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DNA hypermethylation

Tuesday 25 November 2003

Cancers often exhibit an aberrant methylation of gene promoter regions that is associated with loss of gene function.

This DNA change constitutes a heritable state, not mediated by altered nucleotide sequence, that appears to be tightly linked to the formation of transcriptionally repressive chromatin.

Mechanisms of DNA hypermethylation

The underlying mechanisms for the initiation and targeting of ectopic hypermethylation are not known, although it has been suggested that DNMTs may preferentially bind to damaged or mismatched DNA.

Studies of remethylation of the p16INK4A tumor-suppressor gene following genome-wide demethylation indicates a requirement for DNA replication prior to remethylation.

Several model systems has demonstrated that histone methylation imprint may direct DNA methylation. Transcriptional silencing of genes with tumor-suppressive function may also occur via spreading of heterochromatin out from nearby silenced loci of repetitive DNA, and the regulatory regions of many genes (including known tumor suppressors) contain islands of repetitive sequences, some of which have been shown to influence transcriptional regulation.

Spreading of heterochromatin-associated repression may be concurrent with the breakdown of higher-order chromatin structures such as boundary elements.

In normal cells, insulator proteins such as the transcription factor CTCF establish chromatin boundaries, and CTCF is involved in the regulation of imprinting, where it is required to protect against de novo methylation. Intriguingly, methylation of the CTCF recognition sequence abolishes CTCF binding, indicating that specific DNA methylations may have long-range consequences.

Loss of imprinting (LOI) of the IGF2 gene was recently suggested as a predictive marker for colorectal cancer.

DNA hypermethylation and tumorigenesis

DNA hypermethylation is an epigenetic process that acts as an alternative to mutations to disrupt tumor-suppressor gene function and can predispose to genetic alterations through inactivating DNA-repair genes. Oncogenesis can be promoted by local hypermethylation of tumor-suppressor genes.

All three methyltransferase enzymes (DNMT1, DNMT3A, DNMT3B) are overexpressed in human tumors, although to moderate levels only.

DNMT1 was shown to be necessary and sufficient for Fos-induced transformation of mouse fibroblast cells (Bakin and Curran 1999), and DNMT1 knockdown experiments in human cancer cell lines have demonstrated an essential role for DNMT1 in maintaining aberrant repression of tumor-suppressor loci (Robert et al. 2003).

Likewise, cell culture studies have demonstrated an important role for DNMT3A in cancer cell survival (Beaulieu et al. 2002). Germ-line mutations in DNMT3B underlies ICF syndrome, a rare disorder characterized by immunodeficiency, centromeric instability, and facial abnormalities.

Interestingly, mouse embryo fibroblasts deficient for Dnmt3b are resistant to transformation by SV40 largeT and activated Ras oncogenes (Soejima et al. 2003), demonstrating that epigenetic and genetic mechanisms likely act in concert during cellular transformation.

Ectopic cytosine hypermethylation is generally associated with transcriptional repression and, ultimately, tumor formation.

Collaboration between genetic and epigenetic cancer causes has been directly demonstrated by examples in which one tumor-suppressor allele is inactivated by mutations and the other allele is transcriptionally silenced because of hypermethylation (Myohanen et al. 1998; Grady et al. 2000).

Hypermethylation of tumor-suppressor genes may be an early event in cancer development (Waki et al. 2003; Lee et al. 2004; Suter et al. 2004), suggesting that epigenetic and mutational cancer causes may collaborate from an early time point in disease progression.

The list of tumor-suppressor genes found transcriptionally inactivated by hypermethylation in cancer is long and steadily growing, includes genes that are part of every cancer-related pathway, and contains prominent genes such as CDKN2A, pRB , APC , PTEN , BRCA1 , VHL , and CDH1.

By extension, epigenetic silencing may underlie genetic cancer causes. Epigenetic induction of a classical mutator phenotype via transcriptional inactivation of the DNA mismatch repair gene MLH1 has been proposed to account for microsatellite instability in colorectal cancers and silencing of the DNA repair gene coding for O6-methylguanine-DNA methyltransferase has been associated with specific mutations in KRAS and TP53.


- tumorigenesis and oncogenesis

See also

- promoter hypermethylation

  • Promoter hypermethylation is an important and potentially reversible mechanism of tumour suppressor gene silencing in cancer.


- Herman JG, Baylin SB. Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med. 2003 Nov 20;349(21):2042-54. PMID: 14627790

- Baylin SB, Herman JG. DNA hypermethylation in tumorigenesis: epigenetics joins genetics. Trends Genet. 2000 Apr;16(4):168-74. PMID: 10729832