Sam Cusimano ’16
In this episode, I introduce the NeuroEpic Podcast series – who we are, what our podcast series is about, and what we hope to accomplish. Then, I briefly outline some of the basic terms and concepts of genetics and epigenetics. This short run-through prepares listeners for my interview with Dr. David Sweatt (in 2016), one of the leaders in neuroepigenetics and the author of the textbook we use in class. Dr. Sweatt and I discuss what neuroepigenetics is and how it came to be. We also talk about the implications of neuroepigenetics for biology and for philosophical and lay conceptions of human nature. Dr. Sweatt concludes by giving a preview of what kinds of questions neuroepigeneticists hope to address in the near future, and how scientists and healthcare professionals might apply findings in neuroepigenetics towards improving the human condition.
Introduction to the Podcast
Have you ever wondered why you do all the weird things you do? – why you glob ketchup on your pizza, why you sing in the shower, why you always cry at the end of Jurrasic Park? Have you ever caught yourself doing the exact same things that your mother or father would do, and wondered how you could have turned out like them? Do you ever wonder how your life experiences have shaped your personality, or why some people are more prone than others to mental illness?
In this podcast series, we’ll be talking about the blossoming field of neuroepigenetics – the study of how our life experiences lead to epigenetic changes in the brain, and how these epigenetic changes in turn affect our thinking and behavior. This exciting new branch of science promises to help us answer deep questions about who we are as humans – how our brains give rise to our unique personalities and ways of acting, how our early childhood experiences affect our behavior as adults, and how the food and drugs we consume influence the connections that our brains make. In doing so, neuroepigenetics challenges the traditional distinction between “nature” and “nurture” – that is, the supposed division between the hereditary and environmental forces that make us who we are – and shows that the two are in constant interplay.
Even though it’s been less than twenty years since neuroepigenetics emerged from the shadow of neuroscience and epigenetics, this field has already given us striking insights into the nature of aging, Alzheimer’s disease, drugs of addiction, depression and post-traumatic stress disorder, the influence of diet on behavior, and the lifelong effects of maternal care on stress and mental illness. Each episode in this podcast series will present the most groundbreaking findings in each of these areas of recent neuroepeigenetics research.
In this introductory podcast, I’ll be interviewing Dr. David Sweatt, one of the pioneers and leaders in neuroepigenetics research. Dr. Sweatt is currently a professor of neurobiology at the University of Alabama at Birmingham Medical School, as well a professionally trained artist. He has recently appeared on PBS’s NOVA television series.
Before we get to the interview, I’ll briefly outline some of the basic terms and concepts of genetics and epigenetics, which will help orient us for this podcast episode and others in the series.
Introduction to Neuroepigenetics
Neuroepigenetics is an outgrowth of genetics and epigenetics, two older branches of biology. Genetics is the study of genes – that is, the basic instructions that tell our bodies how to operate. To be more precise, our genes tell our bodies how to make proteins. Proteins are one of the molecular building blocks that us living beings are made of. Part of what makes us unique and different from one another is that each of our bodies makes a slightly different set of proteins. The exact set of proteins that our body makes helps to determine many aspects of our physical and mental makeup, from eye color, hair color, and height to our chances of developing mental illnesses such as depression and schizophrenia.
We get our genes from our biological mother and father – in fact, half of our genes come from our mother, and the other half come from our father. That’s one of the reasons why we each have many of the same physical characteristics as our biological parents: our bodies are made of the same proteins as theirs!
Our bodies store gene information in a special type of molecule called DNA, or deoxyribonucleic acid. If we were to view DNA from afar, it would look like a long, winding string – much like a strand of yarn that has been unrolled. If we were to zoom in, however, we would see that each strand of DNA is made up of two smaller strands. These two strands wrap tightly around one another in the iconic double-helix shape.
Each strand of DNA contains two main parts: the nitrogen bases, so called because each base contains at least one nitrogen atom, and the sugar-phosphate backbone, which holds all the nitrogen bases together. There are four different kinds of nitrogen base in DNA: adenine, thymine, cytosine, and guanine. We often abbreviate them as A, T, C, and G, respectively. The exact ordering of bases on a DNA strand determines what kinds of proteins the DNA codes for. That is to say, all our genetic information is stored in the nitrogen base sequence of our DNA molecules. Accordingly, we call the nitrogen base sequence of our DNA the “genetic code.”
Each of the four nitrogen bases preferentially sticks together with one of the others: in particular, A and T like to stick together, and C and G like to stick together. Moreover, each of the two strands in a DNA molecule has a complementary sequence: wherever one strand has an A, the opposite strand has a T; wherever one has a C, the other has a G; and so forth. As such, binding between the nitrogen bases is what holds complementary DNA strands together in the double helix shape. You can think of the DNA double helix as a ladder that we took and twisted up lengthwise. The rungs of the ladder would represent the pairing nitrogen bases, and the walls of the ladder would represent the sugar-phosphate backbone.
Now, simply having genes isn’t enough to run a body effectively. Our genes tell our bodies what kinds of proteins to make, but they don’t dictate exactly when to make these proteins, where to make them, and how much of them to make. To look at it another way, our genetic code tells our bodies what ingredients to use, but not how to put them together.
Different kinds of cells in our bodies perform different kinds of activities, and so each cell type needs to use a different combination of proteins. For example, liver cells use proteins that are specialized for liver function, brain cells use brain-specific proteins, and white blood cells use white blood cell proteins. There are some proteins that all cells use, but in differing amounts. In addition, the parts of our body that help us respond to changes in the environment – especially the brain – need to be able to change how much of each protein they’re making in order to fine tune their activities to the relevant circumstances.
Epigenetics is the study of how our cells know which proteins to make, when to make them, and how much of them to make. Whereas genetic information is stored in the base sequence of DNA, as we’ve seen, epigenetic information is stored in the three-dimensional structure of DNA and in structural elements that DNA is associated with. Within our cells, DNA does not sit all by itself: rather, it is wrapped around special proteins called histones. You can think of the DNA wrapping around histones like a long string of yarn wrapping around tennis balls.
One of the important functions of histones is to keep our DNA compact and organized. Another important function, however, is to control how much protein gets made from each gene. The more tightly a region of DNA wraps around histones, the harder it is for the cell’s machinery to read the genes in that segment of DNA and use them to make protein. Conversely, the more loosely DNA wraps around histones, the more easily the cell’s machinery can read the corresponding genes and use them to make protein. As such, the cell can turn a gene’s protein expression up or down by modifying the structure of the histones near it. Some histone modifications cause the histones to associate more loosely with DNA, thereby turning up the volume on nearby genes, so to speak. Other modifications cause histones to associate more tightly with DNA, thereby turning the volume down on nearby genes.
In particular, there are three major kinds of chemical tags that the cell can add to histones to change their structure: acetyl groups, methyl groups, and phosphoryl groups. Acetyl groups tell histones to loosen their association with DNA, and thus to turn gene expression up. Phosphoryl groups also tell histones to bind DNA less tightly and to turn gene expression up. Methyl groups, on the other hand, can tell the histone to bind DNA either more or less tightly, depending on which part of the histone the methyl group goes on.
Thus, one way the cell can turn up or down the expression of certain genes is by modifying the structure of histone proteins. Another way the cell can modify gene expression is to place special tags on the DNA molecule itself. In this podcast series, the main kind of DNA tag we’ll be discussing is DNA methylation: that is, the addition of a methyl group to a cytosine base on DNA. Notice that DNA methylation is similar to histone methylation in that both modifications involve a methyl group. But the two epigenetic modifications are different because DNA methylation involves the placement of a methyl group on DNA, whereas histone methylation involves the placement of a methyl group on histone proteins.
Methyl groups on DNA near the beginning of a gene sequence tell the cell machinery not to use that particular gene for protein. Importantly, DNA methylation is the only kind of epigenetic tag that can be passed down from generation to generation. As a result, you can inherit some of your biological parents’ and grandparents’ patterns of DNA methylation, but you cannot inherit their histone modifications.
One more important set of terms in epigenetics regards the kinds of enzymes that make epigenetic modifications. We’ll discuss three classes of enzymes: writers, erasers, and readers. Writers put an epigenetic tag on. For example, one kind of writer enzyme called DNA methyltransferase puts a methyl group on DNA. Erasers take an epigenetic tag off. Histone de-acetylases, for example, take an acetyl group off a histone. And readers detect whether certain epigenetic marks are present and convey the information to the cellular machinery responsible for turning genes to protein.
Now that we have discussed some of the basic terms of genetics and epigenetics, let’s turn our attention to neuroepigenetics. Dr. David Sweatt, one of the pioneers of neuroepigenetics, joins us over Skype to talk about what neuroepigenetics is, why we should care about it, and what kinds of insights neuroepigenetics research could afford us in the near future.
Detailed Introduction to Neuroepigenetics
Viewed from one perspective, every living organism – from humans to fish to trees to microscopic bacteria – is an astonishingly intricate web of chemical reactions. As many people have remarked, we living things are like “giant bags filled with chemical reactions.” These chemical reactions harness energy and raw materials from food to help us maintain our bodily structure and to do the things we do.
Although these reactions involve a multitude of different chemicals, we can sort most of the chemicals into four categories: lipids, carbohydrates, proteins, and nucleic acids. Lipids include fats, steroids, and molecules like them. Carbohydrates include sugars and long chains of sugars. Proteins, on the other hand, are long chains of small chemicals called amino acids. (In most living organisms, there are a little more than twenty different kinds of amino acids.) Of the four types of biomolecule, proteins are the most versatile, taking on many different shapes and sizes: some are small and round and serve as hormones; others are large and round and facilitate chemical reactions; others yet, like collagen, are long and skinny and help make up connective tissues like skin and hair. Finally, nucleic acids, including DNA and RNA, are long, stringy molecules that contain “instructions” or “blueprints” for making proteins. We call these blueprints “genes.”
In order to understand how genes work, we’ll have to look a little more closely at the structure of nucleic acids, the molecules that carry them. Like proteins, nucleic acids are polymers of a smaller chemical building block; rather than being made of amino acids, however, nucleic acids are made of nucleotides. Each of these nucleotides contains one of four “nitrogen bases,” so called because they each contain several nitrogen atoms. In DNA, these bases are called adenine, cytosine, guanine and thymine. (RNA has all the same bases except that it substitutes uracil for thymine.) In nucleic acids, nitrogen bases are linked together by a long chain called the “sugar-phosphate backbone,” which consists of alternating subunits of phosphate and sugar.
DNA is usually found in a “double-stranded” or “double-helix” shape, meaning that two DNA chains are stuck together through interactions between their nitrogen bases. In fact, each of the four nitrogen bases has a complementary “partner” with which it’s always stuck together – adenine goes with thymine, and guanine goes with cytosine. The bases stick together in this way because their shapes fit snugly with one another, much like adjacent puzzle pieces: adenine fits with thymine and guanine fits with cytosine. Thus, to illustrate, whenever we see a thymine on one strand of a double-stranded DNA molecule, we should expect to see it bonded with an adenine on the other strand; whenever we see a cytosine on one strand, we should expect to see it bonded with a guanine on the opposite strand.
This bonding between nitrogen bases in double-stranded DNA forms the iconic “double-helix” shape. If we were to zoom in closely on a DNA molecule, it would look something like a spiraling ladder, with the sugar-phosphate backbone of each strand making up the walls of the ladder, and the paired nitrogen bases making up the rungs.
RNA, on the other hand, is often found in single rather than double strands. Sometimes these single strands fold up on themselves when complementary bases on the same strand stick together. Because of this versatility, RNA can generally make up many more kinds of three-dimensional shapes than can DNA.
Now, DNA, or deoxyribonucleic acid, is the place where genes are permanently stored. But what exactly is a “gene”? We’ve said that it’s like a blueprint for a protein product – but how does that relate to nucleotides and nitrogen bases?
Here’s how it works. The exact sequence of nitrogen bases – which biologists aptly call the “base sequence” – specifies the order in which to link certain amino acids together in order to make a functional protein. More specifically, the genetic code is read three bases at a time: these three-base groups are called triplets. Every triplet corresponds to a particular amino acid, and the exact sequence of triplets specifies the exact sequence of amino acids in the corresponding protein. Our bodies contain thousands of proteins, so, accordingly, our DNA molecules are extremely long. To be exact, there are 46 long strands of DNA in most human cells, each of which individual strand we call a chromosome. In summary, then, the exact sequence of nitrogen bases in our DNA tells our cells which proteins to make and how to make them.
In order to turn a gene into a protein, a special type of enzyme complex called a ribosome must read the information from the gene and use it to connect amino acids in the corresponding sequence. But since each cell has only one copy of each chromosome, the cell cannot afford to risk damage to the DNA. As such, the ribosome does not read the DNA directly, but rather reads a temporary, “disposable” copy of the gene. These temporary copies are made on RNA molecules, and these RNA molecules – sometimes called “messenger RNAs” – are read by the ribosome. Because RNA molecules contain the same four bases as DNA, except with uracil substituted for thymine, the RNA generally preserves the DNA’s gene information. Special enzymes called RNA polymerases make messenger RNAs by copying, or transcribing, the genes that are to be turned into protein – or, in the language of biologists, the genes that are to be expressed. In other words, RNA polymerase enzymes use the DNA base sequence as a “template” for synthesizing an RNA molecule to be used by ribosomes to make a protein.
Thus, we have explained basically how genes get turned into proteins. Genes are passed on directly from your parents – in fact, most people get 23 chromosomes from their biological mother and 23 from their biological father. So your cells make the same proteins that your parents’ bodies did! This passing on of genes is the molecular basis of heredity – it’s one of the major reasons why you look, think, and act something like each of your biological parents.
It’s important to note in addition that genes do not generally change much from generation to generation. They stay permanently fixed unless they acquire a random mutation, which results from a rare mistake in the copying of DNA during cell division. Most random mutations, as you can imagine, are destructive. For example, the disease phenylketonuria arises from a single base-substitution. Every once in a while, though, a mutation happens to be useful to the organism that possesses it. These helpful random mutations are the main driving force for evolution.
You might wonder, though, how a mere set of instructions for proteins can account for so much of the amazing complexity and uniqueness of our bodies and minds. But think of it this way: as we’ve seen, every living organism – including me, you, your neighbor’s dog, and your neighbor’s dog’s gut bacteria – is But a dizzyingly intricate meshwork of chemical reactions. Recall also that proteins make up a large fraction of our bodies’ hormones and enzymes. Enzymes, as we’ve seen, help facilitate certain chemical reactions; and one of the main functions of hormones is to tell our enzymes when to turn the “volume” up and down, so to speak, on each of these chemical reactions. As such, our bodies are like symphony orchestras of chemical reactions; genes are the sheet music; and enzymes and hormones are the conductors.
But our genes aren’t the only part of our biology that makes us who we are. There are several facts that assure us of this observation. For one, none of us is a perfect blend of our parents’ characteristics. In fact, many of us turn out to be quite different from our biological parents. Certainly each of us has a set of unique personality characteristics that neither of our parents has.
Moreover, nearly all of the cells in our body have the same exact set of genes, yet our cells show a diverse set of shapes, sizes, and functions. For instance, a neuron, muscle cell, liver cell, and skin cell all have the same DNA, yet they all look and act very differently from one another. So what accounts for this variation over and above genetics? This question makes up the province of epigenetics – or, as the name suggests, the study of organismal variation due to factors “above” the level of genetics.
In order to answer this question, we must examine how RNA polymerase enzymes know which genes to express, when to express them, and how many messenger RNAs to make. As we mentioned earlier, RNA polymerases are a kind of enzyme that makes a temporary RNA copy of a gene using DNA as a template; once synthesized, this RNA molecule gets read by ribosomes to make the protein that the gene specifies. Now, which genes are expressed and when actually determines the identity of a cell. In fact, neurons, liver cells, photoreceptor cells, and pancreas cells all express their own characteristic complement of genes. Some of these genes are common to nearly all cell types, whereas others are specialized to particular cells. For example, genes coding for the enzymes that break down sugars are expressed in nearly all living cells, whereas genes coding for certain hormones are expressed only in structures like the hypothalamus of the brain.
But how do RNA polymerase enzymes know which genes to express and when? The answer lies largely in the three-dimensional structure of DNA. As it happens, most DNA is found in a special complex called chromatin, which consists of one double-stranded DNA molecule wrapped around special proteins called histones. These histones can be packed together more or less tightly so that our cells can compact our DNA molecules into a small space. (Recall that DNA molecules are extremely long: for example, if we were to stretch out all the DNA from one cell in our bodies into a straight line, it would be about six feet long.)
Moreover, different segments of DNA are packed more or less tightly around histones than other segments. And the more tightly a region of DNA is packed around the histone, the harder it is for RNA polymerase enzymes to express that region of the DNA. In this case, you can think of DNA as a long strand of yarn, and the histones as bunches of tennis balls with the yarn wrapped around. The tighter the yarn is wrapped around the tennis balls, the harder it is to get in and grab it; conversely, when the yarn is wrapped around the tennis balls only loosely, it’s much easier to grab hold of it.
So what determines how tightly a region of DNA his packed around histones? In fact, there is another special set of enzymes that modifies the structure of the histone proteins, and yet another set of enzymes responsible for moving different regions of DNA onto different histones. Different histone structures bind DNA more or less tightly. In this podcast series, we’ll be talking mainly about three kinds of histone modifications: acetylation, methylation, and phosphorylation.
Acetylation occurs when we add an acetyl chemical group to certain amino acid residues on a histone. Conversely, de-acetylation occurs when we take one off. Fittingly, enzymes called histone acetyltransferases – or HATs, for short – put acetyl groups onto histones, and enzymes called histone de-acetylases – or HDACs – take them off. Generally speaking, the more acetyl groups a histone has, the less tightly DNA will bind the histone, and the more the corresponding genes will be expressed.
Methylation, on the other hand, occurs when we add a methyl chemical group to certain amino acid residues on the histone; and de-methylation occurs when we take the methyl off. Histone methyltransferases are responsible for methylating histones, and histone de-methylates de-methylate them. Some methylations cause histones to bind DNA more tightly, and other methylations cause histones to bind DNA less tightly. As such, some methylations are “activating,” and others are “deactivating.”
Finally, phosphorylation consists in adding a phosphoryl chemical group to certain amino acid residues on a histone. De-phosphorylation is the process of taking a phosphoryl group off. Generally speaking, phosphorylation is an activating modification, causing DNA to bind histones less tightly.
Histone-modifying enzymes respond to signals from within the cell, which signals result ultimately from environmental signals and experiences. The pattern of histone modifications in each of our cells is a multilayered repository of signals from our early development, our past experiences, and our current lifestyle.
The other major form of epigenetic modification is called DNA methylation. Note that DNA methylation is distinct from histone methylation. Whereas histone methylation occurs when a methyl group gets added to an amino acid on a histone, DNA methylation occurs when a methyl group gets added to a cytosine base on DNA. DNA methyltransferases catalyze this reaction. DNA methylation can be activating or deactivating. When it’s found in a special region of DNA called a promoter, the site where RNA polymerases generally bind, DNA methylation tends to reduce the expression of the corresponding gene. However, when it’s found in the middle of the protein-coding part of the gene, DNA methylation actually tends to increase the expression of the gene.
DNA methylation in a promoter can exert its effects both directly and indirectly. Sometimes, methylated cytosine residues – also called methyl-cytosines for short – attract certain regulatory proteins to that region of DNA. These regulatory proteins can do one of two things. Either they sit on top of the promoter and prevent RNA polymerases from reading the DNA, or they attract histone deacetylase enzymes, causing the histones associated with that region of DNA to bind the DNA more tightly. Both of these modifications result in a reduction in gene expression.
For simplicity’s sake, we often sort the proteins and enzymes involved in epigenetic modifications into three classes: readers, writers, and erasers. Readers involve regulatory proteins that recognize certain epigenetic modifications and effect some kind of response to them – for example, the proteins that recognize DNA methylation and sit on top of methylated regions of DNA are readers. Writers, like histone acetyltransferases and DNA methyltransferases, are enzymes that enact an epigenetic modification by putting a new chemical group onto DNA or histones. Erasers, by contrast, remove chemical groups from DNA and histones. Histone de-methylases are an example of an eraser.
Importantly, DNA methylation is the only epigenetic modification that can be passed down several generations. As such, our parents’ and grandparents’ behaviors and experiences can actually influence the expression of our genes, and hence, to a certain extent, the way that our minds and bodies work. We’ll explore the effects of transgenerational inheritance of DNA methylation in several of our podcasts.
Supplemental Diagrams
Memorable Quotes from Dr. Sweatt
Why “Neuroepigenetics” Needs Its Own Term
“The reason why the people in the field coined the term ‘neuroepigenetics’ is because once we and other people started getting interested in epigenetic molecular mechanisms in the adult nervous system, it sort of raised a conundrum, which is: the classical definition of an “epigenetic” mechanism is one that can be inherited, either across generations or across cell division in dividing cells… But if you’re talking about neurons in the adult nervous system, by definition, they can’t divide. So then, by that definition, nothing that happened in a neuron in the adult nervous system would be ‘epigenetic.’ … it became clear that these epigenetic molecular mechanisms, like DNA methylation and regulation of chromatin structure, were playing important roles in neurons. So we essentially coined a term, ‘neuroepigenetics,’ to describe the role of these epigenetic molecular mechanisms in cells where the signals weren’t heritable. So it sort of violated the typical, the classical definition of epigenetics.”
Early Intuitions as to Why Epigenetic Mechanisms Could Regulate Learning and Memory
“If you’re interested in learning and memory – memories that are behaviorally acquired, that can last a whole lifetime…then maybe it’s appealing to think about epigenetic mechanisms that, in development, are known to be able to trigger effects that last a lifetime, and then ask the question, ‘well, maybe those same mechanisms are involved in behavioral memory in the adult nervous system…’ and that evolution has been, you know, efficient to adapt some of those same mechanisms that are used in development to make a lifelong change – and use them for behaviorally-acquired and experientially-acquired memory in the adult nervous system. So it was really thinking about lifelong changes in development as analogous to lifelong changes in terms of cognitive neuroscience.”
Resistance to Neuroepigenetics from Epigeneticists
“… when we started to see changes in these supposedly permanent marks – epigenetic marks in the adult nervous system – there was, you know, pretty frank skepticism… by the classical epigeneticists. And, you know, sometimes the reviewers of our papers, in the early papers, would just say, basically, ‘I don’t believe that these data are correct, because we know that this is not true. This is not the way things work.’”
The Ascent of Neuroepigenetics into Mainstream Neuroscience
“I think that, over time – and we’re talking about a span of about fifteen years – enough different labs using a wide variety of different kinds of approaches made the same basic observations – that there was dynamic regulation of DNA methylation, in particular – that it got to the point where there was sort of an overwhelming amount of evidence that was consistent with the idea… And, you know, it’s really sort of odd for me now, because now dynamic regulation of cytosine methylation in the nervous system is a standard part of the way people think about [nervous system function]. And so now people – young people like you, taking, you know, classes in neuroepigenetics – just say “Yeah! Of course that’s the way it is!” But that’s a completely different way to think about it than was the case fifteen years ago.
Changes in the Way We Understand Humanity
“… one of the really interesting things about this discovery of epigenetic mechanisms is that they’re actually the molecular interface between genes and experience, or genes and environment – and there really is no dichotomy between genes and environment, or “nature” and “nurture.” There’s a constant dynamic interplay between those two things, and epigenetic mechanisms are, in a very literal sense, those mechanisms that sit right at the face of genes and environment – and are dynamically regulated, and allow environment to influence genes and genes to influence the environmental output of the organism, that is, its behavior… it’s one of the few examples that I can think of where contemporary scientific research has really sort of solved a historical, millennia-long philosophical debate, and come up with, actually, what is a third way to think about it that’s different than what was thought about it before.”
Unsolved Question: How Do Cells Know Which Cytosine to Methylate?
“So there’s about 800 million cytosines in your genome in the cells in your body, and, somehow, it’s clear that one specific cytosine out of the sequence can get picked out to be methylated, and the associated gene silenced, for example. Nobody has any real idea about how that happens.”
Unsolved Question: Are Neuroepigenetic Mechanisms Part of What Makes Us Each Unique?
“It’s interesting to me to think about the role of epigenetic mechanisms in individuality – in humans, for example – and how is it that we become the person that we are, that’s completely unique and distinct from every other human.”
Why We Should Work to Popularize Science
“Being able to help [laypersons] understand modern basic science discoveries can really help them understand how it is that science can improve the human condition, kind of broadly speaking… a more informed public can then understand why it is that it’s important to support research – basic, fundamental research – to try to understand how things work. And, you know, in a real way, allocate some of their hard-earned tax dollars to something that may seem esoteric on its surface, but really can have very important practical applications, and practical ways of improving the way we all go through life.”