or the substitution of an atom or group by a methyl group. Methylation is a form of alkylation

with a methyl group, rather than a larger carbon chain, replacing a hydrogen atom. These

terms are commonly used in chemistry, biochemistry, soil science, and the biological sciences.

In biological systems, methylation is catalyzed by enzymes; such methylation can be involved

in modification of heavy metals, regulation of gene expression, regulation of protein

function, and RNA processing. Methylation of heavy metals can also occur outside of

biological systems. Chemical methylation of tissue samples is also one method for reducing

certain histological staining artifacts.

In biology Epigenetics

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

protein methylation. DNA methylation in vertebrates typically occurs

at CpG sites. This methylation results in the conversion of the cytosine to 5-methylcytosine.

The formation of Me-CpG is catalyzed by the enzyme DNA methyltransferase. Human DNA has

about 80–90% of CpG sites methylated, but there are certain areas, known as CpG islands,

that are GC-rich, wherein none is methylated. These are associated with the promoters of

56% of mammalian genes, including all ubiquitously expressed genes. One to two percent of the

human genome are CpG clusters, and there is an inverse relationship between CpG methylation

and transcriptional activity. Protein methylation typically takes place

on arginine or lysine amino acid residues in the protein sequence. Arginine can be methylated

once or twice, with either both methyl groups on one terminal nitrogen or one on both nitrogens

by peptidylarginine methyltransferases. Lysine can be methylated once, twice or three times

by lysine methyltransferases. Protein methylation has been most studied in the histones. The

transfer of methyl groups from S-adenosyl methionine to histones is catalyzed by enzymes

known as histone methyltransferases. Histones that 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

While chromosomes in the somatic cells retain the parental methylation patterns, during

the development of germ cells their genomes are demethylated. After that, a De novo methylation

of the germ cells occurs, modifying and adding epigenetic information to the genome based

on the sex of the individual. After fertilization of an oocyte and formations

of a zygote, its combined genome is demethylated and remethylated again. By blastula stage,

the methylation of the embryonic cells is complete.

The process of demethylation/remethylation is referred to as "reprogramming". The importance

of methylation was shown in knockout mutants without DNA methyltransferase, which all died

at the morula stage. 5-methylcytosine conversion to 5-hydroxymethylcytosine

is sometimes associated with labile, unstable nucleosomes which are frequently repositioned

during stem cell differentiation. 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, thus influencing

gene expression. Furthermore, processes that are even more dynamic, such as interleukin

signaling, have been shown to be regulated by methylation.

Research in humans has shown that repeated high level activation of the body's stress

system, especially in early childhood, can alter methylation processes and lead to changes

in the chemistry of the individual's DNA. The chemical changes can disable genes and

prevent the brain from properly regulating its response to stress. Researchers and clinicians

have drawn a link between this neurochemical dysregulation and the development of chronic

health problems such as depression, obesity, diabetes, hypertension, and coronary artery

disease. 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 localized 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. Typically, there is hypermethylation of tumor

suppressor genes and hypomethylation of oncogenes. 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

glutathione S-transferase gene appears to be a promising diagnostic indicator of prostate

cancer. In cancer, the dynamics of genetic and epigenetic

gene silencing are very different. Somatic genetic mutation leads to a block in the production

of functional protein from the mutant allele. If a selective advantage is conferred to the

cell, the cells expand clonally to give rise to a tumor in which all cells lack the capacity

to produce protein. In contrast, epigenetically mediated gene silencing occurs gradually.

It begins with a subtle decrease in transcription, fostering a decrease in protection of the

CpG island from the spread of flanking heterochromatin and methylation into the island. This loss

results in gradual increases of individual CpG sites, which vary between copies of the

same gene in different cells. Bacterial host defense

In addition, adenosine or cytosine methylation is part of the restriction modification system

of many bacteria. Bacterial DNAs are methylated periodically throughout the genome. A methylase

is the enzyme that recognizes a specific sequence and methylates one of the bases in or near

that sequence. Foreign DNAs that are introduced into the cell are degraded by sequence-specific

restriction enzymes. Bacterial genomic DNA is not recognized by these restriction enzymes.

The methylation of native DNA acts as a sort of primitive immune system, allowing the bacteria

to protect themselves from infection by bacteriophage. These restriction enzymes are the basis of

restriction fragment length polymorphism testing, used to detect DNA polymorphisms.

Application in Prenatal Diagnosis Recent prenatal diagnostic techniques analyse

cell-free fetal DNA found in maternal blood; however, ffDNA is found in very small amounts

and is difficult to distinguish from a majority of maternal cell-free DNA. Specific regions

of the genome have been found that are differentially methylated when comparing fetal DNA with maternal

DNA. For example, the AIRE gene promoter has been found to be highly methylated in fetal

DNA but under-methylated in maternal DNA. Methylated DNA immunoprecipitation has been

utilized to purify ffDNA from maternal serum for the purpose of pre-natal diagnosis of

Down syndrome. In chemistry

The term methylation in organic chemistry refers to the alkylation process used to describe

the delivery of a CH3 group. This is commonly performed using electrophilic methyl sources

– iodomethane, dimethyl sulfate, dimethyl carbonate, or less commonly with the more

powerful methylating reagents of methyl triflate, diazomethane or methyl fluorosulfonate, which

all react via SN2 nucleophilic substitution. For example a carboxylate may be methylated

on oxygen to give a methyl ester, an alkoxide salt RO− may be likewise methylated to give

an ether, ROCH3, or a ketone enolate may be methylated on carbon to produce a new ketone.

On the other hand, the methylation may involve use of nucleophilic methyl compounds such

as methyllithium or Grignard reagents. For example, CH3Li will methylate acetone, adding

across the carbonyl to give the lithium alkoxide of tert-butanol:

Purdie methylation Purdie methylation is a specific method for

the methylation at oxygen of carbohydrates using iodomethane and silver oxide.

5-O-Methylations 5-O-Methylgenistein

5-O-Methylmyricetin 5-O-Methylquercetin, also known as azaleatin

See also alkylation

Bisulfite sequencing – the biochemical method used to determine the presence or absence

of methyl groups on a DNA sequence MethDB DNA Methylation Database

Microscale thermophoresis – a biophysical method to determine the methylisation state

of DNA References

External links deltaMasses Detection of Methylations after

Mass Spectrometry