What Is DNA Methyltransferase?

a crane lifting a cargo ship container, representing DNA

Methyltransferase Definition

Methyltransferases are a group of enzymes that add a methyl group to their substrates. Over 95% of this group of enzymes use S-adenosylmethionine (SAM) as their methyl donor.

The basic catalytic activity of these enzymes involves the attack of a nucleophile (such as carbon, nitrogen, oxygen, and sulfur) on a methyl group. It leads to the formation of the methylated derivatives of nucleic acids, lipids, proteins, polysaccharides, and other small molecules with SAM converted to S-Adenosyl homocysteine (SAH).

Methylation is an important epigenetic modification in organisms, having roles in gene expression (at transcriptional and post-transcriptional stages), parental imprinting, and the stability of genes

Epigenetic modification has also been implicated in many cancer types, metabolic diseases, and several genetic diseases.

Any abnormalities in the methyltransferase gene lead to critical conditions, such as embryonic lethality, acute monocytic leukemia, and immunodeficiency syndromes. 

For example, aberrant hypermethylation at promoter regions of DNA repair genes has been implicated in several tumors, including breast cancer, lung cancer, colorectal, and glioma.

Methyltransferase Classification

Based on structure

On the basis of structure, methyltransferase is sub-categorized into three classes:

  • Class I methyltransferase: Includes a Rossmann fold, which binds with SAM.
  • Class II methyltransferase: Contains a SET domain, which distinguishes it from other classes of methyltransferase.
  • Class III methyltransferase: Associated with the membrane. 

Based on the substrate utilized

On the basis of the substrate utilized by the methyltransferase, it’s categorized into six groups:

  • DNA/RNA methyltransferases: Causes adenine and cytosine methylation, forming 5’methylcytosine and N6-methyladenine.
  • Histone methyltransferases: Modifies the amino acids (mainly lysine and arginine residues) on the histone tail.
  • N-terminal methyltransferases: Transfers the methyl group to the N-terminal nitrogen of some proteins.
  • Natural product methyltransferases: Modifies naturally produced small molecules at carbon, nitrogen, oxygen, or sulfur atoms.

In this article, we will review what DNA methyltransferases are, what function they perform in organisms, how their functions are inhibited by certain molecules, and provide citations on where you might read more should you so choose.

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Methyltransferase Functions

Methylation plays a critical role in maintaining life. For example, methylation of DNA is crucial for gene expression, mutation repair, and altering the function of expressed proteins.

Here’re some essential roles performed by methyltransferase in organisms:

  • The methylation of chromatin modifies its structure which affects gene transcription.
  • Methylation causes activation or inactivation/silencing of genes without mutation in the nucleotide sequence of the genes. For example, methylation at the CpG island of promoters leads to the inactivation of the expression of genes.
  • The addition of methyl groups to proteins regulates protein activation, protein-protein interaction, and protein-DNA interaction. For example, methylation of RCC1 (a mitotic protein) promotes its binding to the chromosome.
  • Natural product methyltransferases provide insights into the availability of signaling molecules, cofactors, and metabolites and regulate various cellular pathways.
  • Hypermethylation and hypomethylation have been linked to many critical diseases, such as cancer.
  • In mammalian cells, methyltransferase helps to govern gene expression profiles.
  • Methylation (and demethylation) of proteins at certain charged amino acids alter their structural configuration, thereby their function.
  • Methyltransferase has an essential role in epigenetic regulation and its association has been also found in creating many erroneous methylation patterns, leading to severe diseases.
  • The enzymatic activity of methyltransferase is required to maintain methylation at the H3K9 site in cancer cell biol. Moreover, the epigenomic landscape of humans has shown the occurrence of hypermethylated cysteine at the gene or intergenic regions of cancer cells.

DNA Methylation

DNA methylation is the addition of a methyl group at the cytosine and arginine bases in DNA by methylases or DNA methyltransferase (DNMT). It utilizes S-adenosylmethionine (SAM) as a methyl donor.  

The key regulatory mechanisms of DNMT involve alternative splicing, post-translational modification, molecular interactions, and gene loss (or gene duplication).

Figure: An illustration of the reaction of DNA methyltransferase (DNMT) enzyme. 

Mammals have three types of active methyltransferases, with all having variant activities: 

  • DNMT1: This is the most dominant methyltransferase enzyme in mammals, responsible for methylating hemimethylated CpG di-nucleotides in the genome. Cancer cells express DNMT1 as both a de novo and a maintenance methylation enzyme. 

During DNA synthesis DNMT1 functions as a maintenance methyltransferase. For example, Human DNA methyltransferase 1 has been shown to have a role in maintaining histone H3 modification. 

  • DNMT2: This is a homolog of methyltransferase, but instead of DNA, it methylates cytosine-38 in aspartic acid tRNA anticodon loops. And, because of its binding specificity, the enzyme is now known by the name TRDMT1 (tRNA aspartic acid methyltransferase 1).
  • DNMT3: There are four types of DNMT3: DNMT3a, DNMT3b, DNMT3c, and DNMT3L. DNMT3a and DNMT3b enzymes are responsible for methylating unmethylated or hemimethylated CpG islands and maintaining methylation patterns during replication. 

While DNMT3L is catalytically inactive, it has DNA methyltransferase motifs, which are vital for establishing maternal genomic imprints. The characterization of the enzyme by peptide interaction assays has shown that DNMT3L binds specifically to the amino terminus of histone H3.

A DNMT3 complex is also involved in the methylation of histone H3 molecules at lysine 4, which has an essential role in the transcriptional activation of nearby genes.

DNMTs repress transcriptional activity by preventing the binding of transcription factors to DNA. However, it also activates it by preventing the insulator binding and allowing nearby enhancers to induce gene expression.

The association of DNMT has also been found in several metabolic processes including X-chromosome inactivation, genomic imprinting, aging, transposable elements repression, and carcinogenesis. 

How Do DNA Methyltransferase Inhibitors Work?

Altered methylation patterns by DNMTs are often associated with molecular changes in cancer cells. During carcinogenesis, methylation of DNA silences tumor suppressor genes. Therefore, attempts have been made to activate these genes by inhibiting methyltransferase activities.

Image: An illustration of epigenetic alterations in tumorigenesis involving DNMTs.

The activity of methyltransferase can be inhibited by 5‑azacytidine and 2ʹ‑deoxy‑5‑azacytidine. Moreover, these inhibitors have also been approved for treating hematopoietic malignancies.

2ʹ‑deoxy‑5‑azacytidine (decitabine) is a deoxycytidine analog, having a role in gene expression and cellular differentiation. It prevents the β-elimination step of catalysis of DNMTs and traps them on DNA by forming a covalent complex. The reaction results in the inhibition of the activity of DNMTs.

The use of these chemicals is still a question because of each chem’s potential toxicity to the bone marrow and mutations. 

And for this reason, several other approaches, such as antisense RNA therapies, are developed that degrade the DNMT mRNAs and prevent their translation and functional activities.

Figure: Image showing (A) reaction involved in DNA methylation by DNMT; and (B) inhibition of DNMT enzyme.

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