes assigned to 11p15.5: identification and organization of a cluster of genes. Genomics 38, 340–352.
Antequera F., Boyes J., and Byrd A. (1990)High levels of de novo methylation and altered chromatin structure at CpG islands. Cell 62, 503–514.
Barlow D. P. (1992)Preparation, restriction and hybridization analysis of mammalian genomic DNA for pulsed-field gel electrophoresis, in Pulsed-Field Gel Electrophoresis, Methods in Molecular Biology, vol. 12 (Burmeister M. and Vlanovsky L., eds.), Humana, Totowa, NJ, pp. 107–128.
Overhauser J. (1992) Encapsulation of cells in agarose beads, in Pulsed-Field Gel Electrophoresis, Methods in Molecular Biology, vol. 12: (Burmeister M. and Vlanovsky L., eds.), Humana, Totowa, NJ, pp. 129–134.
Boultwood J. (1994) Physical mapping of the human genome by pulsed field gel electrophoresis, in Protocols for Gene Analysis, Methods in Molecular Biology, vol. 31: (Harwood A. J., ed.), Humana, Totowa, NJ, pp. 121–134.
Birren B. and Lai E. (1993) Pulsed Field Gel Electrophoresis. A Practical Guide. Academic, San Diego, CA.
Gendler S. J., Lancaster C. A., Taylor-Papadimitriou J., Duhig T., Peat N., Burchell J. emberton L., Lalani E., and Wilson D. (1990) Molecular cloning and expression of a human tumor-associated polymorphic epithelial mucin. J. Biol. Chem. 265, 15,286–15,293.
Gum J. R., Byrd J. C., Hicks J. W., Toribara N. W., Lamport D. T. A., and Kim Y. S. (1989) Molecular cloning of human intestinal mucin cDNA. Sequence analysis and evi-dence for genetic polymorphism. J. Biol. Chem. 264, 6480–6487.
Gum J. R., Hicks J. W., Swallow D. M., Lagace R. L., Byrd J. C., Lamport D. T. A., Siddiki B. and Kim Y. S. (1990) Molecular cloning of cDNA derived from a novel human intestinal mucin gene. Biochem. Biophys. Res. Commun. 171, 407–415.
Porchet N., Nguyen V.C., Dufossé J., Audié J. P., Guyonnet-Dupérat V., Gross M. S., Denis C., Degand P., Beinheim A., and Aubert J. P. (1991) Molecular cloning and chromosomal localization of a novel human tracheo-bronchial mucin cDNA containing tandemlyrepeated sequences of 48 base pairs. Biochem. Biophys. Res. Commun. 175, 414–422.
Guyonnet-Dupérat V. Audié J. P. Debailleul, V., Laine A., Buisine M. P., GaliègueZouitina S., Pigny P. Degand P., Aubert J. P., and Porchet N. (1995) Characterization of the human mucin gene MUC5AC: a consensus cysteine-rich domain for 11p15 mucin genes? Biochem. J. 305, 211–219.
Dufosé J., Porchet N., Audié J. P., Guyonnet-Dupérat V., Laine A., Van Seuningen I., Marrakchi S., Degand P., and Aubert J. P. (1993) Degenerate 87 base pair tandem repeats create hydrophilic/hydrophobic alternating domains in human mucin peptides mapped to 11p15. Biochem. J. 293, 329–337.
Toribara N. W., Robertson A. M., Ho S. B., Kuo W. L., Gum E., Hicks J. W., Gum J. R., Byrd J. C., Siddiki B., and Kim Y. S. (1993) Human gastric mucin. Identification of a unique species by expression cloning. J. Biol. Chem. 268, 5879–5885.
Burmeister M. (1992) Strategies for mapping large regions of mammalian genomes, in Pulsed-Field Gel Electrophoresis, Methods in Molecular Biology, vol. 12 (Burmeister M. and Vlanovsky L., eds.), Humana, Totowa, NJ, pp. 259–284.
Bickmore W. A. and Byrd A. P. (1992) Use of restriction endonucleases to detect and isolate genes from mammalian cells, in Recombinant DNA, part G, Methods in Enzymology, vol. 216 (Wu R., ed.), Academic, San Diego, CA.
Guyonnet-Dupérat V. (1993) Etude des gènes de mucines humaines localisées en 11p15: mégacartographie et approche de l’organisation génomique de MUC5B et MUC5AC. Thèse de Doctorat d’Université en Sciences de la Vie et de la Santé, Lille, France.
Pigny P. (1997) Les gènes de mucines humaines localisées en 11p15-Polymorphisme, cartographie physique et approches de régulation. Thèse de Doctorat d’Université des Sciences de la Vie et de la Santé.
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Porchet, N., Aubert, JP. (2000). Southern Blot Analysis of Large DNA Fragments. In: Corfield, A.P. (eds) Glycoprotein Methods and Protocols. Methods in Molecular Biology™, vol 125. Humana Press. https://doi.org/10.1385/1-59259-048-9:313
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DOI: https://doi.org/10.1385/1-59259-048-9:313
Publisher Name: Humana Press
Print ISBN: 978-0-89603-720-5
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