Skip to main content
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1987 Feb 11;15(3):1173–1184. doi: 10.1093/nar/15.3.1173

Overabundance of rare-cutting restriction endonuclease sites in the human genome.

D I Smith, W Golembieski, J D Gilbert, L Kizyma, O J Miller
PMCID: PMC340516  PMID: 3029699

Abstract

A human chromosome 3-specific cosmid library was constructed from a somatic cell hybrid containing human chromosome 3 as its only human component. This library was screened to identify 230 human recombinants which contained an average insert size of 37 kilobases. DNA prepared from 54 of these cosmids, representing 2000 kilobases of human DNA, was then tested for restriction endonuclease sites for EcoRI, HindIII, KpnI, XhoI, and DraI, as well as those of the rare-cutting restriction endonucleases NotI, SfiI, NruI, MluI, SacII, and BssHII. Sites for the latter enzymes were much more abundant than would be expected from theoretical calculations, reflecting non-random clustering of these sites. This has important implications for the use of these enzymes in the construction of physical maps of chromosomes. Some individual cosmids contained large numbers of rare sites, offering an alternative means of physically mapping chromosomes based upon identifying clusters of rare restriction sites. These clusters appear to be spaced an average of 1000 kb apart.

Full text

PDF
1175

Selected References

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

  1. 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]
  2. Bernardi G., Olofsson B., Filipski J., Zerial M., Salinas J., Cuny G., Meunier-Rotival M., Rodier F. The mosaic genome of warm-blooded vertebrates. Science. 1985 May 24;228(4702):953–958. doi: 10.1126/science.4001930. [DOI] [PubMed] [Google Scholar]
  3. Bird A. P. CpG-rich islands and the function of DNA methylation. Nature. 1986 May 15;321(6067):209–213. doi: 10.1038/321209a0. [DOI] [PubMed] [Google Scholar]
  4. Bird A., Taggart M., Frommer M., Miller O. J., Macleod D. A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell. 1985 Jan;40(1):91–99. doi: 10.1016/0092-8674(85)90312-5. [DOI] [PubMed] [Google Scholar]
  5. Bishop D. T., Williamson J. A., Skolnick M. H. A model for restriction fragment length distributions. Am J Hum Genet. 1983 Sep;35(5):795–815. [PMC free article] [PubMed] [Google Scholar]
  6. Brown W. R., Bird A. P. Long-range restriction site mapping of mammalian genomic DNA. 1986 Jul 31-Aug 6Nature. 322(6078):477–481. doi: 10.1038/322477a0. [DOI] [PubMed] [Google Scholar]
  7. Byrne B. J., Davis M. S., Yamaguchi J., Bergsma D. J., Subramanian K. N. Definition of the simian virus 40 early promoter region and demonstration of a host range bias in the enhancement effect of the simian virus 40 72-base-pair repeat. Proc Natl Acad Sci U S A. 1983 Feb;80(3):721–725. doi: 10.1073/pnas.80.3.721. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Carle G. F., Olson M. V. An electrophoretic karyotype for yeast. Proc Natl Acad Sci U S A. 1985 Jun;82(11):3756–3760. doi: 10.1073/pnas.82.11.3756. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Carle G. F., Olson M. V. Separation of chromosomal DNA molecules from yeast by orthogonal-field-alternation gel electrophoresis. Nucleic Acids Res. 1984 Jul 25;12(14):5647–5664. doi: 10.1093/nar/12.14.5647. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Carlock L. R., Smith D., Wasmuth J. J. Genetic counterselective procedure to isolate interspecific cell hybrids containing single human chromosomes: construction of cell hybrids and recombinant DNA libraries specific for human chromosomes 3 and 4. Somat Cell Mol Genet. 1986 Mar;12(2):163–174. doi: 10.1007/BF01560663. [DOI] [PubMed] [Google Scholar]
  11. Dana S., Wasmuth J. J. Selective linkage disruption in human-Chinese hamster cell hybrids: deletion mapping of the leuS, hexB, emtB, and chr genes on human chromosome 5. Mol Cell Biol. 1982 Oct;2(10):1220–1228. doi: 10.1128/mcb.2.10.1220. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Drayna D., Davies K., Hartley D., Mandel J. L., Camerino G., Williamson R., White R. Genetic mapping of the human X chromosome by using restriction fragment length polymorphisms. Proc Natl Acad Sci U S A. 1984 May;81(9):2836–2839. doi: 10.1073/pnas.81.9.2836. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Drmanac R., Petrović N., Glisin V., Crkvenjakov R. A calculation of fragment lengths obtainable from human DNA with 78 restriction enzymes: an aid for cloning and mapping. Nucleic Acids Res. 1986 Jun 11;14(11):4691–4692. doi: 10.1093/nar/14.11.4691. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Dynan W. S., Sazer S., Tjian R., Schimke R. T. Transcription factor Sp1 recognizes a DNA sequence in the mouse dihydrofolate reductase promoter. Nature. 1986 Jan 16;319(6050):246–248. doi: 10.1038/319246a0. [DOI] [PubMed] [Google Scholar]
  15. Farnham P. J., Abrams J. M., Schimke R. T. Opposite-strand RNAs from the 5' flanking region of the mouse dihydrofolate reductase gene. Proc Natl Acad Sci U S A. 1985 Jun;82(12):3978–3982. doi: 10.1073/pnas.82.12.3978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Gruenbaum Y., Stein R., Cedar H., Razin A. Methylation of CpG sequences in eukaryotic DNA. FEBS Lett. 1981 Feb 9;124(1):67–71. doi: 10.1016/0014-5793(81)80055-5. [DOI] [PubMed] [Google Scholar]
  17. Gusella J., Varsanyi-Breiner A., Kao F. T., Jones C., Puck T. T., Keys C., Orkin S., Housman D. Precise localization of human beta-globin gene complex on chromosome 11. Proc Natl Acad Sci U S A. 1979 Oct;76(10):5239–5242. doi: 10.1073/pnas.76.10.5239. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Holmquist G., Gray M., Porter T., Jordan J. Characterization of Giemsa dark- and light-band DNA. Cell. 1982 Nov;31(1):121–129. doi: 10.1016/0092-8674(82)90411-1. [DOI] [PubMed] [Google Scholar]
  19. Kunnath L., Locker J. Characterization of DNA methylation in the rat. Biochim Biophys Acta. 1982 Dec 31;699(3):264–271. doi: 10.1016/0167-4781(82)90116-6. [DOI] [PubMed] [Google Scholar]
  20. Lui A. C., McBride B. C., Vovis G. F., Smith M. Site specific endonuclease from Fusobacterium nucleatum. Nucleic Acids Res. 1979 Jan;6(1):1–15. doi: 10.1093/nar/6.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Qiang B. Q., Schildkraut I. A type II restriction endonuclease with an eight nucleotide specificity from Streptomyces fimbriatus. Nucleic Acids Res. 1984 Jun 11;12(11):4507–4516. doi: 10.1093/nar/12.11.4507. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Schwartz D. C., Cantor C. R. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell. 1984 May;37(1):67–75. doi: 10.1016/0092-8674(84)90301-5. [DOI] [PubMed] [Google Scholar]
  23. Skolnick M. H., Francke U. Report of the committee on human gene mapping by recombinant DNA techniques. Oslo Conference (1981): Sixth International Workshop on Human Gene Mapping. Cytogenet Cell Genet. 1982;32(1-4):194–204. doi: 10.1159/000131699. [DOI] [PubMed] [Google Scholar]
  24. Skolnick M. H., White R. Strategies for detecting and characterizing restriction fragment length polymorphisms (RFLP's). Cytogenet Cell Genet. 1982;32(1-4):58–67. doi: 10.1159/000131687. [DOI] [PubMed] [Google Scholar]
  25. Southern E. M. Application of DNA analysis to mapping the human genome. Cytogenet Cell Genet. 1982;32(1-4):52–57. doi: 10.1159/000131686. [DOI] [PubMed] [Google Scholar]
  26. Wolf S. F., Jolly D. J., Lunnen K. D., Friedmann T., Migeon B. R. Methylation of the hypoxanthine phosphoribosyltransferase locus on the human X chromosome: implications for X-chromosome inactivation. Proc Natl Acad Sci U S A. 1984 May;81(9):2806–2810. doi: 10.1073/pnas.81.9.2806. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Wyman A. R., Wolfe L. B., Botstein D. Propagation of some human DNA sequences in bacteriophage lambda vectors requires mutant Escherichia coli hosts. Proc Natl Acad Sci U S A. 1985 May;82(9):2880–2884. doi: 10.1073/pnas.82.9.2880. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Yen P. H., Mohandas T., Shapiro L. J. Stability of DNA methylation of the human hypoxanthine phosphoribosyltransferase gene. Somat Cell Mol Genet. 1986 Mar;12(2):153–161. doi: 10.1007/BF01560662. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES