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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review

CpG Islands

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Disease relevance of CpG Islands


High impact information on CpG Islands

  • Moreover, it has been suggested that Sp1 is linked to the maintenance of methylation-free CpG islands, the cell cycle, and the formation of active chromatin structures [6].
  • As CpG islands overlap with approximately 60% of human genes, the resulting CpG island library can be used to isolate full-length cDNAs and to place genes on genomic maps [7].
  • CpG islands are short stretches of DNA containing a high density of non-methylated CpG dinucleotides, predominantly associated with coding regions [7].
  • We report here that the CpG clusters of the active hprt and g6pd genes are not only undermethylated, but also hypersensitive to MspI, DNase I and S1 nuclease, further supporting the suggestion that they are involved in the control of expression of these genes [8].
  • In an attempt to find the mechanism by which CpG islands remain free of methylation we have undertaken a detailed examination of the mouse adenine phosphoribosyltransferase (aprt) gene [9].

Chemical compound and disease context of CpG Islands


Biological context of CpG Islands


Anatomical context of CpG Islands

  • Studies of DNA, digested with Hpa II and probed with cloned genomic G6PD sequences, indicate that expression of the locus in chorionic villi is associated with hypomethylation of 3' CpG clusters [19].
  • It is more likely that there could be a strong selection process favouring those cells with a reverted full mutation which produced a small and unmethylated FMR-1 CpG island allowing for re-expression of the FMR-1 gene, especially in male germ cells [20].
  • Soggy (Sgy) and Tead2, two closely linked genes with CpG islands, were coordinately expressed in mouse preimplantation embryos and embryonic stem (ES) cells but were differentially expressed in differentiated cells [21].
  • Distinct patterns of E-cadherin CpG island methylation in papillary, follicular, Hurthle's cell, and poorly differentiated human thyroid carcinoma [22].
  • GSTP1 CpG island hypermethylation was not detected in normal epithelium (0 of 48) or in hyperplastic epithelium (0 of 22), but was found in 4 of 64 (6.3%) PIA lesions [11].

Associations of CpG Islands with chemical compounds


Gene context of CpG Islands

  • The tight clustering and juxtaposition of at least five of the surfeit genes (Surf-1-Surf-5) and their associated CpG-rich islands have been found to be conserved over the 600 million years of divergent evolution that separates birds and mammals [28].
  • The BCL3 gene contains 2 cytosine-guanine dinucleotide (CpG) islands, and the intragenic 3' CpG was entirely demethylated in SU-DHL-1 and DEL [29].
  • The Surf-4 gene has heterogeneous transcriptional start sites, and its 5' end lies in a CpG-rich island [30].
  • In contrast, MCF-7/ADR cells contained only unmethylated GSTP1 CpG island alleles and exhibited abundant GSTP1 expression [31].
  • These data suggest that overexpression of DNMT1 and DNMT3a, DNA hypermethylation on CpG islands, and DNA hypomethylation on pericentromeric satellite regions are early events during hepatocarcinogenesis, and that reduced expression of MBD4 may play a role in malignant progression of HCC [32].

Analytical, diagnostic and therapeutic context of CpG Islands


  1. Fragile-X syndrome and myotonic dystrophy: parallels and paradoxes. Tapscott, S.J., Klesert, T.R., Widrow, R.J., Stöger, R., Laird, C.D. Curr. Opin. Genet. Dev. (1998) [Pubmed]
  2. DAP-kinase CpG island methylation in acute myeloid leukemia: methodology versus biology? Aggerholm, A., Hokland, P. Blood (2000) [Pubmed]
  3. Identification of a gene from Xp21 with similarity to the tctex-1 gene of the murine t complex. Roux, A.F., Rommens, J., McDowell, C., Anson-Cartwright, L., Bell, S., Schappert, K., Fishman, G.A., Musarella, M. Hum. Mol. Genet. (1994) [Pubmed]
  4. Demethylation of somatic and testis-specific histone H2A and H2B genes in F9 embryonal carcinoma cells. Choi, Y.C., Chae, C.B. Mol. Cell. Biol. (1993) [Pubmed]
  5. Differential distribution of DNA methylation within the RASSF1A CpG island in breast cancer. Yan, P.S., Shi, H., Rahmatpanah, F., Hsiau, T.H., Hsiau, A.H., Leu, Y.W., Liu, J.C., Huang, T.H. Cancer Res. (2003) [Pubmed]
  6. Transcription factor Sp1 is essential for early embryonic development but dispensable for cell growth and differentiation. Marin, M., Karis, A., Visser, P., Grosveld, F., Philipsen, S. Cell (1997) [Pubmed]
  7. Purification of CpG islands using a methylated DNA binding column. Cross, S.H., Charlton, J.A., Nan, X., Bird, A.P. Nat. Genet. (1994) [Pubmed]
  8. Clusters of CpG dinucleotides implicated by nuclease hypersensitivity as control elements of housekeeping genes. Wolf, S.F., Migeon, B.R. Nature (1985) [Pubmed]
  9. Sp1 sites in the mouse aprt gene promoter are required to prevent methylation of the CpG island. Macleod, D., Charlton, J., Mullins, J., Bird, A.P. Genes Dev. (1994) [Pubmed]
  10. Elevation of breast carcinoma Nm23-H1 metastasis suppressor gene expression and reduced motility by DNA methylation inhibition. Hartsough, M.T., Clare, S.E., Mair, M., Elkahloun, A.G., Sgroi, D., Osborne, C.K., Clark, G., Steeg, P.S. Cancer Res. (2001) [Pubmed]
  11. Hypermethylation of the human glutathione S-transferase-pi gene (GSTP1) CpG island is present in a subset of proliferative inflammatory atrophy lesions but not in normal or hyperplastic epithelium of the prostate: a detailed study using laser-capture microdissection. Nakayama, M., Bennett, C.J., Hicks, J.L., Epstein, J.I., Platz, E.A., Nelson, W.G., De Marzo, A.M. Am. J. Pathol. (2003) [Pubmed]
  12. DNA methylation in ovarian cancer. II. Expression of DNA methyltransferases in ovarian cancer cell lines and normal ovarian epithelial cells. Ahluwalia, A., Hurteau, J.A., Bigsby, R.M., Nephew, K.P. Gynecol. Oncol. (2001) [Pubmed]
  13. Antimitogenic and chemosensitizing effects of the methylation inhibitor zebularine in ovarian cancer. Balch, C., Yan, P., Craft, T., Young, S., Skalnik, D.G., Huang, T.H., Nephew, K.P. Mol. Cancer Ther. (2005) [Pubmed]
  14. Human muscle carbonic anhydrase: gene structure and DNA methylation patterns in fetal and adult tissues. Lloyd, J., Brownson, C., Tweedie, S., Charlton, J., Edwards, Y.H. Genes Dev. (1987) [Pubmed]
  15. Comparison of factor IX methylation on human active and inactive X chromosomes: implications for X inactivation and transcription of tissue-specific genes. Cullen, C.R., Hubberman, P., Kaslow, D.C., Migeon, B.R. EMBO J. (1986) [Pubmed]
  16. Parent-of-origin specific histone acetylation and reactivation of a key imprinted gene locus in Prader-Willi syndrome. Saitoh, S., Wada, T. Am. J. Hum. Genet. (2000) [Pubmed]
  17. Isolation and characterization of the human homologue of rig and its pseudogenes: the functional gene has features characteristic of housekeeping genes. Shiga, K., Yamamoto, H., Okamoto, H. Proc. Natl. Acad. Sci. U.S.A. (1990) [Pubmed]
  18. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Saxonov, S., Berg, P., Brutlag, D.L. Proc. Natl. Acad. Sci. U.S.A. (2006) [Pubmed]
  19. Incomplete X chromosome dosage compensation in chorionic villi of human placenta. Migeon, B.R., Wolf, S.F., Axelman, J., Kaslow, D.C., Schmidt, M. Proc. Natl. Acad. Sci. U.S.A. (1985) [Pubmed]
  20. No mental retardation in a man with 40% abnormal methylation at the FMR-1 locus and transmission of sperm cell mutations as premutations. Rousseau, F., Robb, L.J., Rouillard, P., Der Kaloustian, V.M. Hum. Mol. Genet. (1994) [Pubmed]
  21. DNA methylation may restrict but does not determine differential gene expression at the Sgy/Tead2 locus during mouse development. Kaneko, K.J., Rein, T., Guo, Z.S., Latham, K., DePamphilis, M.L. Mol. Cell. Biol. (2004) [Pubmed]
  22. Distinct patterns of E-cadherin CpG island methylation in papillary, follicular, Hurthle's cell, and poorly differentiated human thyroid carcinoma. Graff, J.R., Greenberg, V.E., Herman, J.G., Westra, W.H., Boghaert, E.R., Ain, K.B., Saji, M., Zeiger, M.A., Zimmer, S.G., Baylin, S.B. Cancer Res. (1998) [Pubmed]
  23. Association of CBP/p300 acetylase and thymine DNA glycosylase links DNA repair and transcription. Tini, M., Benecke, A., Um, S.J., Torchia, J., Evans, R.M., Chambon, P. Mol. Cell (2002) [Pubmed]
  24. Roles of cell division and gene transcription in the methylation of CpG islands. Bender, C.M., Gonzalgo, M.L., Gonzales, F.A., Nguyen, C.T., Robertson, K.D., Jones, P.A. Mol. Cell. Biol. (1999) [Pubmed]
  25. High-resolution methylation analysis of the human hypoxanthine phosphoribosyltransferase gene 5' region on the active and inactive X chromosomes: correlation with binding sites for transcription factors. Hornstra, I.K., Yang, T.P. Mol. Cell. Biol. (1994) [Pubmed]
  26. Chromatin loop structure of the human X chromosome: relevance to X inactivation and CpG clusters. Beggs, A.H., Migeon, B.R. Mol. Cell. Biol. (1989) [Pubmed]
  27. Isolation of estrogen-responsive genes with a CpG island library. Watanabe, T., Inoue, S., Hiroi, H., Orimo, A., Kawashima, H., Muramatsu, M. Mol. Cell. Biol. (1998) [Pubmed]
  28. Conservation of the organization of five tightly clustered genes over 600 million years of divergent evolution. Colombo, P., Yon, J., Garson, K., Fried, M. Proc. Natl. Acad. Sci. U.S.A. (1992) [Pubmed]
  29. High-level expression of BCL3 differentiates t(2;5)(p23;q35)-positive anaplastic large cell lymphoma from Hodgkin disease. Nishikori, M., Maesako, Y., Ueda, C., Kurata, M., Uchiyama, T., Ohno, H. Blood (2003) [Pubmed]
  30. The mouse surfeit locus contains a cluster of six genes associated with four CpG-rich islands in 32 kilobases of genomic DNA. Huxley, C., Fried, M. Mol. Cell. Biol. (1990) [Pubmed]
  31. Methyl-CpG-binding domain protein-2 mediates transcriptional repression associated with hypermethylated GSTP1 CpG islands in MCF-7 breast cancer cells. Lin, X., Nelson, W.G. Cancer Res. (2003) [Pubmed]
  32. Expression of mRNA for DNA methyltransferases and methyl-CpG-binding proteins and DNA methylation status on CpG islands and pericentromeric satellite regions during human hepatocarcinogenesis. Saito, Y., Kanai, Y., Sakamoto, M., Saito, H., Ishii, H., Hirohashi, S. Hepatology (2001) [Pubmed]
  33. Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis. Gitan, R.S., Shi, H., Chen, C.M., Yan, P.S., Huang, T.H. Genome Res. (2002) [Pubmed]
  34. Regional methylation of the 5' end CpG island of BRCA1 is associated with reduced gene expression in human somatic cells. Magdinier, F., Billard, L.M., Wittmann, G., Frappart, L., Benchaïb, M., Lenoir, G.M., Guérin, J.F., Dante, R. FASEB J. (2000) [Pubmed]
  35. Reversal of GSTP1 CpG island hypermethylation and reactivation of pi-class glutathione S-transferase (GSTP1) expression in human prostate cancer cells by treatment with procainamide. Lin, X., Asgari, K., Putzi, M.J., Gage, W.R., Yu, X., Cornblatt, B.S., Kumar, A., Piantadosi, S., DeWeese, T.L., De Marzo, A.M., Nelson, W.G. Cancer Res. (2001) [Pubmed]
  36. The left end of rat L1 (L1Rn, long interspersed repeated) DNA which is a CpG island can function as a promoter. Nur, I., Pascale, E., Furano, A.V. Nucleic Acids Res. (1988) [Pubmed]
  37. Tandem repeats 3' of the IGHA genes in the human immunoglobulin heavy chain gene cluster. Kang, H.K., Cox, D.W. Genomics (1996) [Pubmed]
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