VU LSC Researchers Develop a New Method to Study the Regulation of Gene Activity

Why do different cells in our bodies perform completely different functions despite containing the same genetic information? How does a cell 'decide' which genes to use and which to keep inactive? Scientists are seeking answers to these questions by studying epigenetic processes – mechanisms that regulate gene activity without altering the DNA sequence itself.

A research team led by Prof. Habil. Dr. Saulius Klimašauskas at the Vilnius University Life Sciences Center (VU LSC) has developed a method that makes it possible to distinguish the contributions of individual proteins to one of the most important epigenetic processes – DNA methylation. This achievement opens up new opportunities to understand how gene activity is regulated, how different types of cells develop, and how disruptions in these processes may contribute to the onset and progression of cancer and other diseases.

The Same Genetic Code – Different Cellular Functions 

One of the key mechanisms regulating gene activity is DNA methylation. During this process, small chemical groups are attached to specific sites in DNA, potentially influencing gene activity. But how does a cell 'know' where these chemical marks should be placed, and what effect do they have on gene activity?

Dr. Liepa Gasiulė, a researcher at VU LSC, suggests imagining DNA as a vast map containing information about how an organism functions.

'Epigenetic changes act like additional markers on this map – they help the cell navigate and indicate which regions of DNA to use and which to leave aside at a particular moment. Importantly, the map itself – the DNA sequence – remains unchanged, but the way the cell uses it changes,' explains the researcher.

Although DNA methylation has been studied for decades, scientists still find it difficult to determine which specific protein is responsible for placing a particular chemical mark. This is because several proteins that create such marks operate simultaneously within a cell, making it difficult to distinguish their individual contributions.

The method developed by VU LSC researchers makes it possible to isolate the contribution of a specific protein to the DNA methylation process. It uses a specialised molecular labelling approach to identify the regions of DNA where the protein under investigation has acted.

'It is similar to a situation where, out of a thousand people, we give one person a special pen. Everyone works together and leaves traces of their work, but we can identify the work of that one individual by their distinctive mark,' Dr. Gasiulė explains.

One of the method’s key advantages is that it allows researchers to study the activity of individual proteins while minimally disturbing the cell’s normal state. This makes it possible to gain a better understanding of these processes under conditions that more closely resemble the cell’s natural environment.

New Opportunities to Study Cancer-Related Processes

Using the newly developed method, researchers can independently investigate the activity of two important enzymes involved in DNA methylation – DNMT1 and DNMT3A – in living cells.

These enzymes help establish and maintain chemical marks on DNA that play a role in regulating gene activity. Until now, scientists have largely been able to observe the final DNA methylation patterns, whereas the new method allows them to examine in greater detail how these patterns are formed and the contributions of individual enzymes.

'Until now, we have mostly been able to see the final result of methylation, but now we can observe how it develops. This gives us an opportunity to better understand how the roles of individual enzymes differ and how their activity depends on the specific cellular environment,' says Dr. Vaidotas Stankevičius, a researcher at VU LSC.

This is important for understanding how different cell types emerge from a single initial cell, how they acquire their specialised characteristics, and how they maintain them.

The method is equally significant for disease research.

The Method Could Help Improve Our Understanding of Cancer Development

One of the enzymes studied by the researchers, DNMT3A, is associated with certain cancers, particularly blood cancers. Altered DNMT3A activity can disrupt the normal development of haematopoietic stem cells and contribute to malignant changes.

DNMT3A has been found to play a particularly important role in acute myeloid leukaemia, a type of blood cancer. According to the researchers, mutations in the DNMT3A gene are detected in approximately one-fifth of cases of this disease and are associated with a poorer prognosis.

The ability to determine more precisely where and how this enzyme acts could help scientists better understand the biological processes contributing to the development of the disease.

'If we can determine more precisely how and when epigenetic regulation of DNA becomes disrupted, we can gain a better understanding of the mechanisms underlying disease development. In the long term, such fundamental knowledge may contribute to the search for new disease biomarkers or treatment strategies,' says Dr. Stankevičius.

The potential applications of the method extend beyond cancer research. According to the researchers, it could also prove useful in investigating developmental disorders, neurological and autoimmune diseases, metabolic disorders, and other conditions in which epigenetic changes play an important role.

The First Signal After Years of Research   

The researchers’ journey towards this discovery was far from straightforward. Developing the new method involved unsuccessful experiments, doubts, and moments when it seemed that the proposed approach simply did not work. Nevertheless, one night in the laboratory, the researchers detected signals indicating DNMT3A enzyme activity for the first time.

'It was one of those moments when months or even years of work suddenly produce a tangible result. The first signal was small, but it meant a great deal to us because behind it were countless experiments and hours spent in the laboratory,' recalls Dr. Stankevičius.

However, the first successful experiment was only the beginning. The researchers still needed to confirm that the detected signals genuinely reflected DNMT3A activity. This required numerous additional experiments, control tests, and repeated verification of the results. At least two years passed between the first signal and the final scientific publication.

According to Dr. Gasiulė, this experience once again demonstrated that scientific research requires not only knowledge and experimental skills but also perseverance, critical thinking, and the ability to learn from failure.

'Unsuccessful experiments can also be valuable in scientific research if you are able to learn from them, draw meaningful conclusions, critically assess your assumptions, adjust your plans when necessary, and continue working consistently towards your goal,' says the researcher.

The research was funded by the Lithuanian Ministry of Education, Science and Sport under the University Excellence Initiative programme (Project No. 12-001-01-01-01/S-A-UEI-23-10).