by Frank Ryan
While the evidence for a causative role is not yet strong enough to be definitive, the possible association between this virus—now labeled MSRV/HERV-W—and MS is undergoing extensive further testing, so that in time we shall have an answer to this important question and perhaps to more of the questions that are beginning to accumulate about the potential viral contribution to various cancers as well as a wide range of illnesses that are included under the umbrella description of the autoimmune diseases.
In 2001, when the first draft of the complete human genome showed that roughly 45 percent of the human genome appeared to be made up of retroviruses, or virus-like entities, such as LINEs and SINEs, some biologists dismissed this huge genetic inheritance as junk, the graveyard of past viral infections. But today we have become a good deal more cautious in our interpretations. The 2001 papers in Science and Nature had shown that some 50 percent of the genome was accounted for between the protein-coding genes and the various virus-related sections, but the papers had also revealed that approximately 50 percent of our DNA appeared to code for nothing that we recognized at this time. Of course, some biologists once more labeled it junk, but others were now more cautious. This new mystery would become the raison d’être of a deliberate investigative enterprise, inspired by the very shock of our exposed ignorance beyond the tiny 1.5 percent fraction of protein-coding genes. This investigation, involving a consortium of research groups worldwide, would be encouraged and funded by a public research project launched by the National Human Genome Research Institute in the United States in September 2003. Its acronym was derived from the very nature of the mystery: the “Encyclopedia of DNA coding elements”—ENCODE.
The fact that selection can work simultaneously on both genetic and epigenetic variation complicates matters even further…models that incorporate the effects of epigenetic variations…show how [this] leads to different evolutionary dynamics.
EVA JABLONKA AND MARION J. LAMB
If we look at what happens when a fertilized egg develops into the complex wonder of the human baby, logic would tell us that the process of embryology must be directed by an integrated and coordinated system of control. The fertilized ovum, or “zygote,” is a pluripotent cell—a cell that can develop into any of the organs and tissues that make up the individual human being. When the zygote first begins to divide, the daughter cells retain this pluripotency throughout the very early divisions. If cells separate from the embryo at this stage, each cell is still capable of giving rise to a complete healthy individual. This is how identical twins, triplets, or quadruplets usually arise. But soon the developing mass of cells develops into two different entities: an encircling hollow ball of cells that will become the placenta and an inner cell mass that will become the fetus. At this stage, the symbiotic endogenous retroviruses kick in and express their envelope proteins, which help to create the deeply invasive placenta that, in a quasi-parasitic pattern, burrows into the maternal uterine wall and constructs the fused cell interface between the maternal and the fetal circulations. While this is happening, a complex array of signals takes over the control of the inner cell mass, instructing the cells to divide and multiply, but also recognizing very early the need for the cell types to change, so that selected embryonic cells begin to change into the forerunner cells of the different tissues and organs.
Here we face the enigma that all the cells in an organism have the same DNA, which incorporates the same sum of genes. Therefore different organ and tissue cell types must be determined by mechanisms other than the sum of all the genes they contain. From the studies of the Swedish scientists described in the previous chapter, we now know that the difference between a brain cell and, say, a kidney cell or a circulating blood cell, comes mainly from the profile of expression of genes within the cell. We also recall that each tissue-type cell also expresses a limited number of genes that appear to be particular to that cell—perhaps about half a dozen for each cell type. This fate of cells, and the organization of these cells into the growing complexity of form and function that will make up the different tissues as organs of the head and body parts, is controlled by what geneticists call the epigenetic system.
Some readers might become a trifle worried at this point, since there appears to be a general notion that epigenetics is immensely complicated. It is even fair to say that the world of epigenetics seemed confusing to scientists until recently—but the reason for this was that the definition and scope of epigenetics were undergoing a rapid evolution in themselves. As our understanding has grown, the basic principles have, thankfully, become much easier to grasp. In particular, our growing understanding of the so-called non-coding RNAs has clarified things so that not only can we redefine epigenetics in simpler terms but we can also see how it provides a fascinating answer to the remaining mystery of that huge unknown section of our human DNA.
The epigenetic system is essentially a system of regulatory control of the functioning of the genome. It comprises a number of different mechanisms that act in an integrated and coordinated manner to control the activation and closing down of genes. But its role also extends beyond genes to work in what might be compared to a housekeeping and regulatory coordination affecting the entire genome. The easiest way to understand this is to examine how the various mechanisms operate.
We have seen how a gene is the genetic sequence that codes for a protein, or perhaps more correctly, a parcel of different proteins. Our genome contains roughly 20,500 such genes. We have also seen how a specific cell type, and thus the makeup of the different tissues and organs of the body, is determined mostly by the profile of expression of a large number of genes. The epigenetic system decides that profile of genes, controlling which genes switch on, when they do so, what quantity of protein they express, and so on. Before we examine how it does so, I would like to explain something interesting about this epigenetic system of control.
The DNA that codes for genes and the other functional genetic sequences of the genome is fixed when the parental germ cells unite to form the fertilized cell, or zygote. This aspect of your genome remains exactly the same throughout your life unless changed by a mutation or an invading virus. But your epigenetic system, and its regulatory effects, is not fixed throughout your life. It is capable of changing its regulatory commands, for example by responding to signals coming from your internal physiology and even through signals coming from your environment. In plants, for example, it is the epigenetic system that tells them that spring has arrived. And in animals, including humans, the epigenetic system is similarly sensitive to important changes in your living circumstances, such as the impact of disease, protracted stress, severe pain, or starvation. In other words, although your genes stay the same throughout your life, the expression of those genes in your various tissues and organs can, and will, change because of signals arriving into the systems of epigenetic control. The implications go even deeper: your epigenome is capable of learning from experience and changing to accommodate that experience. More extraordinary still, those changes will sometimes be inherited by future generations of offspring through mechanisms known as epigenetic inheritance systems.
The inheritance of epigenetic changes through epigenetic inheritance systems means that epigenetics has evolutionary potential: this is why I included it as one of the mechanisms of “genomic creativity.” Moreover, the potential for outside influences to bring about epigenetic change offers exciting potential for medicine. For example, it might lead to future medical therapies aimed at changing the expression of disease-causing genes.
Today we recognize four main epigenetic control systems, which can be seen in the figure below:
Would you like to join me in a new journey on our metaphorical train? We find ourselves reversing along the twin track of the DNA of a gene, making our way back past the first exon, to arrive at the nearby stretch of DNA that is the “promoter”—the region that switches the gene on and off. As before, we hop down so we can observe what is happening as one of the
epigenetic mechanisms swings into operation.
We hear a deep buzzing sound nearby and are then startled as a small cloud looms into view, buzzing like a bee. The cloud is a protein called a DNA-methyltransferase. We see that it is bearing tiny clusters of atoms, resembling chemical beads—these are “methyl” chemical groups, made up of a carbon atom attached by covalent bonds to three hydrogen atoms. As we watch, the cloud attaches a methyl bead to a nucleotide in one of the sleepers.
“Go ahead—check which nucleotide.”
“It's a cytosine—a C.”
“Okay—so with the methyl chemical tagged on to this it is now a methylated cytosine. Believe it or not, this simple chemical change is all there is to one of the most powerful epigenetic regulatory mechanisms.”
We follow the progress of the protein cloud as it moves along the promoter, attaching more and more methyl beads, always to cytosines, until most of these within the promoter sequence have been methylated.
“That's it—the promoter has been closed down. So now the gene can't be switched on.”
“You mean it's closed down for good?”
“Nothing in the epigenetic system is quite as fixed as that. To close the promoter down really hard will require some additional silencing—using a second mechanism of epigenetic shutdown. But now I want you to take a look at how methylation can become an epigenetic inheritance system. To understand this you need to take a closer look at the nucleotides adjacent to the cytosines.”
“You mean the other halves of the sleepers?”
“No—we already know that they will be guanines. Because cytosine always binds to guanine. Look at the adjacent sleepers.”
It takes you a minute or two, because you don't see the pattern until you have examined half a dozen or so.
“There always seem to be guanines adjacent to the methylated cytosines.”
“That's right. These cytosine-guanine ‘couplets’ are the key to how the methylation status of genes is inherited to new generations. If we now climb back aboard our train we can actually watch it happen.”
In the blink of an eye we find ourselves entering the genome of a germ-forming cell that is in the process of copying its genome into a sperm or an ovum. We hop down again so we can watch what is happening to another promoter region as it is in the process of being copied. And here we notice something very interesting take place.
To begin with, I draw your attention to one of the C-G couplets. We can hardly miss the fact that the C is methylated—it has its smoky bead attached. We watch as the double helix cleaves apart, and then the process of copying begins, with nucleotides being matched with one another and the new rail forming.
We follow the copying from the “sense” strand to the new “antisense” strand and, with a chuckle of recognition, we observe that wherever there is a C-G couplet on the sense strand, it creates a mirror image copy of G-C in the daughter strand. I bid you wait so we can witness another surprise.
With amazing speed, we observe the arrival of another buzzing cloud, which appears to notice the unmethylated couplets on the daughter strand that stand out in contrast with the methylated couplets opposite on the maternal strand. With that same efficiency as before, it moves along the daughter strand, methylating every complementary couplet on the daughter line.
“The methylation status has been transferred?”
“We have witnessed the operation of an ‘epigenetic inheritance system’ which is a way in which a change in the methylation code can be inherited by future generations. What's more, our train analogy has allowed us to get close enough to witness something definitive. We have seen how methylation can switch off the expression of a gene. If inherited by future generations, this would have evolutionary potential since it would change the heredity of those future individuals through altering gene-profile expression. In other words, methylation status can bring about hereditary change. It's a force within my umbrella of genomic creativity. Yet, as we see, it comprises adding a simple chemical to a preexisting nucleotide, cytosine. There is no actual change in any DNA sequence. Every other force of genomic creativity that we have seen to date—mutation, genetic symbiosis, hybridization—acts through changing DNA sequences, yet this epigenetic mechanism changes heredity without changing genes. An epigenetic inheritance system is a genomic force but it is not a genetic mechanism. This is why I coined the term ‘genomic’ creativity rather than ‘genetic’ creativity.”
Methylation is a very important epigenetic mechanism during the formation of the embryo in the mother's womb. The vitamin folic acid plays an important role in this process of methylation during early embryological development. This is why a lack of folic acid in the mother's diet in those early months of pregnancy can damage the fetus and increase the propensity for developing spina bifida. Extensive defects in the methylation patterns throughout the genome is also a feature of many forms of cancer, a finding that is being extensively investigated in the hope that it will provide enlightenment and potential avenues of treatment in the future.
Another situation where methylation status may be important is morbid obesity, with its tendency to maturity onset diabetes. Some studies have shown that epigenetic factors, particularly changes in methylation status in key areas of the genome, may be playing some part in this.
“Can we do nothing to help ourselves?”
“Yes, we can. Unlike the fixity of genes, epigenetic regulatory systems are amenable to change. And something as simple as regular exercise can change things back to a healthier epigenetic code.”
“But, hold on! What's happening? We appear to be moving again.”
“Time for another trip. I want you to observe another epigenetic mechanism as it actually happens. But this time we are going to restore the double helix in all of its splendor.”
We watch as our train moves away from the genome in the ultramicroscopic landscape, sufficient to observe the spectacular beauty of DNA's natural twist.
“This time we need to observe the actual structure of the chromosome—in this case, human chromosome 6, the chromosome that contains that supremely important Major Histocompatibility Complex. And our first surprise will be to discover, in passing, that those early geneticists who made life difficult for Oswald Avery may have had a point when they insisted that proteins had something to do with the mystery of the gene.”
We discover to our delight that our magical steam engine is capable of hovering within the ultramicroscopic landscape at sufficient distance for us to observe the double helix grow small enough to appear as a fine thread in the distance—far enough away for us to notice things that were not apparent before.
Not only does the incredibly long molecule of DNA spiral within its molecular structure, the twin track then coils for a second time in a broad spiral around some strange globular structures that from this distance resemble tennis balls. The tennis balls are proteins called histones, and they are packed together as structural units of eight balls, in racks of four on four. These eight-packs are themselves wound around a central spine of another linear protein, a central spine unlike the phosphate spines of the DNA molecule. This cruder secondary spiral of the DNA thread winding around the eight-packs of histones extends the entire length of the chromosome, extending away into the fathomless distance.
You appear to be nonplussed.
“It is extraordinary to glimpse the gargantuan wonder of this secondary chromosomal structure—if my mental arithmetic is anywhere near accurate, chromosome 6 is something like 150 million nucleotides long.”
“Where are we headed?”
“To the stretch that codes for the Major Histocompatibility Complex.”
Now you turn to me with a new question on your lips: “What's this new lesson about?”
“We're going to take a look at a second epigenetic system, called the histone code. And like the methylation status, it's really very simple.”
You look a trifle dubious.
“It's all about things the
epigeneticists call histone tails.”
The engine chugs closer to a single section of the chromosome, to a place where we can examine the structure where the eight-packs of tennis balls are inclined to us, side on. These appear to be packaged together like newly harvested onions, bound tight to the central string of the spine.
The tight packaging of the histone eight-packs suddenly opens up. We watch how the thread of DNA loosens up as the individual eight-packs are now teased out into a looser arrangement.
I edge the engine closer. “Look more closely at the eight-packs.”
“There's something poking out…They're sporting tails.”
“Chemical tails—yes.”
Since the histones of the eight-packs are proteins, they are made up of long strings of amino acids. These tails, trailing from the histones, are side chains of amino acids. The key to understanding is that these amino acid tails poke out beyond the broad spiral of DNA thread that is wrapped around the histones. As we watch, one of those buzzing protein clouds hoves into view, hauling one of those chemical beads we saw before. We watch in silence as it attaches the bead to one of the dangling tails. Immediately the whole arrangement begins to change again. The loosened structure of the histone packs begins to tighten into the onion pack again.
“It's coming together.”
“The histone proteins are exceedingly sensitive to the attachment of certain chemical molecules to their tails.”
“Like moths to pheromones?”
Now you have me chuckling with you. “Sometimes it's our old friend, the methyl group. But it can be an acetate group, or a phosphate—there's a range of different simple chemical groups that can trigger the change. And the change can only be one or the other, a local loosening up of the histone packs or a tightening up. The chemicals attach to specific amino acids within the histone. For example, it might be the adding of an acetyl group to the amino acid lysine or the adding of a phosphate group to serine or the adding of a methyl group this time not to cytosine of the DNA but lysine on the histone tail.”
