DNA Methylation

Epigenetic changes affect gene activity or expression without altering the DNA sequence in any way. Epigenetic modifications or marks occur on both histones and DNA via a network of proteins that 1) induce changes by adding epigenetic marks (writers), 2), alter the existing state by removing the epigenetic marks (erasers), or respond to specific epigenetic marks (readers). There are several broad groups of epigenetic modifications: acetylation, methylation, phosphorylation, and ubiquitination.

Methylation is the addition of a -CH3 group directly to DNA (primarily to a cytosine base), or to histone tails at arginine and lysine amino acid residues. Whereas methylation of DNA is generally associated with gene silencing, methyl marks on histones are associated with both gene activation and silencing,

Writers of DNA Methylation

Writers of DNA Methylation are known as DNA methyltransferases (DNMTs). DNMT1, a member of the DNA methyltransferase (DNMT) family of writers, is expressed in proliferating cells and is responsible for reproducing methylation patterns in newly made daughter DNA strands during DNA replication. While expression is reduced in adult somatic tissue, methylation is prominent during early embryonic development and is thought to be carried out by the writers DNMT3A and DNMT3B on nucleosome depleted regions of the genome. DNMT3L helps target and regulate DNMT3A/3B function and plays a role in de novo methylation. DNMT3L is a noncatalytic homolog of DNMT3A/B that aids in their binding to the target DNA. Additional proteins such as PCNA, UHRF1, DMAP1, DNMT3L, and histone deacetylases (HDACs) function to target the DNMT proteins to the appropriate regions of the genome, regulate their methyltransferase activity, and coordinate additional epigenetic marks with DNA methylation.

Typically, CpG islands (regions where cytosine-guanine nucleotides appear in tandem with a frequency >50%) in normal cells are hypomethylated compared to the rest of the genome. However, CpG islands in cancer cells within the promoter region of tumor suppressor genes are hypermethylated by DNMTs, which are typically overexpressed in cancer, thereby increasing tumorigenicity by decreasing tumor suppression. Hypermethylation of CpG islands can disrupt binding of the CTCF protein, leading to loss of key insulator regions and subsequent activation of oncogenes. DNMT1, DNMT3A and DNMT3B are over-expressed in many cancers, including acute and chronic myelogenous leukemias, and colon, breast and stomach carcinomas. Hypomethylation of gene bodies and intergenic regions of DNA also correlates with and may contribute to the onset of cancer.

Erasers of DNA Methylation

5-methylcytosine, a repressive mark written de novo by DNMT3A and DNTM3B and maintained by DNTM1, was originally thought to be passively depleted during DNA replication. However, subsequent studies have shown that the Ten-Eleven-Translocation (TET) family of erasers catalyze the oxidation of methylated cytosine. This occurs specifically through TET1, TET2, or TET3-mediated sequential oxidation of 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC). 5-fC and 5-caC are transient intermediates that are typically excised via a thymine DNA glycosylase (TDG)-dependent base excision repair (BER). In contrast, an increasing number of studies demonstrate that 5-hmC is a unique epigenetic mark that is enriched at promoter regions, able to interact with methyl-CpG-binding protein 2 (MeCP2), and exhibits increasing levels during brain development; while evidence that 5-hmC plays a part in gene activation is demonstrated by an inverse correlation between 5-hmC ad H3K9 and H3K27 trimethylation. Furthermore, demethylation of CpG islands positively regulates gene activation and CTCF insulator functions by allowing for binding of transcription factors and CTCF protein to DNA.

While low levels of 5-hmC are associated with cancers including myeloid leukemia and melanoma, TET2 is the most frequently mutated gene in myeloid dysplastic syndrome. Thus, DNA methylation marks are useful to diagnose and determine prognosis in certain cancers including prostate cancer, melanoma, and oral squamous cell carcinoma.

Readers of DNA Methylation

The de novo methylation pattern that occurs during development can be recognized and read by members of methyl-CpG-binding domain proteins (MBDs) family of readers. In particular, MeCP2, MBD1, and MBD2/4 readers establish and maintain regions of transcriptionally inactive chromatin by reading methylation marks and recruiting several corepressor proteins such as DNMT1 and histone deacetylases HDAC1 and HDAC2. The nucleosome remodeling and histone deacetylation) NURD co-repressor complex contains MBD2 and MBD3 as well as HDAC1 and HDAC2. De novo methylation is important in maintaining genomic imprinting and silencing certain transposable elements. Importantly, mutations in MeCP2, which is abundant in the brain, are associated with Rhett syndrome.

Selected Reviews:

• Jurkowska RZ, Jeltsch A. Enzymology of Mammalian DNA Methyltransferases. Adv Exp Med Biol. 2016;945:87-122.

• Wu X, Zhang Y. TET-mediated active DNA demethylation: mechanism, function and beyond. Nat Rev Genet. 2017;18(9):517-534.

• Ginder GD, Williams DC. Readers of DNA methylation, the MBD family as potential therapeutic targets. Pharmacol Ther. 2018;184:98-111.

• Bergman Y, Cedar H. DNA methylation dynamics in health and disease. Nat Struct Mol Biol. 2013;20(3):274-81.

• Shi DQ, Ali I, Tang J, Yang WC. New Insights into 5hmC DNA Modification: Generation, Distribution and Function. Front Genet. 2017;8:100.

• Clouaire T, Stancheva I. Methyl-CpG binding proteins: specialized transcriptional repressors or structural components of chromatin?. Cell Mol Life Sci. 2008;65(10):1509-22.

• Hendrich B, Bird A. Identification and characterization of a family of mammalian methyl-CpG binding proteins. Mol Cell Biol. 1998;18(11):6538-47.

We would like to thank Dr. Taiping Chen, Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, for reviewing this pathway.

created September 2018