Double helix

What is DNA methylation? Discover the fascinating world of DNA methylation

In the study of genetics, there is an intricate process that goes beyond the sequence of DNA itself. DNA stores multimodal information through a process known as DNA methylation and it plays a crucial role in gene expression and regulation. In this article, we will explore the concept of DNA methylation, its role in various biological processes, and its significance in fields such as cancer research, ageing studies, and precision medicine.

Understanding the methylation of DNA

What is DNA methylation?

DNA methylation is an epigenetic mechanism that modifies DNA without altering its underlying sequence. It involves the addition of a methyl group (CH3) to the DNA molecule, specifically at the 5-carbon position of the cytosine ring. This modification results in the formation of 5-methylcytosine (5mC), often referred to as the “fifth base” of DNA. The addition of a methyl group can impact gene expression by affecting how genes are read and transcribed.

How does DNA methylation affect gene expression?

DNA methylation plays a critical role in regulating gene expression by turning genes “on” or “off.” When certain regions of DNA are methylated, the methyl groups act as a barrier, preventing the binding of proteins that are responsible for gene activation. Consequently, the genes in those regions are silenced or turned off. On the other hand, when DNA is unmethylated, genes can be activated, allowing for the transcription of RNA and subsequent protein synthesis.

DNA methylation patterns: CpG islands and beyond

In somatic cells, DNA methylation predominantly occurs in the context of CpG dinucleotides, where a cytosine nucleotide is followed by a guanine nucleotide. These CpG sites are often found grouped in genetic regions known as CpG islands. Interestingly, CpG islands are often found near gene promoters, which are crucial for gene regulation. In normal somatic cells, CpG islands are typically unmethylated, allowing for gene expression. However, in certain disease states, such as cancer, aberrant DNA methylation can lead to the silencing of tumour suppressor genes or the activation of oncogenes.

The process of DNA methylation

Enzymes involved in DNA methylation

The addition and removal of methyl groups in DNA are controlled by a family of enzymes called DNA methyltransferases (DNMTs). Three key members of this family are DNMT1, DNMT3a, and DNMT3b. DNMT1 is responsible for maintaining existing patterns of DNA methylation during replication, ensuring that the methyl groups are faithfully copied to newly synthesised DNA strands. DNMT3a and DNMT3b, on the other hand, are involved in de novo DNA methylation, establishing new methylation patterns during development or in response to environmental cues.

DNA demethylation: the flip side of methylation

While DNA methylation is essential for gene regulation, the process of DNA demethylation is equally important. DNA demethylation involves the removal of methyl groups from DNA, resulting in changes to gene expression patterns. Demethylation can occur through passive or active mechanisms. Passive demethylation occurs during DNA replication when newly synthesised DNA strands lack methyl groups and slowly replace the methylated DNA strands. In contrast, active demethylation involves enzymatic processes that actively remove methyl groups from specific regions of DNA.

One crucial player in active demethylation is the ten-eleven translocation (TET) family of enzymes, including TET1, TET2, and TET3. These enzymes can promote the conversion of 5mC to other modified forms, such as 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). These modifications can initiate a cascade of events leading to the replacement of methylated cytosines with unmethylated cytosines, effectively reversing the DNA methylation pattern.

The significance of DNA methylation in research and medicine

DNA methylation and cancer

DNA methylation has profound implications in cancer research, as abnormal DNA methylation patterns are commonly observed in various types of cancer. Methylation changes can lead to the silencing of tumour suppressor genes, which are essential for preventing uncontrolled cell growth and the development of tumours. Conversely, the activation of oncogenes through DNA methylation can promote cancer progression. The study of DNA methylation patterns in cancer cells has provided valuable insights into disease mechanisms and has paved the way for the development of epigenetic therapies targeting aberrant DNA methylation.

DNA methylation and ageing

Age-related changes in DNA methylation patterns have also garnered significant attention in the field of ageing research. DNA methylation patterns can serve as biomarkers of biological age, reflecting the cumulative effects of environmental factors and lifestyle choices on the epigenome. Studies have shown that DNA methylation patterns can predict age-related diseases and mortality risk. Moreover, the identification of age-associated differentially methylated regions (aDMRs) has provided valuable insights into the molecular processes underlying ageing and age-related diseases.

DNA methylation in precision medicine

The field of precision medicine aims to tailor medical treatments to an individual’s unique genetic and epigenetic makeup. DNA methylation profiles have shown great promise as diagnostic and prognostic markers in various diseases, including cancer. By analysing DNA methylation patterns, researchers can identify specific biomarkers that can aid in disease detection, prediction of treatment response, and personalised therapeutic interventions. DNA methylation-based assays are also being developed to monitor treatment efficacy and detect minimal residual disease in cancer patients.

5hmC: the sixth base of DNA

As described above, 5mC is often referred to as the “fifth base” of DNA, but recent developments in the understanding of 5hmC have revealed that it has a unique role that differs distinctly from 5mC. Whereas DNA methylation sites that contain 5mC inhibit the expression of genes, 5hmC appears to have an opposing effect. This mark is found mainly in genes that are being actively expressed, or in those that are about to be expressed – sometimes referred to as “poised”. 5hmC is found relatively infrequently in the genome, but it is significantly increased in the brain, where it has been shown to be associated with development and neurodegeneration. This sixth base has been difficult to investigate until recently, where modern techniques are enabling new levels of understanding.

The future of DNA methylation research

As research in the field of epigenetics progresses, our understanding of DNA methylation and its implications continues to expand. Advancements in technology have enabled the high-throughput profiling of DNA methylation patterns across the genome, allowing for comprehensive analyses and the identification of novel biomarkers. Furthermore, the development of targeted epigenetic therapies holds promise for the treatment of various diseases, including cancer and age-related disorders.

In conclusion, DNA methylation plays a crucial role in both the expression and regulation of genes. It is a dynamic process influenced by a range of factors, including environmental cues and lifestyle choices. The study of DNA methylation patterns has provided valuable insights into disease mechanisms, ageing processes, and personalised medicine. As we delve deeper into the fascinating world of epigenetics, DNA methylation remains a key player in understanding and harnessing the power of the epigenome.

“DNA methylation is like adding post-it notes to a book – it doesn’t change the words, but it can affect how often they are read.”

Cambridge Epigenetix is now biomodal