• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of narLink to Publisher's site
Nucleic Acids Res. May 25, 1984; 12(10): 4385–4396.
PMCID: PMC318839

CG dinucleotide clusters in MHC genes and in 5' demethylated genes.


In the DNA of higher vertebrates the dinucleotide CG is unique in two respects: it occurs far less frequently than would be expected on the basis of the content of cytosine and guanine in a given DNA segment ("CG suppression") and it contains predominantly 5-methyl-cytosine, the only modified nucleotide common in vertebrate DNA. Here we point out the existence of CG clusters, i.e. localized lapses in the usual CG suppression, in two categories of DNA segments from vertebrates: around the polymorphic exons of major histocompatibility complex (MHC) genes and in the 5' regions of certain other genes. These observations contradict the recent suggestion that CG frequency is uniform over long contiguous segments of DNA containing several genes. A model for the origin of these CG clusters as a consequence of regional demethylation of germline DNA is supported by analysis of other sequence features of these regions as well as by previously published data on the methylation status in sperm DNA of two of these CG-rich regions.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (835K), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Bird AP. DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res. 1980 Apr 11;8(7):1499–1504. [PMC free article] [PubMed]
  • Lennon GG, Fraser NW. CpG frequency in large DNA segments. J Mol Evol. 1983;19(3-4):286–288. [PubMed]
  • Kimball ES, Coligan JE. Structure of class I major histocompatibility antigens. Contemp Top Mol Immunol. 1983;9:1–63. [PubMed]
  • Evans GA, Margulies DH, Shykind B, Seidman JG, Ozato K. Exon shuffling: mapping polymorphic determinants on hybrid mouse transplantation antigens. Nature. 1982 Dec 23;300(5894):755–757. [PubMed]
  • Shackelford DA, Kaufman JF, Korman AJ, Strominger JL. HLA-DR antigens: structure, separation of subpopulations, gene cloning and function. Immunol Rev. 1982;66:133–187. [PubMed]
  • Smith TF, Waterman MS, Sadler JR. Statistical characterization of nucleic acid sequence functional domains. Nucleic Acids Res. 1983 Apr 11;11(7):2205–2220. [PMC free article] [PubMed]
  • Stein R, Sciaky-Gallili N, Razin A, Cedar H. Pattern of methylation of two genes coding for housekeeping functions. Proc Natl Acad Sci U S A. 1983 May;80(9):2422–2426. [PMC free article] [PubMed]
  • 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. [PubMed]
  • Kvist S, Roberts L, Dobberstein B. Mouse histocompatibility genes: structure and organisation of a Kd gene. EMBO J. 1983;2(2):245–254. [PMC free article] [PubMed]
  • Moore KW, Sher BT, Sun YH, Eakle KA, Hood L. DNA sequence of a gene encoding a BALB/c mouse Ld transplantation antigen. Science. 1982 Feb 5;215(4533):679–682. [PubMed]
  • Steinmetz M, Moore KW, Frelinger JG, Sher BT, Shen FW, Boyse EA, Hood L. A pseudogene homologous to mouse transplantation antigens: transplantation antigens are encoded by eight exons that correlate with protein domains. Cell. 1981 Sep;25(3):683–692. [PubMed]
  • Malissen M, Malissen B, Jordan BR. Exon/intron organization and complete nucleotide sequence of an HLA gene. Proc Natl Acad Sci U S A. 1982 Feb;79(3):893–897. [PMC free article] [PubMed]
  • Malissen M, Hunkapiller T, Hood L. Nucleotide sequence of a light chain gene of the mouse I-A subregion: A beta d. Science. 1983 Aug 19;221(4612):750–754. [PubMed]
  • Saito H, Maki RA, Clayton LK, Tonegawa S. Complete primary structures of the E beta chain and gene of the mouse major histocompatibility complex. Proc Natl Acad Sci U S A. 1983 Sep;80(18):5520–5524. [PMC free article] [PubMed]
  • Larhammar D, Hyldig-Nielsen JJ, Servenius B, Andersson G, Rask L, Peterson PA. Exon-intron organization and complete nucleotide sequence of a human major histocompatibility antigen DC beta gene. Proc Natl Acad Sci U S A. 1983 Dec;80(23):7313–7317. [PMC free article] [PubMed]
  • Benoist CO, Mathis DJ, Kanter MR, Williams VE, 2nd, McDevitt HO. Regions of allelic hypervariability in the murine A alpha immune response gene. Cell. 1983 Aug;34(1):169–177. [PubMed]
  • McNicholas J, Steinmetz M, Hunkapiller T, Jones P, Hood L. DNA sequence of the gene encoding the E alpha Ia polypeptide of the BALB/c mouse. Science. 1982 Dec 17;218(4578):1229–1232. [PubMed]
  • Vogeli G, Ohkubo H, Sobel ME, Yamada Y, Pastan I, de Crombrugghe B. Structure of the promoter for chicken alpha 2 type I collagen gene. Proc Natl Acad Sci U S A. 1981 Sep;78(9):5334–5338. [PMC free article] [PubMed]
  • Wozney J, Hanahan D, Tate V, Boedtker H, Doty P. Structure of the pro alpha 2 (I) collagen gene. Nature. 1981 Nov 12;294(5837):129–135. [PubMed]
  • Crouse GF, Simonsen CC, McEwan RN, Schimke RT. Structure of amplified normal and variant dihydrofolate reductase genes in mouse sarcoma S180 cells. J Biol Chem. 1982 Jul 10;257(13):7887–7897. [PubMed]
  • Nunberg JH, Kaufman RJ, Chang AC, Cohen SN, Schimke RT. Structure and genomic organization of the mouse dihydrofolate reductase gene. Cell. 1980 Feb;19(2):355–364. [PubMed]
  • Simonsen CC, Levinson AD. Isolation and expression of an altered mouse dihydrofolate reductase cDNA. Proc Natl Acad Sci U S A. 1983 May;80(9):2495–2499. [PMC free article] [PubMed]

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


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


  • Compound
    PubChem Compound links
  • PubMed
    PubMed citations for these articles
  • Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...