The INDIVIDUALIST

A Wiki about biochemical individuality

Difference (from prior minor revision)

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> * [http://nar.oxfordjournals.org/cgi/content/full/28/18/3594 Examination of the DNA substrate selectivity of DNA cytosine methyltransferases using mass tagging]


Biochemistry

See Also

Definition

Methylation is a biochemical reaction resulting in the addition of a methyl group (-CH3) to another molecule.

Discussion

DNA methylation in vertebrates typically occurs at CpG sites (that is, where a cytosine is directly followed by a guanine in the DNA sequence); this methylation results in the conversion of the cytosine to 5-methylcytosine. The formation of Me-CpG is catalyzed by the enzyme DNA methyltransferase. CpG sites are uncommon in vertebrate genomes but are often found at higher density near vertebrate gene promoters where they are collectively referred to as CpG islands. The methylation state of these CpG sites can have a major impact on gene activity/expression.

From 'Epigenetics: Genome, Meet Your Environment', by L.A. Pray, In The Scientist (18:14) 2004:

"Duke researchers showed that diet can dramatically alter heritable phenotypic change in agouti mice, not by changing DNA sequence but by changing the DNA methylation pattern of the mouse genome. (1) "This is going to be just massive," Jirtle says, "because this is where environment interfaces with genomics."

One of the prominent features of DNA methylation is the faithful propagation of its genomic pattern from one cellular or organismal generation to the next. When a methylated DNA sequence replicates, only one strand of the next-generation double helix has all its methyl markers intact; the other strand needs to be remethylated. According to Massachusetts Institute of Technology biologist Rudy Jaenisch, the field of epigenetics took its first major step forward more than two decades ago when, upon discovering DNA methyltransferases (DMTs, the enzymes that bind methyl groups to cytosine nucleotides), researchers finally had a genetic handle on how epigenetic information was passed along. Now, it is generally believed that DMTs bind methyl groups to the naked cytosines based on the methylation template provided by the other strand. This is known as the maintenance methylase theory." (2)

Epigenetics

Methylation contributing to epigenetic inheritance can occur either through DNA methylation or protein methylation.

DNA methylation in vertebrates typically occurs at CpG sites (that is, where a cytosine is directly followed by a guanine in the DNA sequence); this methylation results in the conversion of the cytosine to 5-methylcytosine. The formation of Me-CpG is catalyzed by the enzyme DNA methyltransferase. CpG sites are uncommon in vertebrate genomes but are often found at higher density near vertebrate gene promoters where they are collectively referred to as CpG islands. The methylation state of these CpG sites can have a major impact on gene activity/expression.

Protein methylation typically takes place on arginine or lysine amino acid residues in the protein sequence. Arginine can be methylated once (monomethylated arginine) or twice, with either both methyl groups on one terminal nitrogen (asymmetric dimethylated arginine) or one on both nitrogens (symmetric dimethylated arginine) by peptidylarginine methyltransferases (PRMTs). Lysine can be methylated once, twice or three times by lysine methyltransferases. Protein methylation has been most well studied in the histones. The transfer of methyl groups from S-adenosyl methionine to histones is catalyzed by enzymes known as histone methyltransferases. Histones which are methylated on certain residues can act epigenetically to repress or activate "gene" expression. Protein methylation is one type of post-translational modification.

Embryonic development

In early development (fertilisation to 8-cell stage), the eukaryotic genome is demethylated. From the 8-cell stage to the morula, de novo methylation of the genome occurs, modifying and adding epigenetic information to the genome. By blastula stage, the methylation is complete. This process is referred to as "epigenetic reprogramming". The importance of methylation was shown in knockout mutants without DNA methyltransferase. All the resulting embryos died at the morula stage.

Methylation in postnatal development

Increasing evidence is revealing a role of methylation in the interaction of environmental factors with genetic expression. Differences in maternal care during the first 6 days of life in the rat induce differential methylation patterns in some promoter regions and thus influencing gene expression (3). Furthermore, even more dynamic processes such as interleukin signaling have been shown to be regulated by methylation (4).

Cell and Molecular Biology of DNA Methylation

Although it is now recognized that aberrant DNA methylation is a contributing factor in a number of human diseases, and that hypermethylation of normally unmethylated CpG islands surrounding gene transcription start sites is associated with loss of gene expression, the specific effects of aberrant DNA methylation on the cell and molecular biology processes relevant to human diseases are just beginning to be explored.

Epigenetic changes, including those associated with DNA hypermethylation, may be viewed as abnormalities of chromatin patterns. Chromatin, a complex of nucleic acids and protein (primarily histone) dispersed in the nucleus that coils and folds to form chromosomes during cell division, is an important part of the cell machinery for gene control. It is now apparent that methylated DNA can serve as a point of origin for the formation of transcriptionally repressive chromatin. For example, in cancer cells, inappropriate targeting of covalent and structural modifications of chromatin to gene promoters that have hypermethylated DNA leads to the silencing of genes required for cell cycle control. Research shows that methylcytosine binding proteins, which have inherent transcriptional silencing activity, can target transcriptional corepressors, histone deacetylases (HDACs), and chromatin remodeling proteins to methylated DNA.

The loss of gene function associated with promoter hypermethylation of tumor suppressor genes -- for example, APC, BRCA1, MLH1, VHL, p19, E-cadherin, and p16Ink4a -- is functionally equivalent to the loss of gene function resulting from mutations. For hypermethylated genes in cancer cells, there appears to be a synergistic relationship between hypermethylation and HDAC activity with regard to gene silencing, with hypermethylation having the dominant role. In addition, the DNA methyltransferases (Dnmt1, Dnmt3a, Dnmt3b) can interact with HDACs and transcriptional corepressors to repress transcription. Studies indicate that Dnmt1 works at DNA replication foci to methylate DNA and possibly target newly assembled nucleosome histones for deacetylation. Dnmt3a and Dnmt3b may mediate transcriptional silencing in pericentromeric heterochromatin throughout the cell cycle which may be important in carcinogenesis. Interestingly, in a human colon cancer cell line targeting both DNMT1 alleles for deletion results in little change in either the overall pattern of methylation or the abnormal hypermethylation of multiple gene promoters. DNA hypermethylation in gene promoter regions--as measured by PCR techniques in DNA from biological samples such as serum, sputum, bronchial lavage, and urine--has great promise as a molecular marker for cancer detection.

Methylation and cancer

The pattern of methylation has recently become an important topic for research. Studies have found that in normal tissue, methylation of a gene is mainly localised to the coding region, which is CpG poor. In contrast, the promoter region of the gene is unmethylated, despite a high density of CpG islands in the region.

Neoplasia is characterized by "methylation imbalance" where genome-wide hypomethylation is accompanied by localized hypermethylation and an increase in expression of DNA methyltransferase. The overall methylation state in a cell might also be a precipitating factor in carcinogenesis as evidence suggests that genome-wide hypomethylation can lead to chromosome instability and increased mutation rates . The methylation state of some genes can be used as a biomarker for tumorigenesis. For instance, hypermethylation of the pi-class glutathone S-transferase gene (GSTP1) appears to be a promising diagnostic indicator of prostate cancer.

Methylation and bacterial host defense

Additionally, adenosine methylation is part of the restriction modification system of many bacteria. Bacterial DNAs are methylated periodically throughout the genome, and foreign DNAs (which are not methylated in this manner) that are introduced into the cell are degraded by restriction enzymes. Bacteria protect themselves from infection by bacteria viruses, called bacteriophage or phage, through this system.

Dietary effects on DNA methylation

Soy phytoestrogens

Maternal dietary genistein caused a single mouse gene called "agouti" to become methylated at six specific sites near its regulatory region, thereby reducing the gene's expression. The agouti methylation consistently occurred throughout several germ layers of embryonic tissue, indicating that genistein acted during early embryonic development. Moreover, the methylation changes persisted into adulthood, providing the first evidence that in utero dietary genistein alters epigenetic gene regulation, coat color, and susceptibility to adult obesity in animals. (5)

Green tea polyphenols

(-)-epigallocatechin-3-gallate (EGCG), the major polyphenol from green tea, can inhibit DNMT activity and reactivate methylation-silenced genes in cancer cells. (6)

Links

Attribution

References

	 

1. R.A. Waterland, R.A. Jirtle, "Transposable elements: targets for early nutritional effects on epigenetic gene regulation," Mol Cell Biol, 23:5293-300, 2003.

2. Pray LA. Epigenetics: Genome, Meet Your Environment. As the evidence accumulates for epigenetics, researchers reacquire a taste for Lamarckism. New Scientists. 18(13) Jul. 5, 2004

3. Weaver IC, et al. Epigenetic programming by maternal behavior. Nature Neuroscience 7(8): 791-92

4. Bird A. IL2 transcription unleashed by active DNA demethylation. Nature Immunology 4(3): 208-9

5. Dolinoy DC, Weidman JR, Waterland RA, Jirtle RL.Maternal genistein alters coat color and protects Avy mouse offspring from obesity by modifying the fetal epigenome. Environ Health Perspect. 2006 Apr;114(4):567-72.

6. Fang MZ, Wang Y, Ai N, Hou Z, Sun Y, Lu H, Welsh W, Yang CS.Tea polyphenol (-)-epigallocatechin-3-gallate inhibits DNA methyltransferase and reactivates methylation-silenced genes in cancer cell lines. Cancer Res. 2003 Nov 15;63(22):7563-70.

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