Techniques Used to Study Epigenetics

Introduction

Epigenomics deals with the distribution of epigenetic changes genomewide. The gene expression pattern is controlled by epigenetics. Hence, epigenetics can be influenced by the diet and lifestyle of an individual, and epigenetics can also influence the course of any disease like diabetes mellitus.

What Are the Techniques Used to Study Epigenetics?

Epigenetics can be analyzed using the following techniques:

• DNA methylation analysis.

• DNA-protein interaction analysis.

• Chromatic accessibility analysis.

This technique quantitatively assesses the DNA sequence. In simpler terms, with the help of these analysis techniques, the number of methyl groups and their pattern attached to a given DNA sequence can be assessed.

What Are the Applications of These Techniques?

It helps identify biomarkers associated with various disorders, for example, cancer and immunological diseases. Obesity and substance addiction also have a specific methylation pattern which can be assessed using this technique.

What Are the Subtypes of Epigenetic Techniques?

Epigenetic techniques are further divided into subtypes, namely-

• Methylation Sequencing With Next-Generation Sequencing (NGS): It helps in profiling the methylation pattern of the epigenetically significant site in the given DNA sequence.

• Methylation Microarrays: This helps analyze the methylation sites quantitatively, resulting in a reduced time for the analysis. Therefore, it is also considered a cost-effective method.

• DNA-Protein Interaction Analysis: This technique emphasizes alteration in gene expression produced due to chromatin modifications (mixture of DNA and protein which forms a cell’s chromosome) and other structural variations.

• Chromatic Accessibility Analysis: This technique analyzes any discontinuous or open genome through ATAC (adenine-thymine-adenine-cytosine) sequence evaluation. It explains how chromatin packaging influences gene expression. ATAC sequencing is performed under higher resolution; thus, it can analyze a bulk of cells in a short time.

Epigenetic techniques analyze the interactions between DNA, RNA, and proteins. It analyze DNA transcription (transfer of genetic information from DNA to RNA) and translation (it is the process that uses the information given by RNA to form protein). Alterations in the above-mentioned sequential steps lead to changes in gene expression.

Are Disease Progression and Regression Linked With Epigenetics?

Various studies are being conducted to establish the relationship between epigenetics and the cause of disease or its progression.

• The most extensively studied topic is epigenetics and its relation to cancer progression. Various recognized studies in the medical literature suggest that epigenetic changes are responsible for genetic alterations in around one-third to half of the diagnosed cancer patients.

• Besides cancer progression, a positive link between immunological diseases and epigenetics has been established.

The following example can explain epigenetics and its influence on immunological disease.

• It is proven that few patients on blood pressure-reducing drugs like Hydralazine get lupus, but now epigenetics can reverse this condition.

• Firstly, a relation between aberrant histone modification and the underlying etiology of lupus was established. Then, identification of the drug could reverse the lupus disease mechanism by altering the gene expression without changing the DNA sequence.

• Trichostatin A was identified as the drug of choice after researchers experimented on mice.

• Thus, epigenetic techniques can reverse immunological diseases.

Can Epigenetics Influence Reproduction?

Various research studies have shown that epigenetics can also influence the reproduction process. Researchers experimented on mice exposed to high concentrations of insecticide and fungicide. They noted the following points from this experiment:

• Post-exposure to these chemical agents, male infertility, and decreased sperm count were noted in the next generation of mice.

• Moreover, this adverse effect was carried forward up to the next four generations of the mice population, even without additional insecticide exposure.

Hence, this experiment proved that the insecticide used here could alter gene expression, and we can also note this altered gene expression in the future population. Another interesting finding about epigenetics and its influence on the reproduction process is that “epigenetic changes are not only expressed during birth but can be expressed throughout the entire lifespan of an individual.” For example, a study was conducted among two twin pairs. The first twin pair had a similar lifestyle and stayed together for a long period, and the second twin pair had a contrasting or different lifestyle. They had stayed together for a very short period of time.

Researchers noted the following features in the twin pairs:

• The first twin pair noted similar epigenetic changes like DNA methylation and histone acetylation patterns.

• The second twin pair observed many different patterns. So, there was dissimilarity in, for example, intra-abdominal fat distribution, lymphocyte expression, etc.

How Can Lifestyle Modifications Influence Epigenetics?

The term “lifestyle” includes day-to-day habits, which influence one’s way of living.

• The diet taken by the individual.

• Psychological as well as physical stress.

• Harmful habits like cigarette smoking and alcohol consumption.

• Other forms of tobacco intake. All these factors influence the way of living and define an individual'slifestyle.

These lifestyle factors, along with other environmental factors mentioned below, include:

• Climatic changes.

• Pollution triggers epigenetic mechanisms such as DNA methylation as well as the expression of microRNA. Thus, leading to variations in gene expression, which may induce genetic defects.

Unhealthy food items like pizza, burgers, fries, and canned aerated drinks are deficient in basic nutrients and thus induce oxidative stress and free radicals. Free radicals and oxidative stress induce epigenetic mechanisms and cause defects in gene expression, which may increase the risk of cancer and cardiovascular and renal diseases. On the other hand, food items like fruits, dry fruits, and vegetables are rich sources of antioxidants that reduce oxidative stress.

Thus, reducing defective gene expression and the probability of cancer and other systemic disorders. Genes that maintain energy homeostasis influence the body weight of an individual. Thus, people with less physical activity tend to be obese, as epigenetics alter the gene expression associated with energy homeostasis. DNA methylation leads to gene expression during adipogenesis (increased fat deposition). Thus, regular physical activity as a part of lifestyle modification can stimulate gene expression for a fit body.

Conclusion

The techniques that are used to study epigenetics, besides explaining the pattern of altered genetic expressions in individual and future generations, also help identify the cause of the genetic defect. Advancements in epigenetics techniques have led to a better understanding of gene expression without changing the genomic sequence.