Epigenetics and ncRNAS: Open questions
CC Attribution 3.0 Unported:
You are free to use, adapt and copy, distribute and transmit the work or content in adapted or unchanged form for any legal purpose as long as the work is attributed to the author in the manner specified by the author or licensor.
Bellan, Annick Harel
In this workshop, I will review the molecular bases of Epigenetics, as well as some essential but yet unsolved questions, which will be a subject of further discussion. As a part of it, a new hypothesis of the role of small non-coding RNAs in epigenetics will be presented.
 So I've changed a little bit the title actually. I've added, oh, non-coding RNAs in the story. So we'll start with a general view of what is epigenetics for those of you who don't know, essentially, mathematicians, I guess, are not very familiar with the concept. So let's start with genetics. You, of course, know about Mandelian transmission and genetics. You heard about it this morning. Genetics laws allow a same phenotype with different genotypes. For example, when you have a recessive inheritance of a trait. But genetics, if you take it, basically, does not predict different phenotypes with the same genotype. However, it's been known for a very long time, actually, that there are many cases of identical genotypes and different phenotypes, which says that genetics cannot explain everything. So I'll just give you a few examples of that. For example, the queen of the bees and the workers are generated from identical larvae. But they have very different phenotypes, as you can see here. And as you may know, another example, which is closer to us, is the cells from a single organism. All the cells from a complex organism come from a single cell. They have an identical genotype, as far as we can say. But they come from the same cells originally. And then they become quite different when we are with an embryo. And you have completely different cells, brain, muscle, guts. All these cells have the same genotype. But they have different phenotypes. So the question, which has actually been on for a long time, but it's solved now, is how these cells can have the same genotype, but completely different phenotype. And the answer comes from epigenetics. Now, the modern definition of epigenetics is the analysis of stable and reversible changes in gene expression that do not involve modification of genetic information. And how can this happen at the molecular level? So you know that genetic information is burned by DNA. And it's located in the cell nucleus, in blue here in this picture. But DNA is not naked. In fact, in a human cell nucleus, which has about 10 micrometer of diameter, there is about 2 meters of DNA. So these very small nucleus cannot accommodate these two meters of DNA without compaction. And in fact, DNA is compacted in the cells. I apologize for the resolution, which comes from the change of computer, I guess. So you have the naked form of the DNA, and then several degrees of compaction up to the most compacted form, which is the mitotic chromosome. Now, this compaction, in fact, is due to proteins, which are called the histone. So you have several of them. We are not going to go into the details here. But you have two rounds of DNA, which is wrapped around the core of histone proteins and with a regular disposition. So these are called the nucleosomes. And the nucleosomes, so this is the chain of nucleosomes, and then this chain can be compacted. And then the new chain is compacted again. And so you have different level of compaction. Now, the problem is that compacted chromatin, in the compacted chromatin, the DNA is not accessible for proteic cellular machineries. So that, and if you want to express a gene, you have to have access to the DNA, to the RNA transcription machineries, the RNA synthesizing machinery, so that, in fact, compacted chromatin is linked to inactive gene. And open chromatin, decompacted chromatin, are potentially active genes. And indeed, if you look at the cell nucleus, you have different degree of compaction that you can even see by electronic microscopy. And you can distinguish what is called eukromatin, which is little compacted and which includes active genes, from heterochromatin, which is highly compact and which includes inactive genes. Now, chromatin compaction is controlled by chemical modifications of the chromatin. The DNA can be modified. It's methylated. And the histones, the proteins on which it is wrapped, can also be modified. They have little tails protruding out of the nucleosome, which can be either acetylated, methylated, phosphorylated. And you have all sorts of different combinations of all these modifications of the histone tails. So that, and these modifications, these combinations of modifications are specific of the different type of chromatins. In heterochromatin, the highly compacted chromatin, inactive chromatin, DNA is methylated, histones are deacetylated. And you have methylation on certain residues of the histone tail, for example, as we can find. In contrast, when chromatin is active, in eukromatin, you have de-methylated DNA. Histones are acetylated, and they are methylated along all the residues, such as H3K4, for example. You can actually measure at the whole genome level these modifications, one by one. And this will give you the epigenome of the cell. Now, if you take the genome as a book, the epigenome will tell you which are the open pages. It's the epigenetic marks, which will select the open pages of the book. So this, if you want, is the eukromatin. You can read it. This is the heterochromatin. You cannot read it. So if we come back to the question of the cells which come from a single cell and have an identical phenotype, actually the difference is, at least in large part, due to the epigenome, because their epigenome is different. So if you take a stem cell, for example, you will have the genes A, B, and C, which are methylated, et cetera, and compacted. Whereas if you take its daughter cell, other genes will be methylated, compacted, et cetera. So the pattern of genes which are open and the pattern of genes which are closed are different between these two cells. So the main question appears to be solved. We know what make a different phenotype from a single genotype. But there are other open questions. One of the questions which is very important, actually, is, can epigenome be modified by external signal? It's a socially important question, because it includes the relationship between the genome and the environment. And you know all these problems created by the environment. Well, we know that external signals can modify the epigenome. Like you have a ligand, for example, which will bind to a receptor, activates a chain of transduction, and eventually will change the chromatin very locally at very specific loci from compacted to open, and will activate the gene. At a more organism level, if we come back to the B model, it's, in fact, an external signal, which is the royal nectar with which the queen is fed, which makes the whole difference between the worker and the queen. It is the fact that the queen is fed with this type of food, which modifies the epigenome of the larvae, and makes a queen. And it has been proven that some genes are methylated in the absence of royal nectar, and this will give a worker, whereas all the genes will be activated by the royal nectar. And these genes control the size of a reactivity, et cetera, of the future bee. In mammalians also, we have many examples of effect of an external signal on the epigenome. Here, for example, is the example of the dismyse, which are born from a stressed mother. So when the mouse is pregnant, you stress it by noise, different noises, or stuff like that. Now, the mouse, which are born from a mother or a stress during pregnancy, are themselves stressed, whereas the mouse, which is born from a well-treated mother, is not stressed. And it has been linked to the methylation of the gene, which is a gene which is expressed in the neurons, and which actually defects is associated with schizophrenia. And the mouse born from the stressed mother, this gene is methylated, whereas in the mouse born from a well-treated mother, the gene is not methylated. So it's expressed. So this clear environment, nutrition, external conditions affect the epigenome. Now, another very important question, and this one is not solved at all, is can epigenome modifications be transmitted to the next generations? Now, if we take a somatic cell, like for example, we have a culture, let's say fibroblasts. So differentiated cells. Then all the daughter cells of this fibroblast will be fibroblasts, which clearly indicates that the epigenome is transmitted from the mother cell to the daughter cells. Despite the fact, and I think it's a very interesting question actually, that during the mitosis, the chromosomes are highly condensed. It's the most condensed form of the chromosome. And despite this fact, they keep, they maintain this information. And actually, we don't know how. But now, if we take not the somatic cells, but the germ cells, is the epigenome transmitted to the descendants, where there are actually numerous studies in mouse and human, suggesting that it might be the case. And if we go back to the stressed mice, actually, the mice which are born from stressed mothers, they are stressed. But they also have a good probability of giving themselves birth to stressed descendants. Raising the possibility that this epigenomic status of feature has been transmitted. And there are numerous studies like that in the literature. However, this is a very controversial issue. As actually, these experiments are very difficult to interpret. Is the effect due to molecular transmission of the epigenome to the embryo in the germ cells? Or is it due to cultural factors and behavioral transmission? The stressed mother is stressed. She deals with, or it deals, if it's a mouse, with her infants in a very specific way. With a body factor, it's stressed, or they're a particular hormone. Exactly. It can be. Stress is chemical, don't you? The stress is chemical. But the way the children receive the stress, it will induce a chemical reaction in them as well. But it's a transmission is. What's an embryo? We're receiving this hormone. And who cares what you're receiving afterwards? Embryo in development was chemically modified? Yes. But if it gives birth, if it gives birth, the same embryo will give birth. It keeps chemical signature, not behavior. Well, we'll see that it cannot keep this chemical signature, at least not at the epigenomic level. Because if we move directly to the next slide, actually, the epigenetic marks are erased during development. They are erased, almost completely erased. So you can always say that maybe the almost is the fact that it cannot be really. So this is the. It was a chemistry in the blood of a mother. They erased here. But then beyond development, this chemistry of the mother. Yeah. That's why it's developed. That is OK for the. But that is OK for the first generation. No, no, but I see what Michel is saying. This is OK for the first generation, but it's not OK for the second or sometimes the third generation. OK, so at a very important stage. So here are, for example, the methylation marks. So you had the DNA from the mother and from the father. So it's methylated here. And then at a very important stage, which is actually the stage where the embryo appears and the appearance of the embryo in extend cells, then almost everything is erased. So the epigenetic marks are lost. And then they reappear and you have differentiation of the cells. So how could the marks be transmitted if they are erased during the development? This is a completely unsolved issue at this point. But you can ask the question, are the epigenetic marks the only players? Or are there other players involved? At the genomic level, of course. And good candidates are non-coding RNAs. Non-coding RNAs are transcribed from the non-coding genome. So it means that they don't have any open reading frame to make proteins. Previously, the non-coding genome was called JANG DNA because it was thought that it is absolutely useless. Now it's rather called the dark genome. Why? In fact, the complexity of organisms is not correlated with the gene numbers. So if we take, for example, C elegans, which has 90, not far from 20,000 genes, it's a little worm, which has very little complexity. Very little complexity. It's a very small animal as well. And if compared that to human, human is thought to have about 24,000 genes. So you have very little differences in the number of genes. So the complexity of an organism is not linked to the number of genes. However, it is inversely correlated with the percentage of coding sequences. The less coding sequences you have, the more complex the organism is. And in fact, in human, it's 97% of the genome, which is non-coding. All the protein ohm that you heard about this morning represents only 3% of the genome. The rest is non-coding. So if you take, for example, this could be a human chromosome. Well, the coding part is here in red. And all the rest is non-coding. So for long, this non-coding genome has been of no interest at all. Again, it was called the GEN, the GEN DNA. And then the discovery of small, non-coding RNAs triggered the interest for the non-coding genome. So the non-coding RNAs are the microRNAs that I'm sure you heard about many times. So they are, they've been discovered in C. elegans. And they are very small RNA sequences, which bind to the messenger RNA and prevents the synthesis of protein, the translation of the messenger RNA. But small, non-coding RNAs represent a very small part of the non-coding genome. They are very short, and there are a few thousand of them, so they don't represent a whole thing. Now we know that actually almost all the genome, it's even more than 70% of the genome, is transcribed. We know that thanks to these new sequencing technologies, which allow to see molecules which are very little represented in a population. Because what we do in these technologies is that we sequence one molecule, the molecules one by one. So if we do enough molecules, if you have a molecule which is very little represented, you can see it. And because of course the transcription of the whole genome does not give rise to very frequent RNAs, it's been totally ignored up to now. But now we know that almost all the genome is transcribed, and it's mostly transcribed in long, non-coding RNAs. And we actually know that long, non-coding RNAs are able to modify the epigenome. It's been known for very long that there is a non-coding RNA, which is called XIST, which covers one of the X chromosomes in somatic cells of mammalian females, resulting in the epigenetic silencing of the anti-chromosome. You know that you have to have gene dosage on the X chromosome so that male and female have the same level of expression of the genes which are in the X chromosome. So in nature, there are different ways to achieve that. And in mammalian cells, one of the X chromosomes is inactivated. And it's inactivated thanks to this long, non-coding RNA, although the precise mechanism is not known. Do you know that is it known with every single one of those six bits of RNA are actually functional? No, of course not. Not yet. How will you determine that? Well, it's really starting now. It's been started for, I would say, five years now. What you do is, as usual, to analyze the function, you kill the molecule. No, but you have 70% of the genome is. It's even more than that. Well, you just said it's 70%, right? Yeah. So how are you going to walk through 70% of the genome and eliminate every single one? That's insane. Well, you will have to do that. Because there is no way that you can do a cell with only the 3% of DNA. So how would you test that? What people are doing right now is that they are looking at specific long, non-coding RNAs, which are differentially expressed in this or that situation in healthy cells versus whatever disease, or cancer, or whatever. And then they look into these differentially expressed. I think it's a little bit like what was done with the genes at the beginning. At the beginning, people looked at one gene, which is differently, blah, blah. And we didn't have the whole genome sequence, and blah, blah. Now, if the question is, did someone imagine a way to prove that this? I mean, there are many different sequences there. How would you imagine the index of time? Yeah. So the question is, did someone imagine how to prove that the 70% are functional? I don't think anyone did at this point. Come on. We know that most of it is not functional, because most of it is not under constraint. Well, that's not right. I think that's not the right answer. And I have a slide at the end, too. What do you prefer, too? Yeah, yeah, yeah, sure, sure, sure. No, no, no, no, no. No, no, we can have discussion. I don't think it's the right answer, because if you take only the constraint, the evolution constraint, then you will say that only the coding part is. And then you will conclude that there is absolutely or almost no difference between a mouse and a human, because it's 99.9% the same genes. So you have to admit that a zone without constraint plays a role in this. It's not, in fact, being different with a mouse and a human. Biologically, I think, negligible. In a reasonable, unprovaled respect with Serbia, I think objectively, why is there a big difference between mouse and human? The difference is not big, maybe, but it's the most important. We do not have whiskers. No, no, but I have the feeling it's a little bit more than that. Actually, Misha, you know that mouse is not a good model. For most of the diseases, because the mouse does not behave like the human. It's not more complex, but it's different. So to say, well, at least you need to have a measure. What do you mean? At least what you mean? Yeah. But you have this measure. The only point that can be said is that a mouse is different from a human. But if you take the genes, the enzymes and all that, they are very, very alike. The word you say, it's not different. The question is what you emphasize. It's appearance is different. It's not only the appearance. Even biologically, the mouse is different. For example, the lifespan, a mouse lives two years. There's an number of parameters. If you look at the parameters, there are 1,000 parameters in different channels. For example, one parameter the size. Come on. It's not big, big, big. You're being small. Yes. Another parameter is the thinking that the mouse doesn't have at this point. Or maybe yes. But not the same type of thinking. Not the same type of thinking. We tend to overemphasize humanity. Our perspective is just on the view. That's my point. What you're saying is that we are animals. And I think that's absolutely correct. But then there are many differences. And it's not only the mouse and the human. It's also, again, the C. elegans' worm. It's completely different. I mean, there are many, many genes which are in common. Actually, the coding sequence of genes, of the mouse and human, are almost identical. That's actually a good point because what is very diverse is the non-coding region. Exactly. It's my slide, actually. It's my last slide. Let's move to the last slide. The one that could determine, theoretically, what is a mouse? Exactly. That's my last slide. Maybe we can skip the last slide. OK, so what we can think is that maybe a non-coding RNA is to keep the memory. They might be in the cytoplasm of the maternal DNA, or they might be associated with the sperm DNA, whatever. But they can keep maybe the memory of these epigenetic marks. And then we come to the last slide. So there are all the open questions. So non-coding RNAs represent 97% of the genome. They are thus a huge molecular reason where to explain yet unexplained functions. And there are many of the functions which are not explained by genes, simply by genes. Also, and that's exactly the point of the discussion, in contrast to protein coding genes, which may be very similar between the different species. Non-coding RNAs are highly variable. They are not submitted to constraints from one species to the other and from one individual to the other, within the same species. That they have the potential to play an essential role in the differences between species and in the difference between individuals within a species. Yes? I just want to talk to your point about the coding regions being the same. That's like saying that in the human, the eye cells are really different from the cells on your hands, right? Like a difference between a mouse and a human. It has nothing to do with the different coding regions. It has to do with the way how the coding regions are regulated, right? Yeah, yeah, but in total, I mean, yeah, this difference within an organism. But in total, if you take the, it's like, I would say, the, whatever. In total, if you take the human and the mouse, they are, and the genome in total, they are not identical, but very similar. Yeah, but it's not about the actual sequence. It's about what is being regulated. What is being transcribed when? Yeah. The timing of the expression might be different. But actually, the non-coding region can regulate the expression of the coding region. Of course. So because the non-coding region is different, it could determine the difference in the expression. Of course. But my feeling, that's only a feeling, of course, is that the non-coding region doesn't do only, I mean, right now, we see it through the eyes of the genetics and the coding sequences. Everything, the game comes back to the coding sequences, OK? Everything is due to gene and protein. I don't think this is the case. And I have the feeling that the non-coding RNAs, they play a role in the, for example, in the brain functioning. So you started with the difference between different cells in the same organism, with brain and whatever other cells got. And about that, we already asked biologists to record development. And we have the answers already in the genome, because we have the description factors and then hence source. And we have, I'm not saying at all, but we are beginning to, yes, I just wanted to make a point. So we are beginning to understand it without looking at the non-coding. We know, at least one example, exists, that it is functioning. So there will be more. Although we don't know how it works, but we don't. We don't. No, but I mean, at least we know what it does. We are throwing it at 97% of the genome to ask biologists to figure out how we're going to figure out what it does. But the question is a good question, of course. Now, if we think, I don't think that the whole development is due to the genes. And if you take the example of the microRNAs, they were absolutely unknown. And so we didn't even think that this thing were working. So I wouldn't be this. So one point that we cannot, it is not completely true that they are not under constraints, because in different species, they keep the same position in some chromosomes and seems to be related to these chromatin organization maps that are. The sequence is under less constraints. And there are differences in the non-coding genomes. They are parts which are more common or more conserved and parts which are less. There are some, as if their chromosomal organization seem to be conserved across species. And there may be some functions at least for part of them to this chromatin. Yeah. What you're saying, if I understand it properly, is that they can be common functions between species for the non-coding RNAs. And what I'm adding is that might also be species-specific functions or even individual-specific functions. All right. Yeah. Let's suppose that you make an official genome where you get rid of all the everything. And you only have to open the frames. Yeah. Where would that happen? I don't think any. But maybe we should do it. But I don't think that the cell would line. I don't think they would line. It's the kinetics. It's the kinetics. Chromachylamoform. Chromachylamoform. Chromosome. No, no, no, no. I didn't say that. I said that you get rid of this bit. So you make only one small chromosome? You make one small chromosome with a coding sequence? I think actually very, no, but the way it's organized is chromatin in a particular shape. You need this mechanically, yeah? No, no, no. So what I'm just saying is that you convert a human being into a yeast. And I don't mean trans-tune. But I'm not sure that human cell will live. I don't know. I wish I, we have to try. We have to try. We have to try. Because, because the rest, because the rest of the cell has been, no, because I think, I'm not saying that I'm right, okay? It's just what I think is that the rest of the cell has been designed, I'm not designed, but has evolved to work with a complex genome. And I'm not sure, yeah. I'm not sure that if you take, but it would be an interesting experiment to do. And actually, I have a kind of provocative question. You explain us about the genetic marks, which connected with like chromatin, blah, blah, blah. And now you say about non-covinarinase, and of course the third question, how you think, you suggest they interplay between them, how this non-covinarinase can be involved? Yeah, I didn't go into the details. Yeah, yeah. I didn't go into the details. But for example, the XIST. No, but the XIST RNA modifies, yeah. The XIST RNA modifies the epigenetic marks on the chromosome, on the X chromosome, which is inactivated, okay? And there are other examples of that. So the non-covinarinase, they had the capacity to modify the genetic epigenetic mark. But I don't think it's the only way they work, that's my point. Okay, let's go. No, Anik, you choose who you want. You did not speak of plumps. I think it has well been shown some couple of years ago already transmission up to 8 or 10 generations in Arabi. Arabidopsis. I'm not a plant specialist, I have to say. No, no, no. I'm not a plant specialist, I have to say. Yeah, no, no. What is Mr. Antelion? Epigenetic transmission, the Vincent Collore. Yeah, yeah. It made a big jump in the literature, but so I wanted to know what is, since this... But the problem is, well, the problem in plants, I don't know if there is this erasement of the, you know, epigenetic marks. I'm sorry, I'm not a plant specialist, I don't have the answer. I know in Madal it appears, it occurs, but... I don't know if I'm here. So, a few comments. So, first of all, in your experiment of getting rid of most of the genome and seeing what happens, that's been done in nature several times. So, for example, the puffer fish has a genome which is 100 times smaller than other fish and humans, and it's still a fish, okay? So this proves that most of the non-coning genome is not required to make a fish. For this fish. So why do we study all this? Well... Nobody... Please, please, if... No, no, if I may comment, make me comment. If the evolution constraint is so strong and we don't need this 97% of genome, why has it been kept during the evolution? This is population genetics, so genome size is not correlated to complexity in any way. Genome size is to do with the strength of natural selection, so species which have very small, effective population sizes have very big genomes, so plants. Humans have a very small, effective population size. We went through a botanical history. This is why our genome is full of rubbish, okay? This is very well understood. Bacteria, fungi have very effective, very large effect of population sizes, very strong natural selection. Every single base pair is under selection and has a... has a fitness cost when you do something. Actually, it is not absolutely correct because it comes back to plants. In plants it is well known, for example, if you cut half, at least half of non-coding genome of......arabidopsis, it's not coding part. Why is there arabidopsis? It creates a normal plan from this story. But this is only in plants and maybe only arabidopsis, but this is very interesting thing. But maybe it is somehow connected with the case that in animals we have much less plasticity than in plants. But it just made the opposite point. It just made the opposite point. It's a fish that is a natural experiment. I told you, you can film if you said it. I have, so you agree. I agree, I agree. Then I agree, yes. But I don't know about animals. He's telling you about animals. The same thing happens in animals. You have very different genome sizes for animals which are very similar to each other. So the genome size is not related to complexity. You don't need most of the data. But you say about comparison and I say about experiment. It is not the same. Because comparison still don't say the actual result. Okay, but they agree with each other. They agree with each other. Another thing is also this measuring which bits of the genome are important. So there's two ways we can do this. One is by conservation during evolution. And this estimates that roughly 8% of the human genome is under constrained. As in it has been under selection during primary evolution. And the other one now is because we have so many sequences of individual human genomes. We can measure the allele frequency, the frequency of the mutations at every base. So the human population is large enough such that every generation would be in saturation metagenesis for the human genome now. So somebody is born with a mutation everywhere that is compatible with life. And through sequencing millions of genomes now we know the frequency at which you get mutations in the population. But when you say sequencing the whole genome or only the... It's mostly the exomes that are becoming the whole genome. And as this gets bigger and bigger then we will be able to measure exactly how important every base of the human genome is. So this is the other way to answer your experiment. It's like we will have the numbers to do this to say this base is exactly this important for the fitness within... But again, this is not taking into account the individual differences. So maybe this base is very important in general. But this other base which is only present in two people is the one base which makes the difference between these two people. Excuse me, I don't understand where this 97% figure comes from then. I didn't do the experiment myself but it's the percentage of DNA which open reading frame of sufficient size to make a protein. Because what I heard is that like 8% has been shown that has some... Well, it depends on the species. So in human it's 3% but in other species it's more. No, but the 97% is definitely not all non-coding RNAs. This is your point. A lot of it is... A lot of what? It's non-transcribed at all, you mean? Yeah, well, of course. Well, at least there are parts of the genome that we can not even sequence properly. So of course we cannot know if they are transcribed or not. But they are going to come to 100% of course. Yes. So why are you also focused on the genome? There are many more molecules which are passed from one generation to the next. And I'm sure you've talked about germplasm and glycocontregated proteins and whatnot. I'm just curious to know. No, they might be part. But at some point you have to remodel the genome because if you take after the erasement of the marks, you can re-colore the marks. And you start with the stem cell, which is a blah, blah, blah. And so glycoconjugated, they can induce the modification, the epigenetic modification question. Yes, why not? But at this point it has not been proven that any sugar influences the genome. So, I mean, the stretch of the genome. Did anybody ever do an experiment by microinjection of long non-coding RNAs into a protein? Yes, that. Oh, in fertilization. And to show that they actually affect the... Not yet. So how do we know they are important? It's all correlation. It's an open question again. It's not a demonstrated fact. Why do they experiment? She wants us to do it. She's just suggesting an idea. She's just coming up with an idea. That's it. I totally agree that this is not proven. But there are many examples of RNAs, non-coding RNAs, which are modifying the genome. There exists one. And there is another one, which is very interesting, is the parametria. The parametria has two nuclei, micronuclei and a micronuclei. And the micronuclei has actually the whole genome and is very condensed. It's like the storage of the genome. And the other nuclei, nucleus, is very large. It has uncondensed DNA, and it's the part which is expressed. And during the division, the cell division, the micronuclei will give rise to a micro and a micronuclei. And the macronuclei, the sequences which are not expressed, are deleted. And this is directed by RNAs. So there are examples, many examples. But it's parametria. Sure. It's not a mammoth. No, sure, of course. But it is exactly in parametria that you have the heredity, non-DNAs. Oh, no, but... Thomas Sonebaum. That's exactly the history of life. No, no, but I'm not talking about the genetics of the animals. I'm talking about the molecular... I'm talking about the mechanism. About something which is different. Yes. Of course, but the molecular mechanism exists. That's what I'm saying, okay? In C-elegan, it was done in C-elegan. Yeah, of course. In C-elegan, also. Yeah, it was shown genetically. But in a way, microRNAs, not so well-teachable now as an example of non-coding, of this long non-coding RNAs, because they have their genes. They are transcribed as genes, but not protein genes. They are still not this junk of black... Yeah, but those are not protein genes either. No, they are not. They are not protein genes, but they are not on the other... They are transcribed. They are... There is a long association between long-coding RNA and disease. In disease. For example, in cancer. Yeah, yeah, absolutely. I believe in diabetes, maybe, as well. No, no, no. In cancer, very well. There are several long... There are those which are really looked at now. So, 50% are coding from this long non-coding. 50% can code for micro-portings. Right. Yes, that's right. But it has not been proven that these micro-proteins... Some of these micro-portings are very important. Yeah, yeah, yeah. I'm aware of that. They are very small polypeptides. Very small peptides, actually. Yeah. So, it's not proven that they have any function at this point. But it's... Yeah, they are part of this on coding. They have very small open reading plans. Do you synthesize? Many of them are not synthesized? No, they are synthesized and they have a function. Well, the function is not for sure. They are synthesized. Yeah, they are synthesized. Do you think they are only after a long, long, long time synthesized by being digested? Yeah, if they are very small, they can come from... From the point of extension to sideways. Yeah, but one reason also why they are studied is because in different tissues, long RNAs have the same expression pattern. So, if you take a liver or a neurons, you see the same long RNAs expressed in the same tissues. So, this is also one reason why they are... At some point, they try to understand what they do in the cell. Because there are kind of reproducible expression patterns for these long RNAs in osteoarthritis tissues. Well, but that's a correlation and also it can be because of the different types of transcription factors in the different tissues. Right, they said they seem to be under some regulations. Yes. Oh, yeah. Okay, so we can take one last question. Do we have one? Everybody is angry, I think. Everybody is angry.
 So I've changed a little bit the title actually.  I've added, oh, non-coding RNAs in the story.  So we'll start with a general view of what is epigenetics  for those of you who don't know, essentially,  mathematicians, I guess, are not very familiar with the concept.  So let's start with genetics.  You, of course, know about Mandelian transmission  and genetics.  You heard about it this morning.  Genetics laws allow a same phenotype  with different genotypes.  For example, when you have a recessive inheritance  of a trait.  But genetics, if you take it, basically,  does not predict different phenotypes  with the same genotype.  However, it's been known for a very long time, actually,  that there are many cases of identical genotypes  and different phenotypes, which says  that genetics cannot explain everything.  So I'll just give you a few examples of that.  For example, the queen of the bees and the workers  are generated from identical larvae.  But they have very different phenotypes, as you can see here.  And as you may know, another example, which is closer to us,  is the cells from a single organism.  All the cells from a complex organism  come from a single cell.  They have an identical genotype, as far as we can say.  But they come from the same cells originally.  And then they become quite different when we are with an  embryo.  And you have completely different cells, brain, muscle,  guts.  All these cells have the same genotype.  But they have different phenotypes.  So the question, which has actually  been on for a long time, but it's solved now,  is how these cells can have the same genotype,  but completely different phenotype.  And the answer comes from epigenetics.  Now, the modern definition of epigenetics  is the analysis of stable and reversible changes  in gene expression that do not involve  modification of genetic information.  And how can this happen at the molecular level?  So you know that genetic information is burned by DNA.  And it's located in the cell nucleus,  in blue here in this picture.  But DNA is not naked.  In fact, in a human cell nucleus,  which has about 10 micrometer of diameter,  there is about 2 meters of DNA.  So these very small nucleus cannot accommodate these two  meters of DNA without compaction. And in fact, DNA  is compacted in the cells.  I apologize for the resolution, which  comes from the change of computer, I guess.  So you have the naked form of the DNA,  and then several degrees of compaction  up to the most compacted form, which is the mitotic chromosome.  Now, this compaction, in fact, is due to proteins, which  are called the histone.  So you have several of them.  We are not going to go into the details here.  But you have two rounds of DNA, which  is wrapped around the core of histone proteins  and with a regular disposition.  So these are called the nucleosomes.  And the nucleosomes, so this is the chain of nucleosomes,  and then this chain can be compacted.  And then the new chain is compacted again.  And so you have different level of compaction.  Now, the problem is that compacted chromatin,  in the compacted chromatin, the DNA  is not accessible for proteic cellular machineries.  So that, and if you want to express a gene,  you have to have access to the DNA, to the RNA transcription  machineries, the RNA synthesizing machinery,  so that, in fact, compacted chromatin  is linked to inactive gene.  And open chromatin, decompacted chromatin,  are potentially active genes.  And indeed, if you look at the cell nucleus,  you have different degree of compaction  that you can even see by electronic microscopy.  And you can distinguish what is called eukromatin, which  is little compacted and which includes active genes,  from heterochromatin, which is highly compact  and which includes inactive genes.  Now, chromatin compaction is controlled  by chemical modifications of the chromatin.  The DNA can be modified.  It's methylated.  And the histones, the proteins on which it is wrapped,  can also be modified.  They have little tails protruding out  of the nucleosome, which can be either acetylated,  methylated, phosphorylated.  And you have all sorts of different combinations  of all these modifications of the histone tails.  So that, and these modifications, these combinations  of modifications are specific of the different type  of chromatins.  In heterochromatin, the highly compacted chromatin,  inactive chromatin, DNA is methylated,  histones are deacetylated.  And you have methylation on certain residues  of the histone tail, for example, as we can find.  In contrast, when chromatin is active, in eukromatin,  you have de-methylated DNA.  Histones are acetylated, and they are  methylated along all the residues,  such as H3K4, for example.  You can actually measure at the whole genome level  these modifications, one by one.  And this will give you the epigenome of the cell.  Now, if you take the genome as a book,  the epigenome will tell you which are the open pages.  It's the epigenetic marks, which will select the open pages  of the book.  So this, if you want, is the eukromatin.  You can read it.  This is the heterochromatin.  You cannot read it.  So if we come back to the question of the cells which  come from a single cell and have an identical phenotype,  actually the difference is, at least in large part,  due to the epigenome, because their epigenome is different.  So if you take a stem cell, for example,  you will have the genes A, B, and C, which  are methylated, et cetera, and compacted.  Whereas if you take its daughter cell,  other genes will be methylated, compacted, et cetera.  So the pattern of genes which are open and the pattern of genes  which are closed are different between these two cells.  So the main question appears to be solved.  We know what make a different phenotype  from a single genotype.  But there are other open questions.  One of the questions which is very important, actually,  is, can epigenome be modified by external signal?  It's a socially important question,  because it includes the relationship between the genome  and the environment.  And you know all these problems created by the environment.  Well, we know that external signals  can modify the epigenome.  Like you have a ligand, for example,  which will bind to a receptor, activates a chain of transduction,  and eventually will change the chromatin very locally  at very specific loci from compacted to open,  and will activate the gene.  At a more organism level, if we come back to the B model,  it's, in fact, an external signal,  which is the royal nectar with which the queen is fed, which  makes the whole difference between the worker and the queen.  It is the fact that the queen is fed with this type of food,  which modifies the epigenome of the larvae, and makes a queen.  And it has been proven that some genes are methylated  in the absence of royal nectar, and this will give a worker,  whereas all the genes will be activated by the royal nectar.  And these genes control the size of a reactivity, et cetera,  of the future bee.  In mammalians also, we have many examples  of effect of an external signal on the epigenome.  Here, for example, is the example of the dismyse, which  are born from a stressed mother.  So when the mouse is pregnant, you  stress it by noise, different noises, or stuff like that.  Now, the mouse, which are born from a mother  or a stress during pregnancy, are themselves stressed,  whereas the mouse, which is born from a well-treated mother,  is not stressed.  And it has been linked to the methylation of the gene, which  is a gene which is expressed in the neurons,  and which actually defects is associated with schizophrenia.  And the mouse born from the stressed mother,  this gene is methylated, whereas in the mouse born  from a well-treated mother, the gene is not methylated.  So it's expressed.  So this clear environment, nutrition, external conditions  affect the epigenome.  Now, another very important question,  and this one is not solved at all,  is can epigenome modifications be transmitted  to the next generations?  Now, if we take a somatic cell, like for example,  we have a culture, let's say fibroblasts.  So differentiated cells.  Then all the daughter cells of this fibroblast  will be fibroblasts, which clearly indicates  that the epigenome is transmitted from the mother cell  to the daughter cells.  Despite the fact, and I think it's a very interesting question  actually, that during the mitosis,  the chromosomes are highly condensed.  It's the most condensed form of the chromosome.  And despite this fact, they keep, they maintain this information.  And actually, we don't know how.  But now, if we take not the somatic cells,  but the germ cells, is the epigenome  transmitted to the descendants, where there are actually  numerous studies in mouse and human,  suggesting that it might be the case.  And if we go back to the stressed mice,  actually, the mice which are born from stressed mothers,  they are stressed.  But they also have a good probability  of giving themselves birth to stressed descendants.  Raising the possibility that this epigenomic status of feature  has been transmitted.  And there are numerous studies like that in the literature.  However, this is a very controversial issue.  As actually, these experiments are very difficult to interpret.  Is the effect due to molecular transmission  of the epigenome to the embryo in the germ cells?  Or is it due to cultural factors and behavioral transmission?  The stressed mother is stressed.  She deals with, or it deals, if it's a mouse,  with her infants in a very specific way.  With a body factor, it's stressed,  or they're a particular hormone.  Exactly.  It can be.  Stress is chemical, don't you?  The stress is chemical.  But the way the children receive the stress,  it will induce a chemical reaction in them as well.  But it's a transmission is.  What's an embryo?  We're receiving this hormone.  And who cares what you're receiving afterwards?  Embryo in development was chemically modified?  Yes.  But if it gives birth, if it gives birth,  the same embryo will give birth.  It keeps chemical signature, not behavior.  Well, we'll see that it cannot keep this chemical signature,  at least not at the epigenomic level.  Because if we move directly to the next slide,  actually, the epigenetic marks are  erased during development.  They are erased, almost completely erased.  So you can always say that maybe the almost is the fact  that it cannot be really.  So this is the.  It was a chemistry in the blood of a mother.  They erased here.  But then beyond development, this chemistry of the mother.  Yeah.  That's why it's developed.  That is OK for the.  But that is OK for the first generation.  No, no, but I see what Michel is saying.  This is OK for the first generation,  but it's not OK for the second or sometimes the third generation.  OK, so at a very important stage.  So here are, for example, the methylation marks.  So you had the DNA from the mother and from the father.  So it's methylated here.  And then at a very important stage,  which is actually the stage where the embryo appears  and the appearance of the embryo in extend cells,  then almost everything is erased.  So the epigenetic marks are lost.  And then they reappear and you have differentiation  of the cells.  So how could the marks be transmitted  if they are erased during the development?  This is a completely unsolved issue at this point.  But you can ask the question, are the epigenetic marks  the only players?  Or are there other players involved?  At the genomic level, of course.  And good candidates are non-coding RNAs.  Non-coding RNAs are transcribed from the non-coding genome.  So it means that they don't have any open reading  frame to make proteins.  Previously, the non-coding genome was called JANG DNA  because it was thought that it is absolutely useless.  Now it's rather called the dark genome.  Why?  In fact, the complexity of organisms  is not correlated with the gene numbers.  So if we take, for example, C elegans, which has 90,  not far from 20,000 genes, it's a little worm,  which has very little complexity.  Very little complexity.  It's a very small animal as well.  And if compared that to human, human is  thought to have about 24,000 genes.  So you have very little differences  in the number of genes.  So the complexity of an organism is not  linked to the number of genes.  However, it is inversely correlated  with the percentage of coding sequences.  The less coding sequences you have, the more complex  the organism is.  And in fact, in human, it's 97% of the genome,  which is non-coding.  All the protein ohm that you heard about this morning  represents only 3% of the genome.  The rest is non-coding.  So if you take, for example, this could be a human chromosome.  Well, the coding part is here in red.  And all the rest is non-coding.  So for long, this non-coding genome  has been of no interest at all.  Again, it was called the GEN, the GEN DNA.  And then the discovery of small, non-coding RNAs  triggered the interest for the non-coding genome.  So the non-coding RNAs are the microRNAs  that I'm sure you heard about many times.  So they are, they've been discovered in C. elegans.  And they are very small RNA sequences,  which bind to the messenger RNA and prevents  the synthesis of protein, the translation of the messenger  RNA.  But small, non-coding RNAs represent a very small part  of the non-coding genome.  They are very short, and there are a few thousand of them,  so they don't represent a whole thing.  Now we know that actually almost all the genome,  it's even more than 70% of the genome, is transcribed.  We know that thanks to these new sequencing technologies,  which allow to see molecules which are very little  represented in a population.  Because what we do in these technologies  is that we sequence one molecule, the molecules one by one.  So if we do enough molecules, if you  have a molecule which is very little represented,  you can see it.  And because of course the transcription of the whole  genome does not give rise to very frequent RNAs,  it's been totally ignored up to now.  But now we know that almost all the genome is transcribed,  and it's mostly transcribed in long, non-coding RNAs.  And we actually know that long, non-coding RNAs  are able to modify the epigenome.  It's been known for very long that there  is a non-coding RNA, which is called XIST, which covers one  of the X chromosomes in somatic cells of mammalian females,  resulting in the epigenetic silencing  of the anti-chromosome.  You know that you have to have gene dosage on the X chromosome  so that male and female have the same level of expression  of the genes which are in the X chromosome.  So in nature, there are different ways to achieve that.  And in mammalian cells, one of the X chromosomes  is inactivated.  And it's inactivated thanks to this long, non-coding RNA,  although the precise mechanism is not known.  Do you know that is it known with every single one  of those six bits of RNA are actually functional?  No, of course not.  Not yet.  How will you determine that?  Well, it's really starting now.  It's been started for, I would say, five years now.  What you do is, as usual, to analyze the function,  you kill the molecule.  No, but you have 70% of the genome is.  It's even more than that.  Well, you just said it's 70%, right?  Yeah.  So how are you going to walk through 70% of the genome  and eliminate every single one?  That's insane.  Well, you will have to do that.  Because there is no way that you can do a cell  with only the 3% of DNA.  So how would you test that?  What people are doing right now is  that they are looking at specific long, non-coding RNAs,  which are differentially expressed in this or that  situation in healthy cells versus whatever disease,  or cancer, or whatever.  And then they look into these differentially expressed.  I think it's a little bit like what  was done with the genes at the beginning.  At the beginning, people looked at one gene,  which is differently, blah, blah.  And we didn't have the whole genome sequence, and blah, blah.  Now, if the question is, did someone imagine a way  to prove that this?  I mean, there are many different sequences there.  How would you imagine the index of time?  Yeah.  So the question is, did someone imagine  how to prove that the 70% are functional?  I don't think anyone did at this point.  Come on.  We know that most of it is not functional,  because most of it is not under constraint.  Well, that's not right.  I think that's not the right answer.  And I have a slide at the end, too.  What do you prefer, too?  Yeah, yeah, yeah, sure, sure, sure.  No, no, no, no, no.  No, no, we can have discussion.  I don't think it's the right answer,  because if you take only the constraint, the evolution  constraint, then you will say that only the coding part is.  And then you will conclude that there is absolutely  or almost no difference between a mouse and a human,  because it's 99.9% the same genes.  So you have to admit that a zone without constraint  plays a role in this.  It's not, in fact, being different with a mouse  and a human.  Biologically, I think, negligible.  In a reasonable, unprovaled respect with Serbia,  I think objectively, why is there a big difference  between mouse and human?  The difference is not big, maybe, but it's the most important.  We do not have whiskers.  No, no, but I have the feeling it's a little bit more  than that.  Actually, Misha, you know that mouse is not a good model.  For most of the diseases, because the mouse does not  behave like the human.  It's not more complex, but it's different.  So to say, well, at least you need to have a measure.  What do you mean?  At least what you mean?  Yeah.  But you have this measure.  The only point that can be said is that a mouse is different  from a human.  But if you take the genes, the enzymes and all that,  they are very, very alike.  The word you say, it's not different.  The question is what you emphasize.  It's appearance is different.  It's not only the appearance.  Even biologically, the mouse is different.  For example, the lifespan, a mouse lives two years.  There's an number of parameters.  If you look at the parameters, there are 1,000 parameters  in different channels.  For example, one parameter the size.  Come on.  It's not big, big, big.  You're being small.  Yes.  Another parameter is the thinking that the mouse doesn't  have at this point.  Or maybe yes.  But not the same type of thinking.  Not the same type of thinking.  We tend to overemphasize humanity.  Our perspective is just on the view.  That's my point.  What you're saying is that we are animals.  And I think that's absolutely correct.  But then there are many differences.  And it's not only the mouse and the human.  It's also, again, the C. elegans' worm.  It's completely different.  I mean, there are many, many genes which are in common.  Actually, the coding sequence of genes, of the mouse and human,  are almost identical.  That's actually a good point because what is very diverse  is the non-coding region.  Exactly.  It's my slide, actually.  It's my last slide.  Let's move to the last slide.  The one that could determine, theoretically, what is a mouse?  Exactly.  That's my last slide.  Maybe we can skip the last slide.  OK, so what we can think is that maybe a non-coding RNA  is to keep the memory.  They might be in the cytoplasm of the maternal DNA,  or they might be associated with the sperm DNA, whatever.  But they can keep maybe the memory of these epigenetic marks.  And then we come to the last slide.  So there are all the open questions.  So non-coding RNAs represent 97% of the genome.  They are thus a huge molecular reason  where to explain yet unexplained functions.  And there are many of the functions  which are not explained by genes, simply by genes.  Also, and that's exactly the point of the discussion,  in contrast to protein coding genes, which  may be very similar between the different species.  Non-coding RNAs are highly variable.  They are not submitted to constraints  from one species to the other and from one individual  to the other, within the same species.  That they have the potential to play an essential role  in the differences between species  and in the difference between individuals within a species.  Yes?  I just want to talk to your point  about the coding regions being the same.  That's like saying that in the human,  the eye cells are really different from the cells  on your hands, right?  Like a difference between a mouse and a human.  It has nothing to do with the different coding regions.  It has to do with the way how the coding regions are regulated,  right?  Yeah, yeah, but in total, I mean, yeah,  this difference within an organism.  But in total, if you take the, it's like, I would say,  the, whatever.  In total, if you take the human and the mouse,  they are, and the genome in total,  they are not identical, but very similar.  Yeah, but it's not about the actual sequence.  It's about what is being regulated.  What is being transcribed when?  Yeah.  The timing of the expression might be different.  But actually, the non-coding region  can regulate the expression of the coding region.  Of course.  So because the non-coding region is different,  it could determine the difference in the expression.  Of course.  But my feeling, that's only a feeling, of course,  is that the non-coding region doesn't do only, I mean,  right now, we see it through the eyes of the genetics  and the coding sequences.  Everything, the game comes back to the coding sequences, OK?  Everything is due to gene and protein.  I don't think this is the case.  And I have the feeling that the non-coding RNAs,  they play a role in the, for example,  in the brain functioning.  So you started with the difference  between different cells in the same organism, with brain  and whatever other cells got.  And about that, we already asked biologists  to record development.  And we have the answers already in the genome,  because we have the description factors and then hence source.  And we have, I'm not saying at all,  but we are beginning to, yes, I just  wanted to make a point.  So we are beginning to understand it  without looking at the non-coding.  We know, at least one example, exists,  that it is functioning.  So there will be more.  Although we don't know how it works, but we don't.  We don't.  No, but I mean, at least we know what it does.  We are throwing it at 97% of the genome to ask biologists  to figure out how we're going to figure out what it does.  But the question is a good question, of course.  Now, if we think, I don't think that the whole development  is due to the genes.  And if you take the example of the microRNAs,  they were absolutely unknown.  And so we didn't even think that this thing were working.  So I wouldn't be this.  So one point that we cannot, it is not completely true  that they are not under constraints,  because in different species, they  keep the same position in some chromosomes  and seems to be related to these chromatin organization  maps that are.  The sequence is under less constraints.  And there are differences in the non-coding genomes.  They are parts which are more common or more conserved  and parts which are less.  There are some, as if their chromosomal organization  seem to be conserved across species.  And there may be some functions at least for part of them  to this chromatin.  Yeah.  What you're saying, if I understand it properly,  is that they can be common functions between species  for the non-coding RNAs.  And what I'm adding is that might also be  species-specific functions or even  individual-specific functions.  All right.  Yeah.  Let's suppose that you make an official genome where  you get rid of all the everything.  And you only have to open the frames.  Yeah.  Where would that happen?  I don't think any.  But maybe we should do it.  But I don't think that the cell would line.  I don't think they would line.  It's the kinetics.  It's the kinetics.  Chromachylamoform.  Chromachylamoform.  Chromosome.  No, no, no, no.  I didn't say that.  I said that you get rid of this bit.  So you make only one small chromosome?  You make one small chromosome with a coding sequence?  I think actually very, no, but the way it's organized  is chromatin in a particular shape.  You need this mechanically, yeah?  No, no, no.  So what I'm just saying is that you convert a human being  into a yeast.  And I don't mean trans-tune.  But I'm not sure that human cell will live.  I don't know.  I wish I, we have to try.  We have to try.  We have to try.  Because, because the rest, because the rest of the cell has been,  no, because I think, I'm not saying that I'm right, okay?  It's just what I think is that the rest of the cell has been designed,  I'm not designed, but has evolved to work with a complex genome.  And I'm not sure, yeah.  I'm not sure that if you take, but it would be an interesting experiment to do.  And actually, I have a kind of provocative question.  You explain us about the genetic marks, which connected with like chromatin,  blah, blah, blah.  And now you say about non-covinarinase, and of course the third question,  how you think, you suggest they interplay between them,  how this non-covinarinase can be involved?  Yeah, I didn't go into the details.  Yeah, yeah.  I didn't go into the details.  But for example, the XIST.  No, but the XIST RNA modifies, yeah.  The XIST RNA modifies the epigenetic marks on the chromosome,  on the X chromosome, which is inactivated, okay?  And there are other examples of that.  So the non-covinarinase, they had the capacity to modify the genetic epigenetic mark.  But I don't think it's the only way they work, that's my point.  Okay, let's go.  No, Anik, you choose who you want.  You did not speak of plumps.  I think it has well been shown some couple of years ago already transmission up to 8 or 10 generations in Arabi.  Arabidopsis.  I'm not a plant specialist, I have to say.  No, no, no.  I'm not a plant specialist, I have to say.  Yeah, no, no.  What is Mr. Antelion?  Epigenetic transmission, the Vincent Collore.  Yeah, yeah.  It made a big jump in the literature, but so I wanted to know what is, since this...  But the problem is, well, the problem in plants, I don't know if there is this erasement of the, you know, epigenetic marks.  I'm sorry, I'm not a plant specialist, I don't have the answer.  I know in Madal it appears, it occurs, but...  I don't know if I'm here.  So, a few comments.  So, first of all, in your experiment of getting rid of most of the genome and seeing what happens, that's been done in nature several times.  So, for example, the puffer fish has a genome which is 100 times smaller than other fish and humans, and it's still a fish, okay?  So this proves that most of the non-coning genome is not required to make a fish.  For this fish.  So why do we study all this?  Well...  Nobody...  Please, please, if...  No, no, if I may comment, make me comment.  If the evolution constraint is so strong and we don't need this 97% of genome, why has it been kept during the evolution?  This is population genetics, so genome size is not correlated to complexity in any way.  Genome size is to do with the strength of natural selection, so species which have very small, effective population sizes have very big genomes, so plants.  Humans have a very small, effective population size.  We went through a botanical history.  This is why our genome is full of rubbish, okay?  This is very well understood.  Bacteria, fungi have very effective, very large effect of population sizes, very strong natural selection.  Every single base pair is under selection and has a... has a fitness cost when you do something.  Actually, it is not absolutely correct because it comes back to plants.  In plants it is well known, for example, if you cut half, at least half of non-coding genome of... ...arabidopsis, it's not coding part.  Why is there arabidopsis?  It creates a normal plan from this story.  But this is only in plants and maybe only arabidopsis, but this is very interesting thing.  But maybe it is somehow connected with the case that in animals we have much less plasticity than in plants.  But it just made the opposite point.  It just made the opposite point.  It's a fish that is a natural experiment.  I told you, you can film if you said it.  I have, so you agree.  I agree, I agree.  Then I agree, yes.  But I don't know about animals.  He's telling you about animals.  The same thing happens in animals.  You have very different genome sizes for animals which are very similar to each other.  So the genome size is not related to complexity.  You don't need most of the data.  But you say about comparison and I say about experiment.  It is not the same.  Because comparison still don't say the actual result.  Okay, but they agree with each other.  They agree with each other.  Another thing is also this measuring which bits of the genome are important.  So there's two ways we can do this.  One is by conservation during evolution.  And this estimates that roughly 8% of the human genome is under constrained.  As in it has been under selection during primary evolution.  And the other one now is because we have so many sequences of individual human genomes.  We can measure the allele frequency, the frequency of the mutations at every base.  So the human population is large enough such that every generation would be in saturation metagenesis for the human genome now.  So somebody is born with a mutation everywhere that is compatible with life.  And through sequencing millions of genomes now we know the frequency at which you get mutations in the population.  But when you say sequencing the whole genome or only the...  It's mostly the exomes that are becoming the whole genome.  And as this gets bigger and bigger then we will be able to measure exactly how important every base of the human genome is.  So this is the other way to answer your experiment.  It's like we will have the numbers to do this to say this base is exactly this important for the fitness within...  But again, this is not taking into account the individual differences.  So maybe this base is very important in general.  But this other base which is only present in two people is the one base which makes the difference between these two people.  Excuse me, I don't understand where this 97% figure comes from then.  I didn't do the experiment myself but it's the percentage of DNA which open reading frame of sufficient size to make a protein.  Because what I heard is that like 8% has been shown that has some...  Well, it depends on the species.  So in human it's 3% but in other species it's more.  No, but the 97% is definitely not all non-coding RNAs.  This is your point. A lot of it is...  A lot of what? It's non-transcribed at all, you mean?  Yeah, well, of course.  Well, at least there are parts of the genome that we can not even sequence properly.  So of course we cannot know if they are transcribed or not.  But they are going to come to 100% of course.  Yes.  So why are you also focused on the genome?  There are many more molecules which are passed from one generation to the next.  And I'm sure you've talked about germplasm and glycocontregated proteins and whatnot.  I'm just curious to know.  No, they might be part.  But at some point you have to remodel the genome because if you take after the erasement of the marks,  you can re-colore the marks.  And you start with the stem cell, which is a blah, blah, blah.  And so glycoconjugated, they can induce the modification, the epigenetic modification question.  Yes, why not?  But at this point it has not been proven that any sugar influences the genome.  So, I mean, the stretch of the genome.  Did anybody ever do an experiment by microinjection of long non-coding RNAs into a protein?  Yes, that.  Oh, in fertilization.  And to show that they actually affect the...  Not yet.  So how do we know they are important?  It's all correlation.  It's an open question again.  It's not a demonstrated fact.  Why do they experiment?  She wants us to do it.  She's just suggesting an idea.  She's just coming up with an idea.  That's it.  I totally agree that this is not proven.  But there are many examples of RNAs, non-coding RNAs, which are modifying the genome.  There exists one.  And there is another one, which is very interesting, is the parametria.  The parametria has two nuclei, micronuclei and a micronuclei.  And the micronuclei has actually the whole genome and is very condensed.  It's like the storage of the genome.  And the other nuclei, nucleus, is very large.  It has uncondensed DNA, and it's the part which is expressed.  And during the division, the cell division, the micronuclei will give rise to a micro and a micronuclei.  And the macronuclei, the sequences which are not expressed, are deleted.  And this is directed by RNAs.  So there are examples, many examples.  But it's parametria.  Sure.  It's not a mammoth.  No, sure, of course.  But it is exactly in parametria that you have the heredity, non-DNAs.  Oh, no, but...  Thomas Sonebaum.  That's exactly the history of life.  No, no, but I'm not talking about the genetics of the animals.  I'm talking about the molecular...  I'm talking about the mechanism.  About something which is different.  Yes.  Of course, but the molecular mechanism exists.  That's what I'm saying, okay?  In C-elegan, it was done in C-elegan.  Yeah, of course. In C-elegan, also.  Yeah, it was shown genetically.  But in a way, microRNAs, not so well-teachable now as an example of non-coding,  of this long non-coding RNAs, because they have their genes.  They are transcribed as genes, but not protein genes.  They are still not this junk of black...  Yeah, but those are not protein genes either.  No, they are not.  They are not protein genes, but they are not on the other...  They are transcribed.  They are...  There is a long association between long-coding RNA and disease.  In disease. For example, in cancer.  Yeah, yeah, absolutely.  I believe in diabetes, maybe, as well.  No, no, no. In cancer, very well.  There are several long...  There are those which are really looked at now.  So, 50% are coding from this long non-coding.  50% can code for micro-portings.  Right.  Yes, that's right.  But it has not been proven that these micro-proteins...  Some of these micro-portings are very important.  Yeah, yeah, yeah. I'm aware of that.  They are very small polypeptides.  Very small peptides, actually.  Yeah.  So, it's not proven that they have any function at this point.  But it's... Yeah, they are part of this on coding.  They have very small open reading plans.  Do you synthesize? Many of them are not synthesized?  No, they are synthesized and they have a function.  Well, the function is not for sure.  They are synthesized. Yeah, they are synthesized.  Do you think they are only after a long, long, long time synthesized by being digested?  Yeah, if they are very small, they can come from...  From the point of extension to sideways.  Yeah, but one reason also why they are studied is because in different tissues,  long RNAs have the same expression pattern.  So, if you take a liver or a neurons,  you see the same long RNAs expressed in the same tissues.  So, this is also one reason why they are...  At some point, they try to understand what they do in the cell.  Because there are kind of reproducible expression patterns for these long RNAs in osteoarthritis tissues.  Well, but that's a correlation and also it can be because of the different types of transcription factors in the different tissues.  Right, they said they seem to be under some regulations.  Yes. Oh, yeah. Okay, so we can take one last question.  Do we have one?  Everybody is angry, I think. Everybody is angry.
Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_0_431.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_432_1175.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_1176_1919.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_1920_2039.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_2040_2279.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_2280_2339.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_2340_2435.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_2436_6419.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_6420_7727.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_7728_8531.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_8532_9179.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_9180_21743.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_21744_23063.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_23064_25175.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_25176_25823.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_25824_25919.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_25920_29531.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_29532_29639.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_29640_29723.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_29724_30803.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_30804_30863.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_30864_31187.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_31188_32639.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_32640_34043.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_34044_34175.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_34176_34331.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_34332_34655.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_34656_35783.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_35784_36431.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_36432_36539.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_36540_37199.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_37200_37679.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_37680_38075.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_38076_38699.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_38700_38747.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_38748_38999.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_39000_39059.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_39060_39311.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_39312_40583.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_40584_41267.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_41268_42395.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_42396_44555.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_44556_48731.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_48732_48947.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_48948_49211.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_49212_51671.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_51672_52679.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_52680_56819.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_56820_57191.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_57192_58811.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_58812_58883.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_58884_61151.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_61152_64691.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_64692_64751.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_64752_65219.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_65220_65267.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_65268_65687.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_65688_65771.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_65772_65843.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_65844_67475.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_67476_67523.png Annick_Harel_Bellan_-_Epigenetics_and_ncRNAS__Open_F07Kcp56VlE_67524_69647.png