In the chemical sciences, methylation denotes the addition of a methyl group to a substrate
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