CpG islands frequently contain gene promoters or exons1 and are usually unmethylated in normal cells1,2,3. Methylation of CpG islands is associated with delayed replication, condensed chromatin and inhibition of transcription initiation4,5,6,7. The investigation of aberrant CpG-island methylation in human cancer has primarily taken a candidate gene approach, and has focused on less than 15 of the estimated 45,000 CpG islands8 in the genome. Here we report a global analysis of the methylation status of 1,184 unselected CpG islands in each of 98 primary human tumours using restriction landmark genomic scanning9 (RLGS). We estimate that an average of 600 CpG islands (range of 0 to 4,500) of the 45,000 in the genome were aberrantly methylated in the tumours, including early stage tumours. We identified patterns of CpG-island methylation that were shared within each tumour type, together with patterns and targets that displayed distinct tumour-type specificity. The expression of many of these genes was reactivated by experimental demethylation in cultured tumour cells. Thus, the methylation of particular subsets of CpG islands may have consequences for specific tumour types.
Subscribe to Journal
Get full journal access for 1 year
only $18.75 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Cross, S.H. & Bird, A.P. CpG islands and genes. Curr. Opin. Genet. Dev. 5, 309–314 (1995).
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 40, 91–99 (1985).
De Smet, C., Lurquin, C., Lethe, B., Martelange, B. & Boon, T. DNA methylation is the primary silencing mechanism for a set of germ line- and tumor-specific genes with a CpG-rich promoter. Mol. Cell. Biol. 19, 7327–7335 (1999).
Baylin, S.B., Herman, J.G., Graff, J.R., Vertino, P.M. & Issa, J.P. Alterations in DNA methylation: a fundamental aspect of neoplasia. Adv. Cancer Res. 72 , 141–196 (1998).
Jones, P.A. & Laird, P.W. Cancer epigenetics comes of age. Nature Genet. 21, 163– 167 (1999).
Antequera, F., Boyes, J. & Bird, A. High levels of de novo methylation and altered chromatin structure at CpG islands in cell lines. Cell 62, 503– 514 (1990).
Delgado, S., Gómez, M., Bird, A. & Antequera, F. Initiation of DNA replication at CpG islands in mammalian chromosomes. EMBO J. 17, 2426–2435 ( 1998).
Antequera, F. & Bird, A. Number of CpG islands and genes in human and mouse. Proc. Natl Acad. Sci. USA 90, 11995–11999 (1993).
Hatada, I., Hayashizaki, Y., Hirotsune, S., Komatsubara, H. & Mukai, T. A genomic scanning method for higher organisms using restriction sites as landmarks. Proc. Natl Acad. Sci. USA 88, 9523–9527 ( 1991).
Hayashizaki, Y. et al. Identification of an imprinted U2af binding protein related sequence on mouse chromosome 11 using the RLGS method. Nature Genet. 6, 33–40 (1994 ).
Akama, T.O. et al. Restriction landmark genomic scanning (RLGS-M)-based genome-wide scanning of mouse liver tumors for alterations in DNA methylation status. Cancer Res. 57, 3294–3299 (1997).
Costello, J.F. et al. Cyclin-dependent kinase 6 (CDK6) amplification in human gliomas identified using two-dimensional separation of genomic DNA. Cancer Res. 57, 1250–1254 ( 1997).
Yoshikawa, H. et al. Chromosomal assignment of human genomic NotI restriction fragments in a two-dimensional electrophoresis profile. Genomics 31, 28–35 (1996).
Plass, C. et al. An arrayed human not I-EcoRV boundary library as a tool for RLGS spot analysis. DNA Res. 4, 253– 255 (1997).
Smiraglia, D.J. et al. A new tool for the rapid cloning of amplified and hypermethylated human DNA sequences from restriction landmark genomic scanning gels. Genomics 58, 254–262 ( 1999).
Plass, C. et al. Restriction landmark genome scanning for aberrant methylation in primary refractory and relapsed acute myeloid leukemia; involvement of the WIT-1 gene. Oncogene 18, 3159– 3165 (1999).
Lehman, E. Nonparametrics (Holden-Day, San Francisco, 1975).
Barbour, A.D., Holst, L. & Janson, S. Poisson Approximation (Oxford University Press, Oxford, 1992).
Freund, R.J. & Wilson, W.J. Statistical Methods (Academic Press, San Diego, 1997).
Ryan, A.K. & Rosenfeld, M.G. POU domain family values: flexibility, partnerships, and developmental codes. Genes Dev. 11 , 1207–1225 (1997).
Nambu, J.R., Franks, R.G., Hu, S. & Crews, S.T. The single-minded gene of Drosophila is required for the expression of genes important for the development of CNS midline cells. Cell 63, 63–75 (1990).
Stirzaker, C. et al. Extensive DNA methylation spanning the Rb promoter in retinoblastoma tumors. Cancer Res. 57, 2229– 2237 (1997).
Bachman, K.E. et al. Methylation-associated silencing of the tissue inhibitor of metalloproteinase-3 gene suggest a suppressor role in kidney, brain, and other human cancers. Cancer Res. 59, 798– 802 (1999).
Graff, J.R., Herman, J.G., Myöhänen, S., Baylin, S.B. & Vertino, P.M. Mapping patterns of CpG island methylation in normal and neoplastic cells implicates both upstream and downstream regions in de novo methylation. J. Biol. Chem. 272, 22322–22329 (1997).
Gardiner-Garden, M. & Frommer, M. CpG islands in vertebrate genomes. J. Mol. Biol. 196, 261 –282 (1987).
We thank M.S. Berger, A. Asai, A. Tamura and N. Shitara for glioma samples; S. Edge and E. Repasky for help in obtaining primary breast tumour tissue; R. Lothe for testicular tumours, T. Weber and M.A. Rodriguez-Bigas for colon tumour samples; B. Chadwick and J. Weger for nucleotide sequencing; B. Yuan for the automated sequence analysis; J. Eisel, A. Morrow, J. Popovich and Y.-Z. Wu for technical assistance; C. DeSmet for helpful discussions; and Y. Hayashizaki and the late V. Chapman for advice and encouragement. We thank the Cooperative Human Tissue Network (CHTN) Midwestern Division and the CALGB Leukemia Tissue Bank for providing tissue samples. This work was supported in part by the National Cancer Institute grant P30 CA16058 and CA80912 (to C.P.), the Coleman Leukemia Research Foundation grant 3U10CA31946-17S3, the Children's Hospital Research Foundation grant 216398, the Ladies Auxiliary of the Veterans of Foreign Wars grant 216498 and the Roswell Park Alliance Foundation. D.J.S. was supported by the Corixa Corporation and the T32 CA09338-20 Oncology Training Grant from the National Cancer Institute. M.C.F. was supported by a fellowship of the Dr. Mildred Scheel Stiftung für Krebsforschung/Deutsche Krebshilfe. J.F.C. was supported sequentially by the Basic Science Fellowship from the American Association for Cancer Research and by the Frances Goodrich and Albert Hackett Postdoctoral Fellowship from the American Brain Tumor Association.
About this article
Cite this article
Costello, J., Frühwald, M., Smiraglia, D. et al. Aberrant CpG-island methylation has non-random and tumour-type–specific patterns. Nat Genet 24, 132–138 (2000) doi:10.1038/72785
piR-31470 epigenetically suppresses the expression of glutathione S-transferase pi 1 in prostate cancer via DNA methylation
Cellular Signalling (2020)
Frontiers in Oncology (2019)
Stella protein facilitates DNA demethylation by disrupting the chromatin association of the RING finger–type E3 ubiquitin ligase UHRF1
Journal of Biological Chemistry (2019)
Absence of mitochondrial DNA methylation in mouse oocyte maturation, aging and early embryo development
Biochemical and Biophysical Research Communications (2019)
Genome-wide promoter DNA methylation profiling of hepatocellular carcinomas arising either spontaneously or due to chronic exposure to Ginkgo biloba extract (GBE) in B6C3F1/N mice
Archives of Toxicology (2019)