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. 1996 Oct;144(2):609–619. doi: 10.1093/genetics/144.2.609

Macrorestriction Analysis of Caenorhabditis Elegans Genomic DNA

H Browning 1, L Berkowitz 1, C Madej 1, J E Paulsen 1, M E Zolan 1, S Strome 1
PMCID: PMC1207554  PMID: 8889524

Abstract

The usefulness of genomic physical maps is greatly enhanced by linkage of the physical map with the genetic map. We describe a ``macrorestriction mapping'' procedure for Caenorhabditis elegans that we have applied to this endeavor. High molecular weight, genomic DNA is digested with infrequently cutting restriction enzymes and size-fractionated by pulsed field gel electrophoresis. Southern blots of the gels are probed with clones from the C. elegans physical map. This procedure allows the construction of restriction maps covering several hundred kilobases and the detection of polymorphic restriction fragments using probes that map several hundred kilobases away. We describe several applications of this technique. (1) We determined that the amount of DNA in a previously uncloned region is <220 kb. (2) We mapped the mes-1 gene to a cosmid, by detecting polymorphic restriction fragments associated with a deletion allele of the gene. The 25-kb deletion was initially detected using as a probe sequences located ~400 kb away from the gene. (3) We mapped the molecular endpoint of the deficiency hDf6, and determined that three spontaneously derived duplications in the unc-38-dpy-5 region have very complex molecular structures, containing internal rearrangements and deletions.

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Selected References

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  1. Albertson D. G., Thomson J. N. The kinetochores of Caenorhabditis elegans. Chromosoma. 1982;86(3):409–428. doi: 10.1007/BF00292267. [DOI] [PubMed] [Google Scholar]
  2. Brenner S. The genetics of Caenorhabditis elegans. Genetics. 1974 May;77(1):71–94. doi: 10.1093/genetics/77.1.71. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Capowski E. E., Martin P., Garvin C., Strome S. Identification of grandchildless loci whose products are required for normal germ-line development in the nematode Caenorhabditis elegans. Genetics. 1991 Dec;129(4):1061–1072. doi: 10.1093/genetics/129.4.1061. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cohen D., Chumakov I., Weissenbach J. A first-generation physical map of the human genome. Nature. 1993 Dec 16;366(6456):698–701. doi: 10.1038/366698a0. [DOI] [PubMed] [Google Scholar]
  5. Coulson A., Huynh C., Kozono Y., Shownkeen R. The physical map of the Caenorhabditis elegans genome. Methods Cell Biol. 1995;48:533–550. doi: 10.1016/s0091-679x(08)61402-8. [DOI] [PubMed] [Google Scholar]
  6. Coulson A., Kozono Y., Lutterbach B., Shownkeen R., Sulston J., Waterston R. YACs and the C. elegans genome. Bioessays. 1991 Aug;13(8):413–417. doi: 10.1002/bies.950130809. [DOI] [PubMed] [Google Scholar]
  7. Coulson A., Sulston J., Brenner S., Karn J. Toward a physical map of the genome of the nematode Caenorhabditis elegans. Proc Natl Acad Sci U S A. 1986 Oct;83(20):7821–7825. doi: 10.1073/pnas.83.20.7821. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Coulson A., Waterston R., Kiff J., Sulston J., Kohara Y. Genome linking with yeast artificial chromosomes. Nature. 1988 Sep 8;335(6186):184–186. doi: 10.1038/335184a0. [DOI] [PubMed] [Google Scholar]
  9. Fan J. B., Chikashige Y., Smith C. L., Niwa O., Yanagida M., Cantor C. R. Construction of a Not I restriction map of the fission yeast Schizosaccharomyces pombe genome. Nucleic Acids Res. 1989 Apr 11;17(7):2801–2818. doi: 10.1093/nar/17.7.2801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Fire A., Waterston R. H. Proper expression of myosin genes in transgenic nematodes. EMBO J. 1989 Nov;8(11):3419–3428. doi: 10.1002/j.1460-2075.1989.tb08506.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Guo S., Kemphues K. J. par-1, a gene required for establishing polarity in C. elegans embryos, encodes a putative Ser/Thr kinase that is asymmetrically distributed. Cell. 1995 May 19;81(4):611–620. doi: 10.1016/0092-8674(95)90082-9. [DOI] [PubMed] [Google Scholar]
  12. Henderson S. T., Gao D., Lambie E. J., Kimble J. lag-2 may encode a signaling ligand for the GLP-1 and LIN-12 receptors of C. elegans. Development. 1994 Oct;120(10):2913–2924. doi: 10.1242/dev.120.10.2913. [DOI] [PubMed] [Google Scholar]
  13. Herman R. K., Albertson D. G., Brenner S. Chromosome rearrangements in Caenorhabditis elegans. Genetics. 1976 May;83(1):91–105. doi: 10.1093/genetics/83.1.91. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Herman R. K. Analysis of genetic mosaics of the nematode Caneorhabditis elegans. Genetics. 1984 Sep;108(1):165–180. doi: 10.1093/genetics/108.1.165. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Herman R. K., Madl J. E., Kari C. K. Duplications in Caenorhabditis elegans. Genetics. 1979 Jun;92(2):419–435. doi: 10.1093/genetics/92.2.419. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hodgkin J., Plasterk R. H., Waterston R. H. The nematode Caenorhabditis elegans and its genome. Science. 1995 Oct 20;270(5235):410–414. doi: 10.1126/science.270.5235.410. [DOI] [PubMed] [Google Scholar]
  17. Johnson K., Hirsh D. Patterns of proteins synthesized during development of Caenorhabditis elegans. Dev Biol. 1979 May;70(1):241–248. doi: 10.1016/0012-1606(79)90020-4. [DOI] [PubMed] [Google Scholar]
  18. Kramer J. M., French R. P., Park E. C., Johnson J. J. The Caenorhabditis elegans rol-6 gene, which interacts with the sqt-1 collagen gene to determine organismal morphology, encodes a collagen. Mol Cell Biol. 1990 May;10(5):2081–2089. doi: 10.1128/mcb.10.5.2081. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Kramer J. M., Johnson J. J., Edgar R. S., Basch C., Roberts S. The sqt-1 gene of C. elegans encodes a collagen critical for organismal morphogenesis. Cell. 1988 Nov 18;55(4):555–565. doi: 10.1016/0092-8674(88)90214-0. [DOI] [PubMed] [Google Scholar]
  20. Lawrance S. K., Smith C. L., Srivastava R., Cantor C. R., Weissman S. M. Megabase-scale mapping of the HLA gene complex by pulsed field gel electrophoresis. Science. 1987 Mar 13;235(4794):1387–1390. doi: 10.1126/science.3029868. [DOI] [PubMed] [Google Scholar]
  21. Link A. J., Olson M. V. Physical map of the Saccharomyces cerevisiae genome at 110-kilobase resolution. Genetics. 1991 Apr;127(4):681–698. doi: 10.1093/genetics/127.4.681. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. McKim K. S., Rose A. M. Chromosome I duplications in Caenorhabditis elegans. Genetics. 1990 Jan;124(1):115–132. doi: 10.1093/genetics/124.1.115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. McKim K. S., Rose A. M. Spontaneous duplication loss and breakage in Caenorhabditis elegans. Genome. 1994 Aug;37(4):595–606. doi: 10.1139/g94-085. [DOI] [PubMed] [Google Scholar]
  24. McKim K. S., Starr T., Rose A. M. Genetic and molecular analysis of the dpy-14 region in Caenorhabditis elegans. Mol Gen Genet. 1992 May;233(1-2):241–251. doi: 10.1007/BF00587585. [DOI] [PubMed] [Google Scholar]
  25. Meneely P. M., Herman R. K. Lethals, steriles and deficiencies in a region of the X chromosome of Caenorhabditis elegans. Genetics. 1979 May;92(1):99–115. doi: 10.1093/genetics/92.1.99. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Olson M. V., Dutchik J. E., Graham M. Y., Brodeur G. M., Helms C., Frank M., MacCollin M., Scheinman R., Frank T. Random-clone strategy for genomic restriction mapping in yeast. Proc Natl Acad Sci U S A. 1986 Oct;83(20):7826–7830. doi: 10.1073/pnas.83.20.7826. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Paulsen J. E., Capowski E. E., Strome S. Phenotypic and molecular analysis of mes-3, a maternal-effect gene required for proliferation and viability of the germ line in C. elegans. Genetics. 1995 Dec;141(4):1383–1398. doi: 10.1093/genetics/141.4.1383. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Sigurdson D. C., Spanier G. J., Herman R. K. Caenorhabditis elegans deficiency mapping. Genetics. 1984 Oct;108(2):331–345. doi: 10.1093/genetics/108.2.331. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Smith C. L., Econome J. G., Schutt A., Klco S., Cantor C. R. A physical map of the Escherichia coli K12 genome. Science. 1987 Jun 12;236(4807):1448–1453. doi: 10.1126/science.3296194. [DOI] [PubMed] [Google Scholar]
  30. Spieth J., MacMorris M., Broverman S., Greenspoon S., Blumenthal T. Regulated expression of a vitellogenin fusion gene in transgenic nematodes. Dev Biol. 1988 Nov;130(1):285–293. doi: 10.1016/0012-1606(88)90434-4. [DOI] [PubMed] [Google Scholar]
  31. Strome S., Martin P., Schierenberg E., Paulsen J. Transformation of the germ line into muscle in mes-1 mutant embryos of C. elegans. Development. 1995 Sep;121(9):2961–2972. doi: 10.1242/dev.121.9.2961. [DOI] [PubMed] [Google Scholar]
  32. Sulston J., Du Z., Thomas K., Wilson R., Hillier L., Staden R., Halloran N., Green P., Thierry-Mieg J., Qiu L. The C. elegans genome sequencing project: a beginning. Nature. 1992 Mar 5;356(6364):37–41. doi: 10.1038/356037a0. [DOI] [PubMed] [Google Scholar]
  33. Tax F. E., Yeargers J. J., Thomas J. H. Sequence of C. elegans lag-2 reveals a cell-signalling domain shared with Delta and Serrate of Drosophila. Nature. 1994 Mar 10;368(6467):150–154. doi: 10.1038/368150a0. [DOI] [PubMed] [Google Scholar]
  34. Villeneuve A. M., Meyer B. J. The role of sdc-1 in the sex determination and dosage compensation decisions in Caenorhabditis elegans. Genetics. 1990 Jan;124(1):91–114. doi: 10.1093/genetics/124.1.91. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Wilson R., Ainscough R., Anderson K., Baynes C., Berks M., Bonfield J., Burton J., Connell M., Copsey T., Cooper J. 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans. Nature. 1994 Mar 3;368(6466):32–38. doi: 10.1038/368032a0. [DOI] [PubMed] [Google Scholar]

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