Our cells have therefore developed very sophisticated and fast-acting pathways to repair chromosome breaks as rapidly as possible, in order to prevent these sorts of fusions. To do this, our cells must be able to recognise loose ends of DNA. These are created when a chromosome breaks in two.
But there’s a problem. Every chromosome in our cell quite naturally has two loose ends of DNA, one at each end. Something must stop the DNA repair machinery from thinking these ends need to be repaired. That something is a specialised structure called the telomere. There is a telomere at each end of every chromosome, making a total of 92 telomeres per cell in humans. They stop the DNA repair machinery from targeting the ends of chromosomes.
Telomeres play a critical role in control of ageing. The more a cell divides, the smaller its telomeres become. Essentially, as we age, the telomeres get shorter. Eventually, they get so small that they don’t function properly anymore. The cells stop dividing and may even activate their self-destruct mechanisms. The only cells where this is different are the germ cells that ultimately give rise to eggs or sperm. In these cells the telomeres always stay long, so the next generation isn’t short-changed when it comes to longevity. In 2009, the Nobel Prize in Physiology or Medicine was awarded to Elizabeth Blackburn, Carol Greider and Jack Szostak for their work showing how telomeres function.
Since telomeres are so important in ageing, it makes sense to consider how they interact with the epigenetic system. The DNA of vertebrate telomeres consists of hundreds of repeats of the sequence TTAGGG. There are no genes at the telomere. We can also see from the sequence that there are no CpG motifs at the telomeres, so there can’t be any DNA methylation. If there are any epigenetic effects that make a difference at the telomeres they will therefore have to be based on histone modifications.
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 Both abnormal shortening and lengthening of telomeres have potentially deleterious consequences for cells.
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.
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.
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 sub-telomeric 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.
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.
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.