C. David Allis (Rockefeller U.) 1: Epigenetics: Why Your DNA Isn’t Enough

C. David Allis (Rockefeller U.) 1: Epigenetics: Why Your DNA Isn’t Enough Science Communication Lab 182K subscribers Subscribe 1.1K Share Download Clip Save 68,040 views May 2, 2016 https://www.ibiology.org/genetics-and... In the first of his videos, Dr. Allis introduces the concept of epigenetics; a change in a cellular phenotype that is not due to DNA mutation but due to chemical modifications of proteins that result in changes in gene activation. In the nucleus, DNA is wrapped around proteins called histones to form chromatin. How tightly the chromatin is packaged determines whether genes are active or not. This switch between the “on and off” state of chromatin is regulated by chemical modification of histones. Allis describes work from his lab and others that identified the enzymes that add, remove and recognize the histone modifications. Changes in histone modification can cause a number of diseases including cancer. A key difference between genetic mutations and epigenetic modifications is that epigenetic changes are reversible making them an attractive drug target. Dr. Allis focuses on the role of epigenetics in development and disease in his second talk. Histones can be modified on a number of amino acids, particularly lysines, by the addition of acetyl or methyl groups. Combinatorial patterns of these modifications act to enhance or repress gene expression. Allis describes work from his lab and others, which demonstrates that mutations in histone (for instance a lysine to methionine mutation) may block these modifications and, thus, impact gene expression. Sadly, these “onco-histone” mutations have been identified as the cause of many diseases including pediatric brain tumors and pancreatic neuroendocrine tumors. Speaker Biography: C. David Allis is the Joy and Jack Fishman Professor and Head of the Laboratory of Chromatin Biology and Epigenetics at The Rockefeller University. Allis’ lab studies how modifications to histones, the proteins that package DNA, influence gene expression and the implications these changes have for human disease. Allis has been honored with many awards for his pioneering research including the 2015 Breakthrough Prize in Life Sciences, the 2014 Japan Prize, the 2007 Canada Gairdner International Award and many others. Allis is a member of the National Academy of Sciences USA, the American Academy of Arts and Sciences and the French Academy of Sciences. Allis received his BS in biology from the University of Cincinnati and his PhD in biology from Indiana University and he was a post-doctoral fellow at the University of Rochester. Chapters View all Transcript Follow along using the transcript. Transcript Search in video Intro 0:14 Hello. My name is David Allis. I'm a professor and head of laboratory at the Rockefeller University in New York, 0:21 where my lab studies chromatin biology and epigenetics, and I'm very pleased to participate in this wonderful iBiology series. 0:29 I hope that I can enlighten you today in one or both lectures of mine. What is epigenetics? 0:35 Why do we care? And what is it that perhaps might be true about epigenetics such that it's not all our DNA alone? 0:42 Is there more to our heredity than just DNA? I think we all grew up with the notion that A groundbreaking discovery about heredity 0:49 real genetics is deeply founded in our DNA molecule itself. 0:54 I want to use this slide to date myself and say that at Rockefeller University in 1944, 1:00 it wasn't even known that DNA was the macromolecule that is the source of our heredity. 1:06 That was work that was carried out by these researchers -- Avery, MacLeod, and McCarty -- 1:11 and on the left side of the slide you'll get the sort of textbook notion that genes, 1:17 the DNA molecule, really is the molecule that Watson and Crick described the structure of, 1:24 that really is the basis of our heredity. And you can see in the yellow box that 1:31 there are very defined DNA elements that lie upstream of genes, we often know these are transcription factors, transcription regulators, 1:39 they can be positive or negative, but they tell the genes, then, they essentially instruct the genes 1:44 to either be expressed or to be silent. So the idea here is: 1:49 could it be genes are everything? You know, a tour de force, certainly, in 2001 The Human Genome Project 1:55 was the landmark sequencing of the entire human genome. 2:03 It generated a lot publicity, rightfully so, where now we had base-by-base information about our blueprint, 2:10 you know, our heredity. And there were many, many good reasons that the human genome project 2:17 was as exciting and got as much attention as it did: genes might determine again and that, for me, 2:24 someone as old as I am, that would be a really good thing to figure out how to improve that; genes determine disease, 2:32 of course, that would affect many of us; and then genetic analyses might provide us a way 2:37 to diagnose diseases and potentially develop therapeutic strategies, what we now know as personalized medicine or precision medicine. 2:46 So these would all be good things that came from the human genome project. 2:53 So, there are some questions that are sort of nagging that came from the human genome project that I'd sort of like to address to set the stage for epigenetics. 3:01 First of all, there was a surprisingly low number of genes in our sequenced human genome -- only about 21,000. 3:09 So, that seemed remarkably small. It may seem like a big number, but it's a small number, 3:15 especially when you consider that it's about the same number of genes that are in frogs and fish and worms, 3:22 and I think it seems counterintuitive that we would be not including or needing more genes 3:28 than those critters. Where would individual variation come from, 3:33 especially if you had twins? If twins are genetically identical and they're not exactly alike in terms of their outward appearance or phenotype, 3:41 where would that variation come from. Of course, we'd like to know, 3:46 when we traverse through our lifetime and we're influenced by outside factors -- environment, diet, other things -- 3:54 does that influence the genome? It would be, I think arguably, well, the genome's fixed, 4:00 so that can't really explain variation in that way. And ultimately, when genes really became scrutinized 4:07 with precise human diseases, was it the case that in every situation you found a genetic lesion, 4:14 a genetic alteration that accounted for the disease? And it the answer was, 4:20 I didn't find a mistake, I didn't find a change, how might that be explained by another property. Epigenetic "landscapes": genes + environment = phenotypes 4:26 So, this brings us to the theme of what I want to talk about in my first lecture, that will be the term epigenetics. 4:33 It was coined by Conrad Waddington in 1942, and he's very famous for this contour map 4:41 that depicted a ball rolling down a contour map hill. He was a developmental biologist who was interested in why, 4:49 in early embryogenesis, can the same genome give rise to different cell types. 4:55 And so as the ball rolled down either the left side of the contour map or the right side, and ultimately came to lie in different troughs, 5:03 he envisioned that those would be different outward appearances or different phenotypes, but importantly, again, 5:09 all from the same genetic material. And epigenetics stands for... the Greek prefix 'epi' means 'in addition' or 'above' 5:17 or something 'on top of', so something on top of or in addition to genetics. What is epigenetics and why is it so exciting? 5:24 So, I think... here's a nice way to sort of simplify your thinking. If you take a gene 5:31 and think about it in terms of an English word, then it would be... that's genetics, that's genes. 5:37 But, as we know, in English you can stress how words are pronounced 5:43 -- are they pronounced quietly, are they pronounced loudly, do you boldface or underline words 5:49 to get added meaning? Well, you don't change the letters, so the words don't change, 5:55 but how you read them changes, by these simple changes, and those would be the epigenes. 6:01 For those of you who are more tech savvy, I'm not a tech savvy guy, you might think of genes being the computer hardware, 6:08 where epigenes are the computer software. It's the same hardware, but what you're putting into the system changes the meaning. 6:14 And from this cover of ChemBioChem in 2011, a very simple cartoon notion of a puzzle, 6:23 where the authors are trying, or the artist is trying, to show I think some of the exciting connections 6:29 between epigenetics and very diverse parts of biology. So, you can pick your favorite puzzle piece, 6:36 but if I was picking a couple to be fair, developmental biology is where epigenetics 6:41 sort of was founded, and then that's the upper-right-hand corner, but the lower-left-hand corner, these white pieces, 6:48 what about diseases? Again, nothing would be more important than disease states that might not be explained by genetics, 6:55 but might be explained by epigenetics. Another very useful way to think about a genetics situation, 7:02 we're almost to Valentine's Day, how about a cake? We can all bake a cake, perhaps, and that will have a certain taste, 7:08 but if we literally put on different icings, by our choice... 7:13 it's the same cake, we haven't changed the cake a bit, but just by adding different icings -- sugar, non-sugar -- 7:20 you might be able to dramatically change the taste and I think that's a nice way to think about epigenetics, 7:26 and it just happens that frostings normally go on top of a cake. This of the term 'epi' -- on top of genetics. Epi-genetics: something in addition to our "genome" 7:33 More appropriately, in real biology, how do you take a young embryo 7:39 with early cells being established, they're all, again, pretty much underdetermined, 7:44 they all don't know quite who they're going to be or what they're going to become, and then the same genome, 7:50 as it advances through development, is going to give rise to different cell types -- blood, nerve, bone, skin. 7:57 Now, once that has happened, these cells know who they are, and for the most part they're determined 8:03 and they're going to give rise to daughter cells that carry on that identity 8:08 -- blood cells will give rise to other blood cells and so on. Of course, we know now, it's a very hot area of biology, 8:15 there are small populations of cells we refer to as stem cells, that are held in reserve, 8:21 and they seem to have a very much interesting potential because they are pluripotent 8:26 -- they can now still go into different cell fates -- and a very hot area, of course, is, can you take a fully differentiated cell 8:33 and reprogram it, and get it to go backwards into a more pluripotent state? 8:39 But the big point I want to make is that all of these cell types, no matter what cell type they are, they all have the same genetic material. 8:47 And sadly, I think very closely connected to stem cells, when you reprogram 8:54 and you sort of make mistakes in this epigenome layer, you might actually be able to sort of 9:00 push those cells backwards in development, where they would take on a more undifferentiated property, and take on more proliferative capacity, 9:07 and there seems to be many, many examples, now, where those type of cells take on a cancerous phenotype 9:13 that of course if often a very dreaded disease. So, how do we really start to think about epigenetics now 9:22 not so much with the cell biology, but how about the actual mechanisms. 9:27 Now, this might make you think he's crazy. This is I think a wonderful cartoon 9:33 that was drawn by one of my former lab members, Sean Taverna, who's now a faculty member at Johns Hopkins Medical School, 9:40 and, with apologies to the women who might be listening to this, the DNA molecule is clearly stepping out of the shower 9:47 and that DNA molecule is making a choice -- should it grab a towel that's labeled histone or should it grab a towel that's labeled herstone? 9:56 And it looks like nature opted for the histone, so, with apologies. So, what do I really mean when I say histones. Chromatin is the physiological form of our genome 10:02 If you go to a schematic drawing of the nucleus, our DNA in higher cells is not naked DNA, 10:10 it's in fact packaged by these proteins 10:16 that kind of give an impression of a bead on a string. These fundamental repeating units are termed nucleosomes, 10:23 and what nucleosomes really are are histone proteins that are acting as a scaffold 10:28 around which roughly two turns of DNA wrap, and then you can see on this schematic cartoon, 10:36 these beads on a string or nucleosomes will wrap further and further into higher-order structures that truthfully are still being determined. 10:43 But if you take a step back and you think about this structure maybe like a Slinky toy, you might be able to understand right away 10:50 that if you were to pull that Slinky apart or find more of what we term open or decondensed chromatin, 10:56 that might be a better environment for genes to be expressed. Where, in contrast, if you took that Slinky toy 11:02 and just compressed it, more like sort of all that chromatin that's really compacted together, that would be a harder environment for genes to be expressed. 11:10 Even these transcription factors would have a harder time finding their DNA sequence 11:17 to act upon in that really compacted environment. And under some conditions of biology... An electron micrograph of a cell's nucleus showing euchromatin (Eu) and heterochromatin (Het) 11:23 oh, and it's important for me to show you a real nucleus, this is a human cell nucleus stained in such a way that you can see dense and decondensed chromatin, 11:32 this is an electron micrograph, and I hope you can see there are very patchy, very dense domains that are within that nucleus 11:40 that are termed heterochromatin -- that would be this compacted chromatin environment -- where interspersed around these regions 11:49 are more open and decondensed chromatin that's referred to as euchromatin. So here's a real micrograph of a real human cell, Switching genes between 'ON' and 'OFF' states in a chomatin context 11:57 and now under some conditions you can actually tease out that chromatin, flute it, if you will, outside of the nucleus, 12:04 and you can see now these chromatin fibers sort of in their nearly more visible states. 12:11 On the lower panel, you can see this sort of classic bead on a string like a pearl necklace, if you will, 12:16 and somehow that chromatin, that more euchromatin, open chromatin, 12:21 may be able to be flipped into a molecular switch... by a molecular switch 12:27 that will compact that and turn that into the top panel, which is more condensed, compacted chromatin. 12:32 So, of course it became important for my type of lab, a biochemistry lab, 12:38 to try to ask, well, what would those molecular switches be? What would be the target of this sort of switch 12:45 that could throw on and off states between chromatin... euchromatin and heterochromatin? 12:51 So, this takes us to another Rockefeller, I think very pioneering discovery. A second groundbreaking discovery Histone proteins are chemically modified 12:58 Here's a nice look at this individual I want to pay credit to, 13:03 Vince Allfrey, and you can see that the nucleosome unit, now, in atomic structure, 13:10 you can see in different colors the histone proteins wrapping DNA. I think you can just see some of the Watson-and-Crick helix 13:16 wrapping on the outside of the DNA, but you do see these tail projections that are emanating outside of the DNA helix. 13:24 And what Vince Allfrey, who I've shown a picture of, proposed in 1964 was that 13:32 there would be chemical modifications, chemical marks, that would be added to these tail domains 13:38 that would then act as a switch -- they would be a signal, if you will -- that could instruct the cell to either be on or off. 13:47 So, it was his dream, his hypothesis, that these chemical modifications would potentially be that switch 13:55 that I was referring to in that past slide. Now, of course every chemical modification 14:01 would have potentially the need for an enzyme system that would add that mark, 14:08 and in my lab we've nicknamed these "writers", or there could be an opposing enzyme system that would strip these chemical groups off, 14:16 which we've nicknamed "erasers". And they would oppose, they would be the on-off, if you will, switches. 14:22 And this was Allfrey's hypothesis, you know, literally proposed over 50 years ago, 1964. Pick your 'model system' (organism) carefully 14:29 Now, how would you access these enzymes. I think many of you would not have thought 14:36 about this model organism. So, on the top panel is a schematic cartoon of a ciliated protozoan 14:44 that runs its life, remarkably, some very cool biology here, with two nuclei, and a real picture of the Tetrahymena 14:51 is shown below, on a stain, so you can see sort of the organism on a slide. This is a unique property of ciliates, 14:58 that they run their life with two nuclei. The larger, and hence the name, macronucleus, 15:04 is the nucleus that's solely responsible for gene expression. 15:09 This genome is packaged in a way that you might think of it as a mass of euchromatin. 15:16 And in contrast, the smaller, in this slide, micronucleus, that's shown on this slide in red, 15:22 it is very compacted, you might be able to tell that in the slide on the bottom, and it is completely transcriptionally silent. 15:30 What's important about that is that nucleus does no transcription. It's reserved for an important feature in the organism 15:37 that isn't really displayed here until it has the sexual life cycle. 15:42 So, you might think it's not even necessary, and that would be true here. It doesn't play a role in this case. 15:50 Now, when I was a postdoc, I was intrigued by this system. I thought it was a little bit strange to work on something so odd, 15:58 but I want to show you one gel of mine. So, this is prehistoric, 16:03 and what it is is, to the best of my ability, I turned to trying to biochemically separate 16:11 macro- and micronuclei, and I joined a lab, Martin Garofsky's lab, that was able to do that. 16:17 They had pioneered those methods. And what you can see here are two lanes of a gel: 16:22 on the left you can see the macronuclear histone proteins displayed, 16:28 and on the right the micronuclear histones. And I hope you can tell, without going into the details of the gel system, 16:33 there's a much more laddered... there's a much more laddered sort of property, or look, 16:39 to the macronuclear histones, and I've sort of tagged some of those ladders, those rungs of the ladder, 16:45 with these green dots. What was striking is you saw a lot more laddered effect, if you will, 16:52 in the macronuclear histones preps that I made, and you didn't see nearly as much of that ladder in the micronuclear preps. 16:59 That sort of box, that dashed box, shows you where you don't see many of the laddered forms. 17:06 So, I thought that this was pretty exciting and I thought this might give me a handle on using this organism. 17:13 What I need to now explain is that those ladders are due to charge differences, and each rung of the ladder 17:20 is due to an increased chemical group, which is exactly what Allfrey proposed, 17:26 which are these chemical groups called acetyl groups. That's too much detail, maybe, 17:31 but that's what I thought then would give me a good chance, then, to go into the laboratory, purify the macronuclei, and isolate the writer that would be responsible 17:40 for adding acetyl groups to the histones, as you can see here, primarily in macronuclei. 17:48 So, I started my lab group, I was able to attract a few brave students into my lab, one of whom was Jim Brownell, Activity gel assay 17:54 and this is actually right from Jim Brownell's PhD thesis. Jim's long been out of my lab, 18:00 but it was Jim's dream that he could sort of invent or use, I think a quite ingenious, 18:07 in-gel activity assay that I'll quickly describe to you. Jim's idea was to put histones, 18:13 the real proteins that I've been describing in my lecture, into a gel. 18:20 So, that's highlighted by the blue color. So he impregnated an entire gel with blue histones 18:26 -- now, they're not really blue; histones diagrammed in blue -- and as a control he put in another identical gel 18:35 non-histone proteins that would be a control. And then the key was then to take extracts 18:42 from this macronuclei from Tetrahymena and run those out onto the gel, 18:47 and in a perfect world it was his dream that if he then sort of treated this gel 18:54 with steps that I won't necessarily explain well, and then, importantly, add the radioactive cofactor of the reaction, 19:03 which some of us would know as radioactive acetyl-Coenzyme A 19:09 -- so, the acetyl groups come from metabolism -- and he would do this, incubate this gel, wash it, 19:16 and then in a perfect world he might actually see where the enzyme is 19:22 as this red band with the arrow right over here, I'll point to it, 19:27 and in a perfect world you wouldn't see that with the other control gel. And this is actually the very first gel that Jim produced 19:35 after giving this a try. I hope you can see a very strong band on the left 19:41 that was in the histone-containing gel, so pretend that that was the gel impregnated with the blue, 19:46 and to the right is an identically treated identical sample that was... 19:53 I think he used a protein called BSA, bovine serum albumin. It's not a histone, 19:59 the idea was a histone writer wouldn't work on that, and there was no strong band there. It's to Jim Brownell's credit 20:07 that he then purified enough of this p55 band from 200 liters of Tetrahymena 20:14 to get enough of this protein sequenced, and the gene cloned, Reversible acetylation "ON/OFF switches" 1996 20:20 and it came to perhaps be one of the things that my lab is best known for. Jim's mystery band turned out to be, 20:29 shown in this cartoon, look at the top half, a histone acetyltransferase or HAT 20:34 that was already known in yeast experiments to be a positive transcription regulator. 20:41 So, what was not known about this positive transcription regulator was that it was an enzyme, that it was a histone acetyltransferase or HAT, 20:48 so that was really starting to now galvanize certainly our thoughts 20:54 and the field's thoughts that you had to pay attention to this chromatin problem. Just the year... 21:01 Jim's paper was published in March 1996, so remarkably 20 years ago, and another lab, a month later, at Harvard University, 21:09 completely independent of us, Stew Schreiber's group and a graduate student there, too, Jack Taunton, 21:14 found through a really ingenious chemical strategy an enzyme activity that would strip these groups off, 21:22 it would be the opposing enzyme, and it was referred to as a histone deacetylase, or HDAC. 21:29 And remarkably, again, this protein was already known in yeast 21:34 to be a transcription co-repressor. So, already, sort of the magic had happened. 21:41 Our protein was thought to be a positive transcription regulator, the Schreiber/Taunton enzyme was thought to be a repressive in nature protein, 21:50 and what they both were doing was writing or erasing acetyl groups from chromatin. 21:57 Because I think that this is the thing that my lab might be best known for, I want to introduce you to the real Jim Brownell. 22:02 How I think of Jim Brownell is on the left, the before. This is how he looked everyday in my lab, 22:08 he always went into the cold room with a hat because he was going after a HAT and it was cold, 22:13 but he actually won, in 1997, the international prize for the best PhD thesis in the world, 22:22 and he was flown to Stockholm, Sweden to rub shoulders with the Nobel laureates, and my question for you is, where do you think Jim looks more comfortable? 22:31 It's kind of like me standing here. I think he's much more comfortable in the lab as a lab rat and I always sort of made fun of Jim for that, sort of, almost, 22:40 I don't look very happy getting his award. It's a footnote that's unimportant to you, 22:46 but I just think science has to be fun. Jim's paper was published in this journal, Cell. It was published on March 22nd, 1996, 22:53 and that happens to be my birthday, to the day, so that was pretty cool. Unlike mutations in DNA 0 , epigenetic mistakes are reversible, providing many promising drug targets 22:59 So, let's have a little quick summary. If you followed me to this point, classic genetics I think is illustrated on the left. 23:06 We have bona fide important DNA molecules that really are the kingpin of our heredity, 23:13 and that material is relatively fixed -- it can't be altered. 23:19 And of course there are gene regulators that recognize DNA sequences and they really do quite a bit of the activation. 23:26 No question about it. What I've been trying to talk to you about is a much more flexible, fluid system, 23:32 the epigenetic side of the coin, on the right. And the point would be that these chemical groups, 23:38 no matter what they are, they can be added, they can be subtracted, and they give the genome a very important way to be responsive 23:45 to what's going on rapidly. But most importantly, when you look at the DNA molecule, should a mutation occur, 23:53 tragically, whatever, something that you truly inherit from mom or dad, but a genetic mutation, 23:59 we don't have good ways to fix that problem. And should that be a disease-causing mutation, 24:06 we're sort of stuck with that. In contrast, if any of the epigenetic modifications, 24:11 the landscapes, we like to refer to this as an epigenetic landscape... should those be mis-set up and mis-established, 24:19 then there are way to think about reversing those problems, because the DNA has never really been mutated, 24:25 the DNA is fixed. Remember, this is a problem of what's above the DNA template. 24:32 So, as soon as these enzymes began to be recognized, these writers and these erasers, many labs began to try to target them for drug development. 24:41 One was very successful -- right across the street from where I now am at Rockefeller, that's Memorial Sloan-Kettering -- Epigenetic cancer therapy: reversing mistakes in people POST-treatment (wks) 24:48 and in a group led by Paul Marks, he was able to sort of begin to pioneer 24:53 putting these epigenetic drugs into people in clinical trials. This is a patient that was treated in Memorial 25:02 where pre-treatment is shown on the left, this is two different scans of this individual's chest cavity 25:08 -- I hope you can see these arrows point to large tumor masses that were in this individual's chest -- 25:13 it actually was a cancer of the larynx that then spread to the lungs, 25:19 and after 8 weeks of treatment, on the right, is the same individual, where I hope you can see that these tumor masses 25:26 are either almost gone or are much more hollowed out. It's certainly a much better situation for the patient on the right. 25:32 And these kind of very promising things actually led the Marks laboratory to then develop this 25:40 to such a state that this actually has become one of the first FDA-approved drugs 25:45 to treat a specific kind of cancer. Now, this one may be a little bit hard for you to see because it's sort of an internal scan of the body, Cancer epigenetics: reversing mistakes in people 25:53 but, also at Memorial, here's a woman that was treated for a skin cancer. 25:58 This was before the epigenetic drug therapy and, just quickly, I think it's quite easy to see in the visual, 26:04 this is that individual after treatment with these, we'll call them epi-inhibitors. 26:10 So, again, I think... and now this has of course spawned worldwide interest in these enzymes 26:16 as being very powerful drug targets, and they're getting scrutiny worldwide, in part for reasons like this. Epigenetic targets in oncology: histone-modification targets 26:24 So, to sum up this portion of my iBiology talk to this point, 26:29 now, whatever your favorite modification is, think of it as there are classes of enzymes called writers, 26:35 there's a class of enzymes called erasers, and now we even know that some of these chemical modifications can literally become read by reading modules 26:44 that read the modification and plant themselves down on the histone tail in ways that bring about either chromatin opening 26:53 or chromatin closing. And to be accurate to this minute in time, even these readers have become successfully drugged. 27:00 So, every part of the language, if you will -- reading, writing, and erasing -- 27:06 have become now attractive drug targets, some of which are being clinically used. Genetic insights into epigenetics at work: Position Effect Variegation (PEV) in fruit flies 27:13 So, what I have neglected to tell you about, I think, is more on the silencing system. 27:19 So, another chemical modification that Allfrey proposed in his original 1964 studies 27:26 is maybe there's different modifications that can, again, act different ways. 27:32 I've talked to you mainly about acetyl groups as a very promising 'on' mark, 27:38 but what about methyl groups. That's not a very different chemical group, but... you know, how was the field going to get interested in methyl groups? 27:46 Well, this is an elegant epigenetic biology shown here. It's a classic case where, once again, 27:52 the take-home would be that you don't change the DNA but you alter the phenotype. 27:58 So, this is a Drosophila eye. I think it's very easy for you to see on the right side 28:03 two different fly eyes -- one is very red, one is very white -- and what's happened here? 28:08 Now, I think this is odd, but I can't make this go away. There is a gene in Drosophila called the white gene, 28:14 I'm pointing to it, it's on the tip of the X chromosome, and I think it's a little odd and confusing, 28:21 but fly people name their genes based on their mutant property, so when the white gene is active and wild type, 28:28 I hate to say it, but it makes red eyes. So that's just kind of annoying. 28:33 But when that fly chromosome has been treated with X-rays 28:39 and that white gene has been flipped, and that white gene, without any DNA sequence changes, 28:46 lands next to heterochromatin, that gene silences. 28:51 So that concept is called position-effect variegation, and it's a good name. 28:57 It's a positioning of a gene into a new neighborhood. You didn't change the sequence, 29:02 but clearly on the right you can see those fly eyes go from very red to very white, 29:08 and sometimes it's not that black and white and it variegates and that's... hence the name, position-effect variegation. 29:14 Now, because this was Drosophila, researchers realized they could look for mutants 29:20 that didn't do this position-effect variegation very well, and I want to only tell you about one 29:26 that was hugely important in the field of epigenetics. Let me ask you to look at the bottom of this box, 29:31 where you see something called Su(var)3-9. That means it's a mutation that suppresses 29:39 this phenomenon that I've been describing, position-effect variegation. And what's the Su(var)3-9 part all about? 29:46 That stands for... it was a mutation that was mapped on chromosome 3, 29:51 no big deal, and it was mutant number 9. Okay, chromosome 3, mutant number 9, 29:58 and of course the important part is, what did it do? What was its role? 30:04 What were its molecular properties? And I get to tell you one of my most favorite sort of stories in my career 30:09 was when the individual shown here in the lower right, Thomas Jenuwein, 30:15 literally obtained some evidence that the mouse homologue of Su(var)3-9, 30:20 not the Drosophila but the mouse, smelled like it was a methyltransferase writer, 30:26 and he wanted to team up with a lab like mine and see if we could figure out if that was so. 30:32 And so, using a lot of the same sort of approaches that Jim Brownell and we had done with acetyl writers, 30:39 we teamed up with Thomas' lab, and shown here is the blackboard from my office, to this day, 30:46 down the street, and the biochemical take home message 30:51 was that the mammalian Su(var)3-9 was indeed a methyltransferase, 30:57 that means it's a methyl writer and remarkably it's target 31:03 is H3, histone-3. At what position? Lysine 9. 31:08 Unbelievable. So this Su(var)3-9 was named correctly all along, 31:13 and I think Thomas and I still, we're very good friends, we laugh about this, you know, 31:19 it was like it was just unbelievable that the geneticists named this right all along, without even knowing what it did. Similar logic, but two systems for 'ON' vs. 'OFF' states 31:25 So, what's important? I'll give you now sort of a ranging insight 31:31 into what people now think. On the left side, it looks like there are situations where you want to activate genes. 31:38 You might do that by taking these acetyl groups, enzymatically adding them 31:44 with a histone acetyltransferase writer. Now, we know that once that mark has been written, there are proteins that read that mark, 31:52 like shown here, protein X, they'll dock on that acetyl group, 31:58 they'll bring about gene activation, and when you really want to shut that gene off, all you have to employ are those HDACs 32:05 that will strip that acetyl group off. And so that's a very, you know, sort of attractive, 32:10 well-worked out paradigm in the field. In contrast, let's take a situation where you want to silence a gene epigenetically. 32:17 No mutations, just silence a gene epigenetically. Well, in this case you're going to have to make sure 32:23 that that lysine residue, that's the blue K in these slides, that's the one-letter code for lysine, 32:29 you're going to have to make sure that you don't have an acetyl group there, so you might employ the HDAC 32:34 to remove the acetyl group as step 1. Then you'll go to the histone methyltransferase, shown in red, 32:40 and you'll add a methyl group, so that's this HMT, that's the methyltransferase writer, 32:46 you might think of that as the Su(var)3-9, and then once that's methyl mark has been put on, 32:52 they'll be readers, like shown here in Y in red, that literally silence and compact that chromatin 32:57 by reading the methyl mark. And I have to say, it's funny to me that 33:04 when this slide was made, I thought it was pretty nice, but we didn't know and I don't show in this cartoon, was there a demethylase? 33:11 Was there an enzyme that took the methyl groups off and now, indeed, Yang Shi and his colleagues, 33:16 and now many others, have found that even these methyl marks can be enzymatically removed. 33:22 So, in this sense, this slide is even out of date. But nonetheless, acetyl marks generally track on-ness, 33:30 and methyl groups generally track off-ness in chromatin. So, a couple biology examples... 33:36 here's another cartoon, it wasn't drawn by someone in my lab. You can see, it's a mom and a dad doin' their thing, 33:43 but the sister is clearly irritating the brother by saying her epigenome -- now, I put in the epi -- 33:49 her epigenome is more complex than his. And I think that this is a case where she's right, 33:55 because every woman has two X chromosomes, so that's underneath her are the two pink chromosomes... 34:00 two X chromosomes, where every male, young boy, father, whatever, XY. 34:07 So, you know, how does nature create a balance on those X chromosomes? 34:12 There's two in the female, there's one in the male, and what they've learned to do is to literally shut off, 34:18 early in development, one of those X chromosomes. That's called X inactivation and you'll think I'm making this up, Epigenetic silencing of 'identical genomes: Calico cats 34:25 but when you take female mammalian cells and stain them... there's an example of two, 34:31 you can't see much staining on the left panel, but if you stain with a methyl antibody, 34:37 that's a methyl histone antibody, I hope you can see there's little patches that light up red, 34:43 and those are the completely shut down, heterochromatic, inactive X chromosome. 34:50 If you did the same staining experiment in a male cell line, you won't see any of that. 34:55 And as a footnote, if ever you've seen a calico cat, shown on the right, 35:01 that coat color... coat color patches is all a reflection of female X inactivation in the cat 35:09 that happens to be tracking to a coat color gene, and that happens early in development, 35:15 and it makes different coat colors in different patches, hence the calico coat properties, 35:21 and calico cats are always female. They're female because of this coat color phenomenon that tracks back to X inactivation and methylation. 35:30 Identical twins I mentioned, you know, we should know that they are absolutely identical genetically, 35:37 but I think, if any of you know identical twins, they're often not identical, and it's becoming an attractive model system 35:44 -- not these two individuals -- when people have studied behavioral properties, different disease properties 35:51 from monozygotic twins and found out that they're not identical with respect to their epigenome. 35:57 And that now becomes a nice model system for identical genetics but not identical epigenetics. 36:05 And then of course, you know, I certainly grew up thinking that if I wanted to be abusive to myself, 36:10 that's not so cool, but at least I'm only hurting myself, so it was a life choice that I was making, 36:16 and I think a lot of people might have said, "We are what we eat," but much more recently, because of this revolution in epigenetics, 36:25 others have written other alterations of that quote, that might be, "We are also what our parents ate"... 36:32 and maybe our parents before them." And I'll give you a nice visual of that. These are identically genetic mice Genetically-identical mice, but mothers ate different diets 36:40 but the only thing that was varied in this experiment by these researchers was the diet that their mother was given 36:48 when these babies were in utero. So, the question was, wow, 36:54 I just altered the diet of the mother -- in too much detail, these were alterations in a diet that would foster the methyl modification -- 37:01 and you can see that the different pups, all genetically identical, are phenotypically very different, 37:09 very different sizes, very different coat colors, and that's kind of a scary thought. 37:15 They're identically genetic in terms of genetic terms, but the diet of the mother impacted the outcome of the children. 37:22 And if you take this to one more extreme level, Michael Meaney and his colleagues Behavioral epigenetics: nurturing one generation to the next 37:28 have been asking questions that fall more in the realm of social behavior, and that would be: 37:35 what about having a model system that might mimic good moms versus bad moms? 37:40 And he's got mice that actually are very, very "good Moms", meaning that they lick their pups a lot, 37:47 they kind of hold and cuddle their babies quite a bit, and he's found some strains of mice that are just the opposite, 37:55 so we'll sort of call them "bad Moms", they don't cuddle, they don't lick, 38:01 and he's then asked, what happens if I can expose genetically identical mice pups 38:08 to good moms or bad moms? And as you might guess, 38:13 he's now paying a lot of attention to epigenetic marks and he's finding out that the marks change 38:20 in the brain regions that he studies that are responsive to, ultimately, 38:26 alterations in gene expression that lead to alterations in stress and inherited phenotypes, 38:31 and it's quite amazing to then think that this may be socially relevant in our society 38:37 when we have unfortunate situations that track good moms versus not-so-good moms, 38:44 not only in terms of the tragedy of it all, but also in terms of the upbringing of children. 38:50 And perhaps can traits be passed on to even their children 38:55 that are inherited through this epigenome layer? So, this would be a summary slide, I think you've seen it before. 39:01 I want to leave you with the impression that on the left slide is the classic textbook genetics, 39:06 there's nothing wrong with that, and in fact, you know, it's very clear that some things that are... 39:12 like smoking, too much sunlight, they can indeed alter the DNA, mutations that can cause disease, 39:18 and that's certainly something we do want to protect and hopefully inherit good copies from mom and dad. 39:26 But there is now an emerging, if you will, revolution in an understanding that genetics 39:32 doesn't explain everything, and there seems to be, in hindsight, you might think, a much more dynamic opportunities for these genomes 39:39 to be responsive much more quickly in time 39:45 to needs that might be epigenetic in nature. I should mention for completeness: 39:50 it's not just the histones that are chemically modified, the DNA is as well, and these things are now a raging topic for biochemists like myself. 39:58 Again, writers, erasers, readers, and what's really rapidly ramped up the interest in these modifications 40:07 is that many if not all of them are now associated with human diseases, notably cancer, 40:12 and many are being targeted for drug development. Why? Again, because the genome is relatively unfixable; 40:20 the epigenome is much more responsive to fixing... being fixed. One new textbook on epigenetics EPIGENETICS 40:27 So, if you're interested in this topic... I'm not trying to plug this book, but a pleasurable sort of challenge for... it's a complicated field, 40:36 so some time ago Cold Spring Harbor approached some small number of us to write a textbook on the subject, 40:43 and if you're interested this is the second edition of a textbook that was just published, it came out this last year, 40:49 and importantly, it makes me sort of want to introduce you to the editorial team. You might recognize Thomas Jenuwein on the far left 40:57 because he's actually the scientist that we enjoyed working with on the methylation and the Su(var)3-9. 41:04 That's been a long-lived friendship. And Monica Lachner, Danny Reinberg, myself, and Marie-Laure Caparros 41:10 are all part of the editorial team, which helps me make the point that, besides your labmates in the lab, 41:17 it's equally a privilege and run to sort of carry out worldwide interactions and collaborations, 41:25 and in this case an academic project, with so many talented people. 41:30 So, I'm done with my first lecture. I would be remiss if I didn't thank many people. Of course, anything I referred to 41:36 -- I showed you a few lab people's pictures, like Jim Brownell, but I've had a rich career of many, many talented students and postdocs and technicians. 41:46 We don't do many of our projects without many important collaborators, the iBiology staff here has been wonderful, 41:53 I'm not used to being filmed or any of these productions, but they've treated me really nicely, 41:58 the Lasker Foundation for allowing this to happen here, and my funding sources, Rockefeller University, 42:05 and you all for your time and attention. Thank you very much. Show transcript Science Communication Lab 182K subscribers Videos About LinkedIn Twitter Facebook 76 Comments rongmaw lin Add a comment... @ddarhe 6 years ago this man is such a delight; his politeness and measured manner of speech is truly something to learn from. i bet that working at his lab is remarkably enjoyable. looking forward to watching part 2! thanks for the video; keep up the good work iBiology team, you are certainly one of the best (i honestly cannot even think of others) advanced-level education sources in molecular biology! 15 Reply @evelyne7071 3 years ago Years ago I was a laboratory technologist and I started seeing these articles regarding methylation. After your lecture, even though I didn’t get a some of the more detailed technical; information, I now understand a little better the significance of your interesting work. So, thank you. 3 Reply @ahmadzamy4357 3 years ago In youtube i think this channel is very different and informative and the best biology learning channel 3 Reply @vastg5453 3 years ago Very easy to understand, what a great speaker! Thank you so much. 3 Reply @graemelaubach3106 2 years ago Very interesting. Many thanks to Allis and this channel, ya'll are killin it. 1 Reply @twitchalmighty 4 years ago I've always look at all of the sciences a being fun, Learning is something to be enjoyed. I see Self-education in life as being more of a hobby. 12 Reply @timblackburn1593 1 year ago Share it with your kids! Thank you sir Reply @StewartChaimson 6 years ago Thank you, I enjoyed this lecture very much! 5 Reply @DancesWithSpiders 5 months ago Hello Dr. Ellis - is anybody looking at the placenta in relation to epigenetics? If I understand it correctly, it is genetically identical to the embryo but develops in a completely different way, which would suggest that a different set of epigentic switches is present in the descendents of the fertilised egg that goes on to form the placenta and those that go on to form the embryo. I thought there might be some interesting finds to be made through a comparison of the two. On a side note, who do we inherit the epigenetic switches from that kickstart the developments of the embryo and the placenta respectively - the mother or father or a bit of both? Reply @numericalcode 1 year ago Great explanation Reply @TheTopfearless 1 year ago He was such a pioneer and a great scientist.. sadly he did not get the Nobel Reply @webmelomaniac 3 years ago Very enlightening, thank you! 1 Reply @usmanasghar1127 3 years ago Just awesome 1 Reply @ardd.c.8113 2 years ago 200 liters... 1 Reply @superoxidedismutase5757 5 years ago Great stuff 2 Reply @joechang8696 4 years ago it would seem that quantity of genes does not correlate to "intellect" or whatever makes people special? perhaps quantity of genes matters more in ability to survive varied or difficult environments, which are obviously not that good at, in terms of genetic ability, not ability to alter the environment 1 Reply 1 reply 1 year ago Peoples thinking all this complexities comes from randomness must be crazy. Reply @russ1618 5 years ago Why is it so often said that it is unintuitive that humans should have a similar number of genes as fish and frogs and whatever? They have skin and spines and eyes and hearts and lungs and bones and so on and so on. Why should we expect to be anything more than a different sculpture made from the same clay? 2 Reply 3 replies @lucasqwert1 3 years ago Fly People: when the gen is activated and inside euchromatin, the eyes are red, so lets name our gene "white" 😂😂😂 1 Reply @kavikumar4440 4 years ago fall in love Reply @小猪飞天-f5j 4 years ago 现在想想中国古代胎教思想：“古者妇人妊子，寝不侧，坐不边，立不跸（单脚站立），不食邪味，割不正不食，席不正不坐，目不视邪色，耳不听淫声，夜则令瞽颂诗，道正事。如此，则生子形容端正，才过人矣。故妊子之时，必慎所感。感于善则善，感于恶则恶。人生而肖万物者，皆其母感于物，故形音肖之。”是真的牛逼 2 Reply 1 reply @patldennis 8 years ago Alternatively this talk could be entitled Epigenetics: It's not the magic bullet against evolution that Intelligent design creationists think it is. 9 Reply 28 replies @jimmcnicholas9670 4 years ago When will scientists learn that immortality would be very bad for everyone Reply @ashsomers1 5 years ago nup. Reply @MichaelHarrisIreland 6 years ago He's assuming there is a good and bad mother, and he and some elite are the judge of it. The reality of life makes no such call. The bad mother could be the one that rears kittens that survive. So many of these studies have a "support the status quo agenda" without them even realising it. I don't mean the status quo of science but of society. Real change might very well come from the worst treated survivor. I admit I only browsed through the video and the subject is new to me so maybe I'll change my mind on further study. 1 Reply 2 replies @andrew64J 6 years ago Fail Reply 1 reply @twitchalmighty 4 years ago I enjoy all of these lectures very much. 2 Reply