The Epigenetics Revolution (40 page)
Read The Epigenetics Revolution Online
Authors: Nessa Carey
Tags: #Science/Life Sciences/Genetics and Genomics
In between the telomeres and the main parts of the chromosome are stretches of DNA referred to as sub-telomeric regions. These contain lots of runs of repetitive DNA. These repeats are less restricted in sequence than the telomeres. The sub-telomeric regions contain a low frequency of genes. They contain some CpG motifs so these regions can be modified by DNA methylation, in addition to histone modifications.
The types of epigenetic modifications normally found at telomeres and the sub-telomeric regions are the ones that are highly repressive. Because there are so few genes in these regions anyway, these modifications probably aren’t used to switch off individual genes. Instead, these repressive epigenetic modifications are probably involved in ‘squashing down’ the ends of the chromosomes. The epigenetic modifications attract proteins that coat the ends of the chromosomes, and help them to stay as tightly coiled up, and as dense and inaccessible as possible. It’s a little like covering the ends of a pipe in insulation.
It’s potentially a problem for a cell that all its telomeres have the same DNA sequence, because identical sequences in a nucleus tend to find and bind to one another. Such close proximity creates a big risk that the ends of different chromosomes will link up, especially if they get damaged and opened up. This can lead to all sorts of errors as the cell struggles to sort out chains of chromosomes, and may result in ‘mixed-up’ chromosomes similar to the one that causes chronic myeloid leukaemia. By coating the telomeres with repressive modifications that make the ends of the chromosomes really densely packed, there’s less chance that different chromosomes will join up inappropriately.
The cell is, however, stuck with a dilemma, as shown in
Figure 13.1
.
Figure 13.1
.
If the telomeres get too short, the cell tends to shut down. But if the telomeres get too long, there’s an increased risk of different chromosomes linking up, and creating new cancer-promoting genes. Cell shut-down is probably a defence mechanism that has evolved to minimise the risk of creating new cancer-inducing genes. This is one of the reasons why it’s likely to be very difficult to create drugs that increase longevity without increasing the risk of cancer as well.
What happens when we create new pluripotent cells? This could be through somatic cell nuclear transfer, as we saw in
Chapter 1
, or through creation of iPS cells, as we saw in
Chapter 2
. We may use these techniques to create cloned non-human animals, or human stem cells to treat degenerative diseases. In both cases, we want to create cells with normal longevity. After all, there is little point creating a new prize stallion, or cells to implant into the pancreas of a teenager with diabetes, if the horse or the cells die of telomere ‘old age’ within a short time.
Chapter 1
, or through creation of iPS cells, as we saw in
Chapter 2
. We may use these techniques to create cloned non-human animals, or human stem cells to treat degenerative diseases. In both cases, we want to create cells with normal longevity. After all, there is little point creating a new prize stallion, or cells to implant into the pancreas of a teenager with diabetes, if the horse or the cells die of telomere ‘old age’ within a short time.
That means we need to create cells with telomeres that are about the same length as the ones in normal embryos. In nature, this occurs because the chromosomes in the germline are protected from telomere shortening. But if we are generating pluripotent cells from relatively adult cells, we are dealing with nuclei where the telomeres are already likely to be relatively short, because the ‘starter’ cells were taken from adults, whose chromosomes are getting shorter with age.
Figure 13.1
Both abnormal shortening and lengthening of telomeres have potentially deleterious consequences for cells.
Both abnormal shortening and lengthening of telomeres have potentially deleterious consequences for cells.
Luckily, something unusual happens when we create pluripotent cells experimentally. When iPS cells are created, they switch on expression of a gene called telomerase. Telomerase normally keeps telomeres at a healthy long length. However, as we get older, the telomerase activity in our cells starts to drop. It’s important to switch on telomerase in iPS cells, or the cells would have very short telomeres and wouldn’t create very many generations of daughter cells. The Yamanaka factors induce the expression of high levels of telomerase in iPS cells.
But we can’t use telomerase to try to reverse or slow human ageing. Even if we could introduce this enzyme into cells, perhaps by using gene therapy, the chances of inducing cancers would be too great. The telomere system is finely balanced, and so is the trade-off between ageing and cancer.
Both histone deacetylase inhibitors and DNA methyltransferase inhibitors improve the efficiency of the Yamanaka factors. This might be partly because these compounds help to remove some of the repressive modifications at the telomeres and subtelomeric regions. This may make it easier for telomerase to build up the telomeres as the cells are reprogrammed.
The interaction of epigenetic modifications with the telomere system takes us a little further away from a simple correlation between epigenetics and ageing. It moves us closer to a model where we can start to develop confidence that epigenetic mechanisms may actually play a causative role in at least some aspects of ageing.
Is your beer getting old?
To investigate this more fully, scientists have made extensive use of an organism we all encounter every day of our lives, whenever we eat a slice of bread or drink a bottle of beer. The scientific term for this model organism is
Saccharomyces cerevisiae
, but we generally know it by its more common name of brewer’s yeast. We’ll stick with yeast, for short.
Saccharomyces cerevisiae
, but we generally know it by its more common name of brewer’s yeast. We’ll stick with yeast, for short.
Although yeast is a simple one-celled organism, it is actually very like us in some really fundamental ways. It has a nucleus in its cells (bacteria don’t have this) and contains many of the same proteins and biochemical pathways as higher organisms such as mammals.
Because yeast are such simple organisms, they’re very easy to work with experimentally. A yeast cell (mother) can generate new cells (daughters) in a relatively straightforward way. The mother cell copies its DNA. A new cell buds off from the side of the mother cell. This daughter cell contains the correct amount of DNA, and drifts off to act as a completely independent new single-celled organism. Yeast divide to form new cells really quickly, meaning experiments can be run in a few weeks rather than taking the months or years that are required for some higher organisms, and especially mammals. Yeast can be grown either in a liquid soup, or plated out onto a Petri dish, making them very easy to handle. It’s also fairly straightforward to create mutations in interesting genes.
Yeast have a specific feature that has made them one of the favourite model systems of epigeneticists. Yeast never methylate their DNA, so all epigenetic effects
must
be caused by histone modifications. There’s also another helpful feature of yeast. Each time a yeast mother cell gives rise to a daughter cell, the bud leaves a scar on the mother. This makes it really easy to work out how many times a cell has divided. There are two types of ageing in yeast and these each have parallels to human ageing, as shown in
Figure 13.2
.
must
be caused by histone modifications. There’s also another helpful feature of yeast. Each time a yeast mother cell gives rise to a daughter cell, the bud leaves a scar on the mother. This makes it really easy to work out how many times a cell has divided. There are two types of ageing in yeast and these each have parallels to human ageing, as shown in
Figure 13.2
.
Most of the emphasis in ageing research has been on replicative ageing, and trying to understand why cells lose their ability to divide. Replicative ageing in mammals is clearly related to some obvious symptoms of getting older. For example, skeletal muscle contains specialised stem cells called satellite cells. These can only divide a certain number of times. Once they are exhausted, you can’t create new muscle fibres.
Figure 13.2
The two models of ageing in yeast, relevant for dividing and non-dividing cells.
The two models of ageing in yeast, relevant for dividing and non-dividing cells.
Substantial progress has been made in understanding replicative ageing in yeast. One of the key enzymes in controlling this process is called Sir2 and it’s an epigenetic protein. It affects replicative ageing in yeast through two pathways. One seems to be specific to yeast, but the other is found in numerous species right through the evolutionary tree, all the way up to humans.
Sir2 is a histone deacetylase. Mutant yeast that over-express Sir2 have a replicative lifespan that is at least 30 per cent longer than normal
8
. Conversely, yeast that don’t express Sir2 have a reduced lifespan
9
, about 50 per cent shorter than usual. In 2009, Professor Shelley Berger, an incredibly dynamic scientist at the University of Pennsylvania whose group has been very influential in molecular epigenetics, published the results of a really elegant set of genetic and molecular experiments in yeast.
8
. Conversely, yeast that don’t express Sir2 have a reduced lifespan
9
, about 50 per cent shorter than usual. In 2009, Professor Shelley Berger, an incredibly dynamic scientist at the University of Pennsylvania whose group has been very influential in molecular epigenetics, published the results of a really elegant set of genetic and molecular experiments in yeast.
Her research showed that the Sir2 protein influences ageing by taking acetyl groups off histone proteins, and not through any other roles this enzyme might carry out
10
. This was a key experiment, because Sir2, like many histone deacetylases, has rather loose molecular morals. It doesn’t just remove acetyl groups from histone proteins. Sir2 will take acetyl groups away from at least 60 other proteins in the cell. Many of these proteins have nothing to do with chromatin or with gene expression. Shelley Berger’s work was crucial for demonstrating that Sir2 influences ageing precisely because of its effects on histone proteins. The altered epigenetic pattern on the histones in turn influenced gene expression.
10
. This was a key experiment, because Sir2, like many histone deacetylases, has rather loose molecular morals. It doesn’t just remove acetyl groups from histone proteins. Sir2 will take acetyl groups away from at least 60 other proteins in the cell. Many of these proteins have nothing to do with chromatin or with gene expression. Shelley Berger’s work was crucial for demonstrating that Sir2 influences ageing precisely because of its effects on histone proteins. The altered epigenetic pattern on the histones in turn influenced gene expression.
These data, showing that epigenetic modifications of histones really do have a major influence on ageing, gave scientists in this field a big confidence boost that they were on the right track. The importance of Sir2 doesn’t seem to be restricted to yeast. If we over-express Sir2 in our favourite worm,
C. elegans
11
,
the worm lives longer. Fruit flies that over-expressed Sir2 had up to a 57 per cent increase in lifespan
12
. So, could this gene also be important in human ageing?
C. elegans
11
,
the worm lives longer. Fruit flies that over-expressed Sir2 had up to a 57 per cent increase in lifespan
12
. So, could this gene also be important in human ageing?
There are seven versions of the
Sir2
gene in mammals, called
SIRT1
through to
SIRT7
. Much of the attention in the human field has focused on
SIRT6
, an unusual histone deacetylase. The breakthroughs in this field have come from the laboratory of Katrin Chua, a young Assistant Professor at the Stanford Center on Longevity (and also the sister of Amy Chua who wrote the highly controversial mothering memoir
Battle Hymn of the Tiger Mother
).
Sir2
gene in mammals, called
SIRT1
through to
SIRT7
. Much of the attention in the human field has focused on
SIRT6
, an unusual histone deacetylase. The breakthroughs in this field have come from the laboratory of Katrin Chua, a young Assistant Professor at the Stanford Center on Longevity (and also the sister of Amy Chua who wrote the highly controversial mothering memoir
Battle Hymn of the Tiger Mother
).
Katrin Chua created mice which never expressed any Sirt6 protein, even during their development (they are known as
Sirt6
knockout mice). These animals seemed normal at birth, although they were rather small. But from two weeks of age onwards they developed a whole range of conditions that mimicked the ageing process. These included loss of fat under the skin, spinal curvature, and metabolism deficits. The mice died by one month of age, whereas a normal mouse can live for up to two years under laboratory conditions.
Sirt6
knockout mice). These animals seemed normal at birth, although they were rather small. But from two weeks of age onwards they developed a whole range of conditions that mimicked the ageing process. These included loss of fat under the skin, spinal curvature, and metabolism deficits. The mice died by one month of age, whereas a normal mouse can live for up to two years under laboratory conditions.
Most histone deacetylases are very promiscuous. By this we mean they will deacetylate any acetylated histone they can find. Indeed, as mentioned above, many don’t even restrict themselves to histones, and will take acetyl groups off all sorts of proteins. However, SIRT6 isn’t like this. It only takes the acetyl groups off two specific amino acids – lysine 9 and lysine 56, both on histone H3. The enzyme also seems to have a preference for histones that are positioned at telomeres. When Katrin Chua knocked out the
SIRT6
gene in human cells, she found that the telomeres of these cells got damaged, and the chromosomes began to join up. The cells lost the ability to divide any further and pretty much shut down most of their activities
13
.
SIRT6
gene in human cells, she found that the telomeres of these cells got damaged, and the chromosomes began to join up. The cells lost the ability to divide any further and pretty much shut down most of their activities
13
.
This suggested that human cells need SIRT6 so that they can maintain the healthy structures of telomeres. But this wasn’t the only role of the SIRT6 protein. Acetylation of histone 3 at amino acid 9 is associated with gene expression. When SIRT6 removes this modification, this amino acid can be methylated by other enzymes present in the cell. Methylation at this position on the histone is associated with gene repression. Katrin Chua performed further experiments which confirmed that changing the expression levels of SIRT6 changed the expression of specific genes.
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