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What is Methylation? 

In organic chemistry, methylation is the addition of a methyl group (CH3) to chemical compounds. Methylation reactions also involve the substitution of a functional group with a methyl group. It can be considered as a specific case of alkylation reaction as given in the following example we see that cytosine which is one of the four bases in DNA undergoes methylation by methyltransferase to yield methylated cytosine. These reactions and their enzymes operate at various phases such as embryonic development, aging, cancer, diseases such as atherosclerosis, B cell differentiation, and other events. Their most common case being DNA methylation and gene regulation.

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Electrophilic Methylation

Methylation can occur in a variety of ways. One of them is electrophilic methylation.

Electrophiles are species that accept electron pairs (or are generally electrons seeking species). Hence, in electrophilic methylation, the source of the methyl group is an electrophile.

Some of these agents are methyl triflate, diazomethane, methyl iodide; dimethyl carbonate.SN2 mechanism of the reaction is followed in these processes.

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Nucleophilic Methylation

Similarly, in Nucleophilic methylation, the source of a methyl group or methylating agent is a nucleophile such as methyl lithium or Grignard reagent of the form R-Mg-X where R is an alkyl group and X denotes a halogen. In the below figure we can see that the Nucleophilic methylating agent methyl lithium adds a  CH3 group to the carbonyl atom of ketones and aldehydes.

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The Eschweiler-Clarke Reaction

It is also popularly known as Eschweiler-Clarke methylation in which the chemical reaction involves the methylation of a primary or secondary amine after treatment with excessive formaldehyde and formic acid. In the following example, a primary amine undergoes double methylation after treatment with CH2O.

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DNA Methylation and its Significance in Gene Regulation

DNA methylation is an inherent mechanism of gene suppression in many biological entities.DNA is a sequence of base pairs that undergo transcription and then the translation to express them into proteins. However, there are some cases where a gene shouldn’t be transcribed to mRNA as the gene products will most likely harm other biological processes. Hence, with the action of methyltransferase, a methyl group is added to one of the bases present in the gene and that gene can no longer take part in transcription and hence cannot be expressed.

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This is called gene repression. Related to the earlier example, in this picture, the white substances represent the newly added methyl groups attached to cytosine bases thus rendering the whole gene repressed.


Also called Biomethanation, it is the production of methane gas by microbial producers called methanogens. Methane production is a critical element of microbial metabolism in anaerobic digesters. It is the final step in biomass degradation.

Methanogenesis can be used to treat organic waste & produce methane that can be collected and used as biogas.

It can be used side by side with landfills.

Methanogenesis is the last stage of anaerobic digestion following the process of Hydrolysis, Acidogenesis, and Acetogenesis.

Methanogens utilize the products of the past stages and form methane, carbon dioxide, and water. These components comprise a huge portion of biogas emitted from the system

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What is Methyltransferase? 

Methyltransferases are a family of enzymes that all catalyze the addition of methyl groups to a substrate. In the biological system, these enzymes play a huge role in methylating bio substrates and regulate various biological processes. The enzymes can be categorized into:

  • Histone methyltransferases which are important for genetic regulation

  • N-terminal methyltransferases methylate protein targets

  • DNA/RNA methyltransferases: gene regulation

  • Natural product methyltransferases

  • Radical methyltransferases 

  • Non-SAM dependent methyltransferases

What Are Methanogens?

These are prokaryotic, Archaea microorganisms that produce methane in hypoxic conditions. They are common in wetlands and in the digestive tracts of ruminants where they are responsible for the production of methane

Did You Know 

In some bacteria, the body fights against viral invasions through endonucleases (enzymes that cut up DNA making viral DNA harmless). However, to protect its own host DNA from being cut too, bacteria employed the method of methylation. By methylating their DNA at certain sites the enzyme could no longer cut host DNA and since the viral DNA doesn’t have the same addition it is susceptible to enzymatic action and is destroyed

Methylation serves as an excellent example of the change in gene activity of an organism without actually changing the gene itself. Suppression of genes is the basis of epigenetics and it describes how phenotypes are expressed.

FAQ (Frequently Asked Questions)

Q1. What Does Methylation Do to DNA?

Generally, DNA that has been modified by the addition of a methyl group at one of the bases is unable to be acted upon by enzymes such as enzymes involved in transcription and endonuclease. In the first case, the gene that is harmful to the body is repressed by adding a methyl group to it so it can no longer express itself. 

These are some of the most prominent methods of gene regulation & phenotype expression in epigenesis.  In the second case, a bacteria “marks” its DNA by methylating it, and therefore the exposed viral invasive DNA is vulnerable to enzymatic action of the endonucleases and is cut into smaller pieces rendering them inactive.

Q2. What are the Applications of Methylation?

DNA methylation is arising as a biomarker that can be used for diagnosis of diseases, prognosis, and even treatment for many diseases, most prominent being cancer. DNA methylation is now considered to be an important molecular mechanism in biological processes that include genomic imprinting, X-inactivation, tissue-specific gene expression. Assays have been developed where radiolabelled methyl groups can be enzymatically attached to CpG sites of DNA and can later be used to localize these sites using an autoradiograph. 

Methylated cytosine can be immune precipitated using specific antibodies that have been prepared for array hybridization. Bacteria can be made viral attack resistant by recombining the DNA responsible for DNA methylation into the viral susceptible bacterial genome.