Conjuring over a tangle
Molecular biologists unravel the intricacies of the 3D genome
Yuri Drize, "Search"
At the end of the last century, biologists began to master a global project to decode the human genome. It seemed that by determining its primary structure, the researchers would reveal all the secrets, first of all, they would understand how the fine regulation of gene expression is carried out. It is difficult to overestimate the importance of the Human Genome program for the science of life and medicine, but so far it has not revealed much, for example, the mysteries of the functioning of the genome, in particular, understanding how chromosomes are stacked in the nucleus, how distant parts of the genome interact with each other.
Molecular biologists have been interested in this question for a long time, and at every stage of its study they try to move forward. The Department of Cellular Genomics of the Institute of Gene Biology of the Russian Academy of Sciences, headed by Doctor of Biological Sciences Omar Kantidze, has achieved tangible success in this. The team's research "Mechanisms for maintaining the stability of the 3D genome and technologies for its directional modification to solve fundamental and applied problems" was supported by a large grant from the Russian Science Foundation.
– The problem is that it is not enough to "read" the genome, – explains Omar Levanovich. – It is important to understand how individual and often very remote parts of it interact, what influence they have on each other. The knowledge gained in a certain sense reverses our understanding of the mechanisms of regulation of gene expression. For example, earlier we considered the sequence of genes and regulatory elements controlling their activity on a linear scale, but it turned out that they function in 3D space.
– What does a 3D volumetric genome look like? What is the approximate length of its molecule?
– The length of the DNA molecule of one human cell is approximately 2 meters, but in other dimensions it has a nanometer scale. At the same time, DNA is very compactly folded in the space of the cell nucleus, the average diameter of which is about 10 micrometers. If you try to imagine what one chromosome in the interphase nucleus looks like, then the closest thing will be ... a ball of threads or spaghetti pasta mixed up with each other. The spatial organization of the genome has been studied for many decades, but it is in recent years that significant progress has been achieved in this area. It became clear not only how the chromosomes are arranged in the nucleus and how the elements of the genome that are removed from each other interact, but also what molecular processes underlie such an organization. Today it is one of the hottest spots of molecular biology. Many laboratories in the world conduct fundamental research in this area. Interest in them is increased, because it also has an applied value: it is directly related to understanding the mechanisms of regulation of gene expression. These changes are the root cause of cellular disorders, they lead to the emergence of various diseases, including cancer. And in some cases, this is really due to changes in the 3D genome. That is why it is so important to understand how it is laid in the nucleus, how it affects gene expression and other molecular processes inside the cell nucleus.
– Is it possible to influence the laying of the genome?
– Yes, in recent years, in various laboratories (including in our department), researchers have been developing ways to manipulate the 3D genome. Actually, the RNF grant provides not only for the study, but also for the development of methods of point changes in it. For example, it is possible to destroy or, conversely, stabilize interactions between remote parts of the genome in order to make the necessary transformations in gene expression. Mastering such approaches is very important for the development of our field of research and, in general, for the life sciences, but not only. These methods also have the prospect of clinical application. In a sense, manipulation of the 3D genome is the editing of the genome, but not at the level of the primary sequence, but the interaction of its elements. There are already examples of the use of such technologies in animal research for the treatment of hereditary diseases.
– How to restore order in the "tangle"?
– Before putting things in order, it is necessary to determine exactly what is wrong with the 3D genome of the diseased cell, the violation of which processes led to changes. To do this, it is necessary to compare the spatial arrangement of chromosomes of normal (healthy) cells and pathologically transformed ones. It sounds simple, but every time it is a big, complex and self-sufficient scientific task that brings us closer to discovering the mechanisms of development of a particular disease. If we solve this problem, we can think about how and what changes in the 3D genome should be reversed or, conversely, induced for therapeutic purposes. Point transformations can be made into it using specially designed chimeric proteins consisting of several functional modules. The most important of them are responsible for attracting the chimeric protein to a certain place in the genome and, in fact, for "changing" its 3D structure. One of the activities of various laboratories in the world is the search and research of new variants of such protein modules to create technologies for high–precision and efficient manipulation of the 3D genome.
– How does he feel about the invasion, does it cause consequences?
– Like all gene therapy developments (and any drugs), 3D genome editing methods should be effective, but safe. Its transformation as a whole is a less traumatic technology compared, for example, with genomic editing. However, please note that we (I mean all researchers of the 3D genome) have just moved from the process of accumulating knowledge to their possible practical application, that is, the creation of the technologies I mentioned. The next stage, in all likelihood, is a comprehensive study of the accuracy and safety of such manipulations.
– Let's go back to the RNF grant. Why do you think the Foundation supported you?
"It's not the first time he's done this, I'll note. Our team has been awarded RNF grants since the Foundation was established. I think it's because we've managed to prove ourselves well: projects are interesting and often complex, but we know how to implement them. And our results are published by the best international scientific journals. It seems to me that every time the Foundation asks itself the same main questions. Can he, for example, trust our team, will we cope with the task? And, of course, how relevant, significant and attractive is our project? We received the last grant last year (the Foundation has just approved the report for the first year, and the reviews are very good), it is designed for four years and can be extended for another three. I must say that the RNF has brought a lot of useful things to the system of allocating funds for research: these are clear, transparent examination criteria, and the publication of reviews of applications and reports, which can be extremely useful for applicants and grant performers, and focus on quality, not only on the number of reporting publications.
– What are the grant funds used for?
– We have no problems with scientific equipment. The IBG RAS successfully operates a Center for Collective Use, and our department has expanded and updated its instrument base over the years of cooperation with the Foundation. The main item of our expenses is the purchase of reagents and payment for sequencing. Both are very expensive. The size of the RNF grants is comparable to good foreign ones, but in fact it turns out to be three times less. The reason is known – it is an overpayment for reagents. Unfortunately, very few reagents and consumables suitable for our research are produced in our country. And the institute cannot buy foreign ones directly, so we all use the services of supplier companies. As a result, prices increase several times. In addition, the extreme overregulation of procurement requirements leads to delivery times that are unthinkable by modern standards. The problems have been known for many years, they are constantly reminded of them, but for some reason the situation does not change.
– How do your colleagues evaluate your research?
– The fact that our work is known in the world is evidenced by the number of citations of our articles, and the fact that employees of the department are often invited to make presentations at international conferences. I would like to note that in this field of genetics we cooperate with many people both in our country and abroad. The merit in this, in my opinion, belongs to the powerful scientific school established at our institute, the pioneer of research on the structural and functional organization of chromosomes, Sergei Vladimirovich Razin.
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