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. 1983 Feb 11;11(3):647–658. doi: 10.1093/nar/11.3.647

Unmethylated domains in vertebrate DNA.

D N Cooper, M H Taggart, A P Bird
PMCID: PMC325743  PMID: 6188105

Abstract

We have detected a fraction that is rich in unmethylated HpaII and HhaI sites by end-labelling HpaII fragments of chicken DNA. The fraction is not obvious when DNA fragments are stained with ethidium bromide as it amounts to less than 2% of the genome. The average frequency of sites for HpaII is over thirteen times greater in the unmethylated fraction than in total DNA. Partial digests indicate that the unmethylated sites are clustered in the genome. Similar unmethylated fractions were detected in six other vertebrates in both somatic and germ line DNA.

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Selected References

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

  1. Bird A. P. DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res. 1980 Apr 11;8(7):1499–1504. doi: 10.1093/nar/8.7.1499. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bird A. P., Southern E. M. Use of restriction enzymes to study eukaryotic DNA methylation: I. The methylation pattern in ribosomal DNA from Xenopus laevis. J Mol Biol. 1978 Jan 5;118(1):27–47. doi: 10.1016/0022-2836(78)90242-5. [DOI] [PubMed] [Google Scholar]
  3. Bird A. P., Taggart M. H., Gehring C. A. Methylated and unmethylated ribosomal RNA genes in the mouse. J Mol Biol. 1981 Oct 15;152(1):1–17. doi: 10.1016/0022-2836(81)90092-9. [DOI] [PubMed] [Google Scholar]
  4. Bird A. P., Taggart M. H., Smith B. A. Methylated and unmethylated DNA compartments in the sea urchin genome. Cell. 1979 Aug;17(4):889–901. doi: 10.1016/0092-8674(79)90329-5. [DOI] [PubMed] [Google Scholar]
  5. Bird A. P., Taggart M. H. Variable patterns of total DNA and rDNA methylation in animals. Nucleic Acids Res. 1980 Apr 11;8(7):1485–1497. doi: 10.1093/nar/8.7.1485. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Cedar H., Solage A., Glaser G., Razin A. Direct detection of methylated cytosine in DNA by use of the restriction enzyme MspI. Nucleic Acids Res. 1979;6(6):2125–2132. doi: 10.1093/nar/6.6.2125. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. DOSKOCIL J., SORM F. Distribution of 5-methylcytosine in pyrimidine sequences of deoxyribonucleic acids. Biochim Biophys Acta. 1962 Jun 11;55:953–959. doi: 10.1016/0006-3002(62)90909-5. [DOI] [PubMed] [Google Scholar]
  8. Fedoroff N. V., Brown D. D. The nucleotide sequence of oocyte 5S DNA in Xenopus laevis. I. The AT-rich spacer. Cell. 1978 Apr;13(4):701–716. doi: 10.1016/0092-8674(78)90220-9. [DOI] [PubMed] [Google Scholar]
  9. Gautier F., Bünemann H., Grotjahn L. Analysis of calf-thymus satellite DNA: evidence for specific methylation of cytosine in C-G sequences. Eur J Biochem. 1977 Oct 17;80(1):175–183. doi: 10.1111/j.1432-1033.1977.tb11869.x. [DOI] [PubMed] [Google Scholar]
  10. Grippo P., Iaccarino M., Parisi E., Scarano E. Methylation of DNA in developing sea urchin embryos. J Mol Biol. 1968 Sep 14;36(2):195–208. doi: 10.1016/0022-2836(68)90375-6. [DOI] [PubMed] [Google Scholar]
  11. JOSSE J., KAISER A. D., KORNBERG A. Enzymatic synthesis of deoxyribonucleic acid. VIII. Frequencies of nearest neighbor base sequences in deoxyribonucleic acid. J Biol Chem. 1961 Mar;236:864–875. [PubMed] [Google Scholar]
  12. Kunnath L., Locker J. Variable methylation of the ribosomal RNA genes of the rat. Nucleic Acids Res. 1982 Jul 10;10(13):3877–3892. doi: 10.1093/nar/10.13.3877. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Macleod D., Bird A. DNAase I sensitivity and methylation of active versus inactive rRNA genes in xenopus species hybrids. Cell. 1982 May;29(1):211–218. doi: 10.1016/0092-8674(82)90105-2. [DOI] [PubMed] [Google Scholar]
  14. Mandel J. L., Chambon P. DNA methylation: organ specific variations in the methylation pattern within and around ovalbumin and other chicken genes. Nucleic Acids Res. 1979 Dec 20;7(8):2081–2103. doi: 10.1093/nar/7.8.2081. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Maniatis T., Jeffrey A., van deSande H. Chain length determination of small double- and single-stranded DNA molecules by polyacrylamide gel electrophoresis. Biochemistry. 1975 Aug 26;14(17):3787–3794. doi: 10.1021/bi00688a010. [DOI] [PubMed] [Google Scholar]
  16. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  17. McGhee J. D., Ginder G. D. Specific DNA methylation sites in the vicinity of the chicken beta-globin genes. Nature. 1979 Aug 2;280(5721):419–420. doi: 10.1038/280419a0. [DOI] [PubMed] [Google Scholar]
  18. McKeon C., Ohkubo H., Pastan I., de Crombrugghe B. Unusual methylation pattern of the alpha 2 (l) collagen gene. Cell. 1982 May;29(1):203–210. doi: 10.1016/0092-8674(82)90104-0. [DOI] [PubMed] [Google Scholar]
  19. Miller J. R., Cartwright E. M., Brownlee G. G., Fedoroff N. V., Brown D. D. The nucleotide sequence of oocyte 5S DNA in Xenopus laevis. II. The GC-rich region. Cell. 1978 Apr;13(4):717–725. doi: 10.1016/0092-8674(78)90221-0. [DOI] [PubMed] [Google Scholar]
  20. Molitor H., Drahovsky D., Wacker A. Unmethylated DNA in mouse L cells. I. DNA fibre autoradiography. Biochim Biophys Acta. 1976 Apr 15;432(1):28–36. doi: 10.1016/0005-2787(76)90038-1. [DOI] [PubMed] [Google Scholar]
  21. Naveh-Many T., Cedar H. Active gene sequences are undermethylated. Proc Natl Acad Sci U S A. 1981 Jul;78(7):4246–4250. doi: 10.1073/pnas.78.7.4246. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Naveh-Many T., Cedar H. Topographical distribution of 5-methylcytosine in animal and plant DNA. Mol Cell Biol. 1982 Jul;2(7):758–762. doi: 10.1128/mcb.2.7.758. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. SWARTZ M. N., TRAUTNER T. A., KORNBERG A. Enzymatic synthesis of deoxyribonucleic acid. XI. Further studies on nearest neighbor base sequences in deoxyribonucleic acids. J Biol Chem. 1962 Jun;237:1961–1967. [PubMed] [Google Scholar]
  24. Singer J., Roberts-Ems J., Riggs A. D. Methylation of mouse liver DNA studied by means of the restriction enzymes msp I and hpa II. Science. 1979 Mar 9;203(4384):1019–1021. doi: 10.1126/science.424726. [DOI] [PubMed] [Google Scholar]
  25. Urieli-Shoval S., Gruenbaum Y., Sedat J., Razin A. The absence of detectable methylated bases in Drosophila melanogaster DNA. FEBS Lett. 1982 Sep 6;146(1):148–152. doi: 10.1016/0014-5793(82)80723-0. [DOI] [PubMed] [Google Scholar]
  26. Waalwijk C., Flavell R. A. MspI, an isoschizomer of hpaII which cleaves both unmethylated and methylated hpaII sites. Nucleic Acids Res. 1978 Sep;5(9):3231–3236. doi: 10.1093/nar/5.9.3231. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Weintraub H., Larsen A., Groudine M. Alpha-Globin-gene switching during the development of chicken embryos: expression and chromosome structure. Cell. 1981 May;24(2):333–344. doi: 10.1016/0092-8674(81)90323-8. [DOI] [PubMed] [Google Scholar]
  28. Whittaker P. A., McLachlan A., Hardman N. Sequence organisation in nuclear DNA from Physarum polycephalum: methylation of repetitive sequences. Nucleic Acids Res. 1981 Feb 25;9(4):801–814. doi: 10.1093/nar/9.4.801. [DOI] [PMC free article] [PubMed] [Google Scholar]

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