As a world outside the genome, imprinted genes like to "huddle together". As we age, the state of our epigenetic information will only get worse. We're trying to find specific ways to reverse or slow down the DNA methylation "clock" moving forward....
Producer: Gezhi Pulpit.
The following is a transcript of the speech of Zhu Bing, a researcher at the Institute of Biophysics, Chinese Academy of Sciences
Hello everyone, I am Zhu Bing, a researcher at the Institute of Biophysics, Chinese Academy of Sciences. It is an honor to come to Gezhi and introduce you to the knowledge of epigenetics.
Seeing today's topic, you may first ask: What is epigenetics? Why do I call it "The World Beyond the Genome"?
Mom and Dad, you can't leave anyone.
Everyone is familiar with the genome, and probably all know about heredity. When we encounter something less than ideal, we can at least complain. For example, if I say that I am not good-looking, it is because of my dad and my mom, which is genetically determined, right? Because our genes come from our parents. But what is epigenetic? Even when you have the same gene, its effect may not be the same.
We know that everyone's genome comes from their father and mother, and that our parents will give us a set of genomes. This begs the question: do mom and dad give us the same genome?
About three weeks ago, my youngest son asked me a question: Daddy, if you take out the nucleus of a fertilized egg and put in two sets of nuclei from both eggs, will it survive? Can it become an embryo, or even a child?
I said, "You know what?" My main research direction is related to this, and I will tell you about it next.
At the top of this diagram, there is a relatively large egg and a smaller sperm. Of course, the size of sperm is much smaller than this, and it is even more disproportionate.
Once fertilized, the DNA from the egg and the DNA from the sperm do not immediately mix, but become two pronuclei: one called the female pronucleus and the other called the male pronucleus. These two prokaryotes are morphologically different, so under the light microscope it is clear which one came from Mom and which one came from Dad.
Based on such characteristics, scientists have done an exploration many years ago: they pierced a capillary into the fertilized egg of a mouse, and then sucked out the female pronucleus from the mother; After sucking it up, a male pronucleus from Daddy is inserted. It's the equivalent of a mouse without a mother, it has two fathers, right? As a result, they found that the embryo was lethal and the single male had failed.
Two dads can't do it, so can those two mothers do it? Neither can two mothers. Scientists also did this experiment, sucking out the male pronucleus from the father and injecting a female pronucleus from the mother, so that the embryo could not develop, and the embryo was also lethal.
Some readers may think that if you prick this capillary around, you may also prick the fertilized egg to death. But a scientist is a scientist because he does controlled experiments. So what does a controlled experiment look like?
After the researchers inserted a capillary into the fertilized egg, they sucked out both the female and male pronuclei, and then injected it with a female pronucleus and a male pronucleus, respectively. As a result, this embryo is alive and can develop into a mouse, and the mouse is alive and kicking around without much of a problem. This fertilized egg is fine after two more punctures, so it is not because it is pierced, but it tells us a very simple truth: we need both a father and a mother.
We know this from a young age, but from a scientific point of view, it is not particularly easy to understand. Because what we knew before was: Dad provided one genome, Mom provided one genome, and we had two genomes, so we survived. In nature, we do need to fertilize the sperm and egg to achieve this process, but if we do a human experiment, like just now, you can have two genomes, why not?
This tells us that, for some reason that mom and dad don't provide exactly the same genome. What does this involve? There is a classical epigenetic phenomenon involved called genetic imprinting.
Magical imprint genes.
What is genetic imprinting? We humans have about 20,000 or 30,000 genes, but only two or three hundred of them are imprinted genes. The reason why it is called a sigil is because it knows whether it is from its mother or from its father. Although there are two copies of the imprinted gene, the DNA or sequence of these two copies is exactly the same, and the genetic information it carries is exactly the same, but only one is expressed in our cells, or only one is functional.
It's kind of confusing. Because in one of our cells, either we have this gene or we don't have this gene. Now there is, and not only that, but there are two, and the two gene sequences are exactly the same, but only one is expressed, and the other is not.
Traditionally, it has been believed that the expression of a gene depends on the presence or absence of upstream regulatory factors, and it is clear that in this cell, regulatory factors exist. Why? Because the one that can be expressed is well expressed, but the other one is still not expressed even if there is an upstream regulatory factor. That's a pretty confusing thing.
So how many imprinted genes are in our genome? There were two or three hundred. Interestingly, these two or three hundred imprinted genes are not scattered in our genome, they are often clustered, and there are many imprinted genes in one pile. Of course, there are many other piles, so that there will be two or three hundred.
Imprinted genes: Only one of the paternal or maternal origins works.
There are two chromosomes on this diagram, the top one is from the mother, which we call the mother's chromosome; The one below comes from the father and is the chromosome of the paternal origin. Each small square represents a gene, and an arrow indicates that the gene is being expressed, or that it is working.
We note that the leftmost gene is expressed in both copies. It's not an imprint gene, it's a very common gene, and most of our genes are like that.
But for the two genes on the second and third left, we see that only the small red arrow is drawn on the maternal source, and a circle and a bar are drawn on the paternal source, which means that it does not express or work. In other words, these two genes know that they can only express themselves if they come from their mother, and they can't express them if they come from their father, even if they look exactly the same.
What's even more interesting? These imprinted genes are often clustered together, but there is often the "other way around" in this pile.
What does it mean to be "reversed"? For example, the penultimate gene on the right, there is a small blue arrow on the paternal one, which means that the copy from the father can be expressed; But the one from the mother has a circle and a bar on it, which means that the gene cannot be expressed. This is a paternally specific expression of the imprint gene - only those from Dad work, and those from Mom are useless.
What are the consequences of this? Let's take a look.
Left: Chubby Willi syndrome.
Right: Angelman syndrome.
Both the children on the left and right have specific diseases. The one on the left is called Chubby Willi syndrome, and the one on the right is called Angel syndrome. I'd like to say something that might surprise you: these two types of patients actually come from the same genetic family, and they have the same genetic defects.
What is a genetic pedigree? For example, in a family, the grandfather has this disease, the mother is not sick and is a carrier, but the granddaughter has this disease, which is a genetic family. In general, there is only one disease in a genetic family.
But there are two different diseases in this genetic lineage. The damage to the DNA they have is the same, but the results are not the same, and different diseases occur. Why? It's because I just said that some genes come from mom and some come from dad, and they will be different.
Left: Chubby Willi syndrome (paternal loss).
Right: Angelman syndrome (maternal loss).
We now know that the missing part of DNA in Chubby Willi syndrome comes from the father, and the part of Angelman syndrome comes from the mother. So why does missing the same chromosomal segment cause two different diseases? This is because the missing segment happens to cover a certain group of imprinted genes, and there are several imprinted genes in it.
As I mentioned earlier, some imprinted genes are only expressed by mothers, and some imprinted genes are only expressed by fathers. In the case of Chubby Willi syndrome, the one from the father is missing, and the one from the mother is fine, but one of the imprint genes can only be expressed by the father, and the one from the mother is there, but it will not be expressed and will not work, which is equivalent to not having this gene, so you will get this disease.
But in other children, the defect comes from the mother. As we have just mentioned, imprinted genes often exist in clusters, and some are in reverse, in which it also has several "reversed": only the mother ** expresses it, and the father ** does not express it. In patients with Angelman syndrome, what is missing is the gene of the mother, although there is the father's one, but it does not work, so it is equivalent to nothing.
In patients with Angelman syndrome and Chubby Willi syndrome, the gene "equivalent to nothing" is not the same, so the phenotype is different, the symptoms of the disease are different, and of course, the ** plan is also different.
The next thing I want to tell you is, why do these imprint genes know that they come from their mother or from their father? How are they different? This is where epigenetic modifications exist genetically.
The 5th letter in the genome.
I'm sure you've all learned in middle school that there are 4 main letters (bases) in our genome: A, T, G, C (ADENINE, THYMINE, CYTOSINE, GUANINE). A and T are paired, G and C are paired, and 3 bases can form a triple codon that codes for an amino acid to synthesize proteins.
What I want to tell you is that in addition to these 4 letters, there is a 5th letter on our genome, which is the 5-methylcytosine in the figure. The one on the left is cytosine, which is called C, and the one on the right is 5-methylcytosine. We can see that they look almost identical, the only difference is that the right one has an extra methyl group on the ring, and the presence of this methyl group makes it called 5-methylcytosine.
However, when DNA is synthesized, there is no 5-methylcytosine, only four letters: A, T, G, and C. After the synthesis is completed, there is an enzyme that can carry out a methylation modification on it, and catalyze it through a chemical reaction, then this enzyme is the DNMT in the figure, that is, DNA methyltransferase.
What problems can the presence of DNA methyltransferases cause? With methylation, there are differences in the proteins that recognize it: some proteins selectively recognize methylated cytosine, while others selectively reject methylated cytosine, so that the methylated copy and the non-methylated copy have different binding to the protein.
Of course, the combination of different proteins may have different consequences, or expression or non-expression. In general, methylated genes are not expressed, and unmethylated genes are actively expressed.
As I mentioned earlier, methylation regulates genes, and imprinted genes are known to be from their father or from their mother because they have DNA methylation that is different from their parents. In other words, in one of our adult cells, one gene comes from the father and one from the mother, and the imprinted gene from the father is not methylated differently than the imprinted gene from the mother. Why is it different? This is because there is a significant difference in the DNA methylation profile established at the time of sperm and egg production.
The DNA methylome of sperm and egg is not the same, so it is inherently different, and some of these differences can be copied in the process of cell**. Therefore, after the replication of cells and DNA, the original methylated ones will still be methylated, and the non-methylated ones will still not be methylated. In this way, the cell keeps replicating and this methylation message can be maintained forever.
Even when we reach adulthood, some cells still know that my gene comes from my father, because the DNA methylome of my gene is exactly the same as that in sperm. And the other gene knows: I came from my mother, because my spectrum is exactly the same as the methylome from the egg. This is how the main molecular mechanism of the difference, which we talked about earlier, is recognized.
The ticking of the methylation clock, can it be reversed?
There is another interesting question. Can DNA methylation profiles be copied, and can such copies be faithfully completed forever? Actually, that's not the case, so let's show you this picture.
There are three "paths" on this picture, what are they? It is the part of our chromosomes that reflects the condition of the T cells in our lymphocytes: the yellow area represents a high degree of methylation, and the blue area represents a low level of methylation.
The aging process is accompanied by a selective loss of DNA methylation.
What's the top one? is a newborn baby's T cells. We can see that this chromosome is yellow, indicating that he was highly methylated when he was born.
What is the second one? It is a 103-year-old T cell. We can clearly see that there is selective demethylation in certain locations, and those places are blue.
What's even more interesting is the third one, which comes from the T cells of lymphoma or tumor patients. It's very similar to the second one, right? They all appear blue in the same area, with a loss of selective DNA methylation, but it's a little more severe.
What's behind this? We first need to know that if a blood draw is taken to test the DNA methylome of white blood cells, it is the best molecular marker for our age. After the measurement, you can know the age range of 3 years, and its judgment is very accurate. This is also often referred to as the methylation clock, the methylation clock of human age.
How did this clock come about? It is because in the process of aging, it will be accompanied by the selective loss of DNA methylation just mentioned. But what is not clear is that it is because the demethylase enzyme likes these places and then removes the methylation of these places? Or is it that in the process of replication, DNA methylation needs to be copied, but this copy is not ideal, and the copy is slowly lost?
This is one of the things that our research group studied a few years ago. The white blood cells in our blood have a methylation group, and with age, DNA methylation increases with aging in some places, stabilizes with aging in others, and decreases in others.
We did something that allowed us to precisely measure the dynamics of DNA methylation reconstitution in a cell cycle, a single cell.
There are three lines on this picture, but what are the two on it? During the aging process, DNA methylation grows or stabilizes in those places. We can see that their copy profiles are almost the same within a cell cycle, and the dynamics, or velocity, are just as fast.
But we clearly see that the red line below is different. What is that line? These are the places where DNA methylation is gradually lost during aging. We can see that in one cell cycle, it is significantly slower than the other two, and by the far right point in time, which is when the entire cell cycle has been completed for 24 hours, it basically catches up, but not completely.
We Chinese have an old saying, called "a small mistake is a thousand miles". Cells are lost a little at a time, and a lot of them are lost after many times. It's a bit like giving you a document and having you copy it, and when you're done, it always looks pretty much the same. But if you take the copied version and make a copy, wait until you have copied it a hundred times, and you will find that it is miserable.
This tells us that as we age, the state of our epigenetic information will only get worse and worse, and this is a predestined thing because the copies of our DNA methylation are not so ideal, not so absolutely precise.
Of course, from my personal point of view, now that we have discovered this phenomenon, we are very keen to study it further in the next few years. Is there a way to find a specific way to reverse, even slow, the ticking of the DNA methylation clock? If we could intervene in it, would it be possible to have a more ideal life? This is the direction we are currently working on, and I hope that in many years, we will have the opportunity to report to you on new developments.
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