The Epigenetics Revolution (11 page)
Read The Epigenetics Revolution Online
Authors: Nessa Carey
Tags: #Science/Life Sciences/Genetics and Genomics
Figure 4.4
The chemical structures of the amino acid lysine and its epigenetically modified form, acetyl-lysine. C: carbon; H: hydrogen; N: nitrogen; O: oxygen. For simplicity, some carbon atoms have not been explicitly shown, but are present where there is a junction of two lines.
The chemical structures of the amino acid lysine and its epigenetically modified form, acetyl-lysine. C: carbon; H: hydrogen; N: nitrogen; O: oxygen. For simplicity, some carbon atoms have not been explicitly shown, but are present where there is a junction of two lines.
So back in 1996 there was a nice simple story. DNA methylation turned genes off and histone acetylation turned genes on. But gene expression is much more subtle than genes being either on or off. Gene expression is rarely an on-off toggle switch; it’s much more like the volume dial on a traditional radio. So perhaps it was unsurprising that there turned out to be more than one histone modification. In fact, more than 50 different epigenetic modifications to histone proteins have been identified since David Allis’s initial work, both by him and by a large number of other laboratories
9
. These modifications all alter gene expression but not always in the same way. Some histone modifications push gene expression up, others drive it down. The pattern of modifications is referred to as a histone code
10
. The problem that epigeneticists face is that this is a code that is extraordinarily difficult to read.
9
. These modifications all alter gene expression but not always in the same way. Some histone modifications push gene expression up, others drive it down. The pattern of modifications is referred to as a histone code
10
. The problem that epigeneticists face is that this is a code that is extraordinarily difficult to read.
Imagine a chromosome as the trunk of a very big Christmas tree. The branches sticking out all over the tree are the histone tails and these can be decorated with epigenetic modifications. We pick up the purple baubles and we put one, two or three purple baubles on some of the branches. We also have green icicle decorations and we can put either one or two of these on some branches, some of which already have purple baubles on them. Then we pick up the red stars but are told we can’t put these on a branch if the adjacent branch has any purple baubles. The gold snowflakes and green icicles can’t be present on the same branch. And so it goes on, with increasingly complex rules and patterns. Eventually, we’ve used all our decorations and we wind the lights around the tree. The bulbs represent individual genes. By a magical piece of software programming, the brightness of each bulb is determined by the precise conformation of the decorations surrounding it. The likelihood is that we would really struggle to predict the brightness of most of the bulbs because the pattern of Christmas decorations is so complicated.
That’s where scientists currently are in terms of predicting how all the various histone modification combinations work together to influence gene expression. It’s reasonably clear in many cases what individual modifications can do, but it’s not yet possible to make accurate predictions from complex combinations.
There are major efforts being made to learn how to understand this code, with multiple labs throughout the world collaborating or competing in the use of the fastest and most complex technologies to address this problem. The reason for this is that although we may not be able to read the code properly yet, we know enough about it to understand that it’s extremely important.
Build a better mousetrap
Some of the key evidence comes from developmental biology, the field from which so many great epigenetic investigators have emerged. As we have already described, the single-celled zygote divides, and very quickly daughter cells start to take on discrete functions. The first noticeable event is that the cells of the early embryo split into the inner cell mass (ICM) and the trophoectoderm. The ICM cells in particular start to differentiate to form an increasing number of different cell types. This rolling of the cells down the epigenetic landscape is, to quite a large degree, a self-perpetuating system.
The key concept to grasp at this stage is the way that waves of gene expression and epigenetic modifications follow on from each other. A useful analogy for this is the game of
Mousetrap
, first produced in the early 1960s and still on sale today. Players have to build an insanely complex mouse trap during the course of the game. The trap is activated at one end by the simple act of releasing a ball. This ball passes down and through all sorts of contraptions including a slide, a kicking boot, a flight of steps and a man jumping off a diving board. As long as the pieces have been put together properly, the whole ridiculous cascade operates perfectly, and the toy mice get caught under a net. If one of the pieces is just slightly mis-aligned, the crazy sequence judders to a halt and the trap doesn’t work.
Mousetrap
, first produced in the early 1960s and still on sale today. Players have to build an insanely complex mouse trap during the course of the game. The trap is activated at one end by the simple act of releasing a ball. This ball passes down and through all sorts of contraptions including a slide, a kicking boot, a flight of steps and a man jumping off a diving board. As long as the pieces have been put together properly, the whole ridiculous cascade operates perfectly, and the toy mice get caught under a net. If one of the pieces is just slightly mis-aligned, the crazy sequence judders to a halt and the trap doesn’t work.
The developing embryo is like
Mousetrap
. The zygote is pre-loaded with certain proteins, mainly from the egg cytoplasm. These egg-derived proteins move into the nucleus and bind to target genes, which we’ll call
Boots
(in honour of
Mousetrap
), and regulate their expression. They also attract a select few epigenetic enzymes to the
Boots
genes. These epigenetic enzymes may also have been ‘donated’ from the egg cytoplasm and they set up longer-lasting modifications to the DNA and histone proteins of chromatin, also influencing how these
Boots
genes are switched on or off. The
Boots
proteins bind to the
Divers
genes, and switch these on. Some of these
Divers
genes may themselves encode epigenetic enzymes, which will form complexes on members of the
Slides
family of genes, and so on. The genetic and epigenetic proteins work together in a seamless orderly procession, just like the events in
Mousetrap
once the ball has been released. Sometimes a cell will express a little more or a little less of a key factor, one whose expression is on a finely balanced threshold. This has the potential to alter the developmental path that the cell takes, as if twenty
Mousetrap
games had been connected up. Slight deviations in how the pieces were fitted together, or how the ball rolled at critical moments, would trigger one trap and not another.
Mousetrap
. The zygote is pre-loaded with certain proteins, mainly from the egg cytoplasm. These egg-derived proteins move into the nucleus and bind to target genes, which we’ll call
Boots
(in honour of
Mousetrap
), and regulate their expression. They also attract a select few epigenetic enzymes to the
Boots
genes. These epigenetic enzymes may also have been ‘donated’ from the egg cytoplasm and they set up longer-lasting modifications to the DNA and histone proteins of chromatin, also influencing how these
Boots
genes are switched on or off. The
Boots
proteins bind to the
Divers
genes, and switch these on. Some of these
Divers
genes may themselves encode epigenetic enzymes, which will form complexes on members of the
Slides
family of genes, and so on. The genetic and epigenetic proteins work together in a seamless orderly procession, just like the events in
Mousetrap
once the ball has been released. Sometimes a cell will express a little more or a little less of a key factor, one whose expression is on a finely balanced threshold. This has the potential to alter the developmental path that the cell takes, as if twenty
Mousetrap
games had been connected up. Slight deviations in how the pieces were fitted together, or how the ball rolled at critical moments, would trigger one trap and not another.
The names in our analogy are made up, but we can apply this to a real example. One of the key proteins in the very earliest stages of embryonic development is Oct4. Oct4 protein binds to certain key genes, and also attracts a specific epigenetic enzyme. This enzyme modifies the chromatin and alters the regulation of that gene. Both Oct4 and the epigenetic enzyme with which it works are essential for development of the early embryo. If either is absent, the zygote can’t even develop as far as creating an ICM.
The patterns of gene expression in the early embryo eventually feed back on themselves. When certain proteins are expressed, they can bind to the
Oct4
promoter and switch off expression of this gene. Under normal circumstances, somatic cells just don’t express Oct4. It would be too dangerous for them to do so because Oct4 could disrupt the normal patterns of gene expression in differentiated cells, and make them more like stem cells.
Oct4
promoter and switch off expression of this gene. Under normal circumstances, somatic cells just don’t express Oct4. It would be too dangerous for them to do so because Oct4 could disrupt the normal patterns of gene expression in differentiated cells, and make them more like stem cells.
This is exactly what Shinya Yamanaka did when he used Oct4 as a reprogramming factor. By artificially creating very high levels of Oct4 in differentiated cells, he was able to ‘fool’ the cells into acting like early developmental cells. Even the epigenetic modifications were reset – that’s how powerful this gene is.
Normal development has yielded important evidence of the significance of epigenetic modifications in controlling cell fate. Cases where development goes awry have also shown us how important epigenetics can be.
For example, a 2010 publication in
Nature Genetics
identified the mutations that cause a rare disease called Kabuki syndrome. Kabuki syndrome is a complex developmental disorder with a range of symptoms that include mental retardation, short stature, facial abnormalities and cleft palate. The paper showed that Kabuki syndrome is caused by mutations in a gene called
MLL2
11
. The MLL2 protein is an epigenetic writer that adds methyl groups to a specific lysine amino acid at position 4 on histone H3. Patients with this mutation are unable to write their epigenetic code properly, and this leads to their symptoms.
Nature Genetics
identified the mutations that cause a rare disease called Kabuki syndrome. Kabuki syndrome is a complex developmental disorder with a range of symptoms that include mental retardation, short stature, facial abnormalities and cleft palate. The paper showed that Kabuki syndrome is caused by mutations in a gene called
MLL2
11
. The MLL2 protein is an epigenetic writer that adds methyl groups to a specific lysine amino acid at position 4 on histone H3. Patients with this mutation are unable to write their epigenetic code properly, and this leads to their symptoms.
Human diseases can also be caused by mutations in enzymes that remove epigenetic modifications, i.e. ‘erasers’ of the epigenetic code. Mutations in a gene called
PHF8
, which removes methyl groups from a lysine at position 20 on histone H3, cause a syndrome of mental retardation and cleft palate
12
. In these cases, the patient’s cells put epigenetic modifications on without problems, but don’t remove them properly.
PHF8
, which removes methyl groups from a lysine at position 20 on histone H3, cause a syndrome of mental retardation and cleft palate
12
. In these cases, the patient’s cells put epigenetic modifications on without problems, but don’t remove them properly.
It’s interesting that although the MLL2 and PHF8 proteins have different roles, the clinical symptoms caused by mutations in these genes have overlaps in their presentation. Both lead to cleft palate and mental retardation. Both of these symptoms are classically considered as reflecting problems during development. Epigenetic pathways are important throughout life, but seem to be particularly significant during development.
In addition to these histone writers and erasers there are over 100 proteins that act as ‘readers’ of this histone code by binding to epigenetic marks. These readers attract other proteins and build up complexes that switch on or turn off gene expression. This is similar to the way that MeCP2 helps turn off expression of genes that are carrying DNA methylation.
Histone modifications are different to DNA methylation in a very important way. DNA methylation is a very stable epigenetic change. Once a DNA region has become methylated it will tend to stay methylated under most conditions. That’s why this epigenetic modification is so important for keeping neurons as neurons, and why there are no teeth in our eyeballs. Although DNA methylation
can
be removed in cells, this is usually only under very specific circumstances and it’s quite unusual for this to happen.
can
be removed in cells, this is usually only under very specific circumstances and it’s quite unusual for this to happen.
Most histone modifications are much more plastic than this. A specific modification can be put on a histone at a particular gene, removed and then later put back on again. This happens in response to all sorts of stimuli from outside the cell nucleus. The stimuli can vary enormously. In some cell types the histone code may change in response to hormones. These include insulin signalling to our muscle cells, or oestrogen affecting the cells of the breast during the menstrual cycle. In the brain the histone code can change in response to addictive drugs such as cocaine, whereas in the cells lining the gut, the pattern of epigenetic modifications will alter depending on the amounts of fatty acids produced by the bacteria in our intestines. These changes in the histone code are one of the key ways in which nurture (the environment) interacts with nature (our genes) to create the complexity of every higher organism on earth.
Histone modifications also allow cells to ‘try out’ particular patterns of gene expression, especially during development. Genes become temporarily inactivated when repressive histone modifications (those which drive gene expression down) are established on the histones near those genes. If there is an advantage to the cell in those genes being switched off, the histone modifications may last long enough to lead to DNA methylation. The histone modifications attract reader proteins that build up complexes of other proteins on the nucleosome. In some cases the complexes may include DNMT3A or DNMT3B, two of the enzymes that deposit methyl groups on CpG DNA motifs. Under these circumstances, the DNMT3A or 3B can ‘reach across’ from the complex on the histone and methylate the adjacent DNA. If enough DNA methylation takes place, expression of the gene will shut down. In extreme circumstances the whole chromosome region may become hyper-compacted and inactivated for multiple cell divisions, or for decades in a non-dividing cell like a neuron.
Why have organisms evolved such complex patterns of histone modifications to regulate gene expression? The systems seem particularly complex when you contrast them with the fairly all-or-nothing effects of DNA methylation. One of the reasons is probably because the complexity allows sophisticated fine-tuning of gene expression. Because of this, cells and organisms can adapt their gene expression appropriately in response to changes in their environment, such as availability of nutrients or exposure to viruses. But as we shall see in the next chapter, this fine-tuning can result in some very strange consequences indeed.
There are two things in life for which we are never prepared: twins.
Josh Billings
Identical twins have been a source of fascination in human cultures for millennia, and this fascination continues right into the present day. Just taking Western European literature as one source, we can find the identical twins Menaechmus and Sosicles in a work of Plautus from around 200 B.C.; the re-working of the same story by Shakespeare in
The Comedy of Errors
, written around 1590; Tweedledum and Tweedledee in Lewis Carroll’s
Through the Looking-Glass, and What Alice Found There
written in 1871; right up to the Weasley twins in the
Harry Potter
novels of J. K. Rowling. There is something inherently intriguing about two people who seem exactly the same as one another.
The Comedy of Errors
, written around 1590; Tweedledum and Tweedledee in Lewis Carroll’s
Through the Looking-Glass, and What Alice Found There
written in 1871; right up to the Weasley twins in the
Harry Potter
novels of J. K. Rowling. There is something inherently intriguing about two people who seem exactly the same as one another.
But there is something that interests all of us even more than the extraordinary similarities of identical twins, and that is when we can see their differences. It’s a device that’s been repeatedly used in the arts, from Frederic and Hugo in Jean Anhouil’s
Ring around the Moon
to Beverley and Elliott Mantle in David Cronenberg’s
Dead Ringers
. Taking this to its extreme you could even cite Dr Jekyll and his alter ego Mr Hyde, the ultimate ‘evil twin’. The differences between identical twins have certainly captured the imaginations of creative people from all branches of the arts, but they have also completely captivated the world of science.
Ring around the Moon
to Beverley and Elliott Mantle in David Cronenberg’s
Dead Ringers
. Taking this to its extreme you could even cite Dr Jekyll and his alter ego Mr Hyde, the ultimate ‘evil twin’. The differences between identical twins have certainly captured the imaginations of creative people from all branches of the arts, but they have also completely captivated the world of science.
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