Many of the processes that explain life occur at the microscopic level. That greatly complicates your observation. Hence, scientists seek solutions to overcome these limitations. That is what Antonio Giráldez (Jerez de la Frontera, 1975) has just done, who together with other colleagues from Yale University (USA), where he has had his own laboratory for almost 17 years, have developed a technique that allows the physical volume of zebrafish embryonic cell nuclei to be increased 4,000 times. "It's like having a lighter and amplifying it to the size of a refrigerator," he explains to La Vanguardia. He assures that they will now be able to "observe the events that occur in the genome." His work has just been published in the journal Science.
How have they managed to achieve that level of increase?
We have put the cell in a kind of jelly. There, the molecules are anchored to the gel. When we add water to it, it expands, and that allows us to see each of the molecules, which are separated from each other thanks to this expansion. The cell grows, in volume, 4,000 times.
And what implications can this new technique have?
In science, many of the processes are so microscopic that we have to intuit them with experiments. This technique, however, allows us to see many of the processes that we have intuited and hypothesized. We can observe how genes are transcribed, how they are activated, and the arrangement of different molecules. In addition, it opens a window to see what other processes are like.
Which is it?
For example, how DNA is repaired when a mutation occurs, which is essential for cancer. Or how DNA replicates. We will also be able to see in the future how genes interact with each other, something that is very important for their regulation.
Is this the first time that it is possible to see live how genes are activated and regulated in the cell?
It is the first time that we can see in this incredible resolution how genes are activated and how the polymerase protein, which reads DNA, creates the carbon copies, which are RNA. It's a basic process applicable to all cells, not just the zebrafish embryo we used in our research. What had not been seen until now, and that this technique allows, is how the molecules interact.
Is it also the first time that the molecules imagined by Severo Ochoa can be seen at high resolution?
Yes, it is the first time that we see with this resolution the molecules that Severo Ochoa imagined and studied in his day and how they act inside the cell. Also how these proteins participate in the activation of genes, which is the first process that occurs when life starts after fertilization.
Based on this technique, they have developed a new model, which they have called kiss and kick, which explains how genes are regulated and in which the regulatory zone and the promoter interact.
The regulatory region of the gene has to stick to the promoter to attract the polymerase. The promoter region is at the beginning of the genome and the regulatory region may be far away. If a gene is a thousand nucleotides long, or a thousand letters, the regulatory region may be more than 50,000 letters away. The genome has to fold for both areas to interact.
It bends over and they touch (kiss).
Correct. There the polymerase is recruited, which is what allows the gene to be activated. But what's interesting is that when the gene is turned on, the polymerase kicks the regulatory zone to downregulate the gene.
What is gene regulation?
It's how it turns on and off. When the regulatory area hits, the gene is turned on; and when the polymerase kicks it, it shuts down.
And the gene happens to be in a state, let's say, dormant?
When the regulatory zone detaches, what it does is that the polymerase does not read the gene all the time.
And what would happen if it did?
The cell could not function. It is as if all the traffic lights in a city were green at the same time. It would be chaos. At some times you need a type of protein; and in others, another. The genes are activated at the right time, it is something fundamental.
Will they be able to test hypotheses so far unverifiable?
Yes. For example, how the genome is packaged in the cell. The genome is a huge thing. There are two meters of DNA in a cell, which on the contrary is something tiny. And we will not only be able to see how it is packaged, but also how its shape influences the way in which genes are regulated: how cancer is activated, how genes are activated to prevent it... It is to observe how the shape influences the function.
Will they study other processes?
We will also be able to observe how different transcription factors (proteins), which regulate different types of genes, activate the latter. Until now, we have not been able to see how these proteins, which bind to DNA, activate genes in cells. We have seen it indirectly, through biochemistry, but not directly. We will also be able to see how DNA duplicates itself. We have never seen it with this level of resolution in the cell.
And how can it help?
Between people, there are many differences in the genome, and we don't know how these influence whether one is more prone to disease. In the case of the covid, for example, there were people who were greatly affected and others who were not. This is an example of how our genome (among other factors) can respond to external agents through internal agents.
Do genes interact through contact?
That's what we believe. Also through its prevention. Sometimes, a specific area of the genome prevents two different points from contacting each other, and this is also important for regulation, because a gene may be regulated at the wrong time.
Earlier he told us about DNA duplication. Are we constantly replicating ourselves?
Yes, although not in all types of cells. Since fertilization there is a lot of replication. Later, once we grow, it decreases a bit, although there are tissues that replicate all the time, such as the skin (it is thanks to this that the wounds we make on it heal). In fact, many cancer processes are explained by replication that is reactivated and cannot be controlled. Part of this process is also genome repair. We are acquiring mutations all the time. Genes are constantly mutating and repairing themselves. Our technique will allow us to see how this happens
The idea is to further improve the resolution of the technique.
Exact. Although we can currently visualize molecules that interact with the genome, it is not yet possible to identify individual genes.
It remains to take one more step.
Although we can see individual genes, we don't know who they are. I explain. Imagine that we see two people who interact a lot, but we do not know their identity. If we knew, however, their name and that, for example, they are sister and brother, then we would have more context in that relationship and understand why they are interacting. Now we see how genes can interact, but we don't know who they are. Thanks to the technique we have developed, it will be possible to create new processes that will allow us to know the identity of these genes. We can name them, something that is not currently possible.