Toward a physical map of the genome of the nematode Caenorhabditis elegans (original) (raw)

Abstract

A technique for digital characterization and comparison of DNA fragments, using restriction enzymes, is described. The technique is being applied to fragments from the nematode Caenorhabditis elegans (i) to facilitate cross-indexing of clones emanating from different laboratories and (ii) to construct a physical map of the genome. Eight hundred sixty clusters of clones, from 35 to 350 kilobases long and totaling about 60% of the genome, have been characterized.

Keywords: ordered clone bank, genomic data base, clone matching

7821

Images in this article

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Albertson D. G. Mapping muscle protein genes by in situ hybridization using biotin-labeled probes. EMBO J. 1985 Oct;4(10):2493–2498. doi: 10.1002/j.1460-2075.1985.tb03961.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Birnboim H. C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. doi: 10.1093/nar/7.6.1513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Blumenthal T., Squire M., Kirtland S., Cane J., Donegan M., Spieth J., Sharrock W. Cloning of a yolk protein gene family from Caenorhabditis elegans. J Mol Biol. 1984 Mar 25;174(1):1–18. doi: 10.1016/0022-2836(84)90361-9. [DOI] [PubMed] [Google Scholar]
  4. Cami B., Kourilsky P. Screening of cloned recombinant DNA in bacteria by in situ colony hybridization. Nucleic Acids Res. 1978 Jul;5(7):2381–2390. doi: 10.1093/nar/5.7.2381. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cox G. N., Carr S., Kramer J. M., Hirsh D. Genetic mapping of Caenorhabditis elegans collagen genes using DNA polymorphisms as phenotypic markers. Genetics. 1985 Mar;109(3):513–528. doi: 10.1093/genetics/109.3.513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Ellis R. E., Sulston J. E., Coulson A. R. The rDNA of C. elegans: sequence and structure. Nucleic Acids Res. 1986 Mar 11;14(5):2345–2364. doi: 10.1093/nar/14.5.2345. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Files J. G., Hirsh D. Ribosomal DNA of Caenorhabditis elegans. J Mol Biol. 1981 Jun 25;149(2):223–240. doi: 10.1016/0022-2836(81)90299-0. [DOI] [PubMed] [Google Scholar]
  8. Garoff H., Ansorge W. Improvements of DNA sequencing gels. Anal Biochem. 1981 Aug;115(2):450–457. doi: 10.1016/0003-2697(81)90031-2. [DOI] [PubMed] [Google Scholar]
  9. Gergen J. P., Stern R. H., Wensink P. C. Filter replicas and permanent collections of recombinant DNA plasmids. Nucleic Acids Res. 1979 Dec 20;7(8):2115–2136. doi: 10.1093/nar/7.8.2115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Ish-Horowicz D., Burke J. F. Rapid and efficient cosmid cloning. Nucleic Acids Res. 1981 Jul 10;9(13):2989–2998. doi: 10.1093/nar/9.13.2989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Karn J., Matthes H. W., Gait M. J., Brenner S. A new selective phage cloning vector, lambda 2001, with sites for XbaI, BamHI, HindIII, EcoRI, SstI and XhoI. Gene. 1984 Dec;32(1-2):217–224. doi: 10.1016/0378-1119(84)90049-0. [DOI] [PubMed] [Google Scholar]
  12. Klass M. R., Kinsley S., Lopez L. C. Isolation and characterization of a sperm-specific gene family in the nematode Caenorhabditis elegans. Mol Cell Biol. 1984 Mar;4(3):529–537. doi: 10.1128/mcb.4.3.529. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Little P. F., Cross S. H. A cosmid vector that facilitates restriction enzyme mapping. Proc Natl Acad Sci U S A. 1985 May;82(10):3159–3163. doi: 10.1073/pnas.82.10.3159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Murray N. E., Brammar W. J., Murray K. Lambdoid phages that simplify the recovery of in vitro recombinants. Mol Gen Genet. 1977 Jan 7;150(1):53–61. doi: 10.1007/BF02425325. [DOI] [PubMed] [Google Scholar]
  15. 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]
  16. Peacock A. C., Dingman C. W. Molecular weight estimation and separation of ribonucleic acid by electrophoresis in agarose-acrylamide composite gels. Biochemistry. 1968 Feb;7(2):668–674. doi: 10.1021/bi00842a023. [DOI] [PubMed] [Google Scholar]
  17. Rosenberg S. M. EcoK restriction during in vitro packaging of coliphage lambda DNA. Gene. 1985;39(2-3):313–315. doi: 10.1016/0378-1119(85)90330-0. [DOI] [PubMed] [Google Scholar]
  18. Sanger F., Coulson A. R. The use of thin acrylamide gels for DNA sequencing. FEBS Lett. 1978 Mar 1;87(1):107–110. doi: 10.1016/0014-5793(78)80145-8. [DOI] [PubMed] [Google Scholar]
  19. Staden R. A new computer method for the storage and manipulation of DNA gel reading data. Nucleic Acids Res. 1980 Aug 25;8(16):3673–3694. doi: 10.1093/nar/8.16.3673. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Sternberg N., Tiemeier D., Enquist L. In vitro packaging of a lambda Dam vector containing EcoRI DNA fragments of Escherichia coli and phage P1. Gene. 1977 May;1(3-4):255–280. doi: 10.1016/0378-1119(77)90049-x. [DOI] [PubMed] [Google Scholar]
  21. Sulston J. E., Brenner S. The DNA of Caenorhabditis elegans. Genetics. 1974 May;77(1):95–104. doi: 10.1093/genetics/77.1.95. [DOI] [PMC free article] [PubMed] [Google Scholar]