A team led by Dr Jeffrey Craig in 2010 at the Royal Children’s Hospital in Melbourne also examined DNA methylation in identical and fraternal twin pairs[32]. They investigated a few relatively small regions of the genome in greater detail than in Manel Esteller’s earlier paper. Using samples just from newborn twin pairs, they showed that there was a substantial amount of difference between the DNA methylation patterns of fraternal twins. This isn’t unexpected, since fraternal twins are genetically non-identical and we expect different individuals to have different epigenomes. Interestingly, though, they also found that even the MZ twins differed in their DNA methylation patterns, suggesting identical twins begin to diverge epigenetically during development in the uterus. Combining the information from the two papers, and from additional studies, we can conclude that even genetically identical individuals are epigenetically distinct by the time of birth, and these epigenetic differences become more pronounced with age and exposure to different environments.
These data are consistent with a model where epigenetic changes could account for at least some of the reasons why MZ twins aren’t phenotypically identical, but there’s still a lot of supposition involved. That’s because for many purposes humans are a quite hopeless experimental system. If we want to be able to assess the role of epigenetics in the problem of why genetically identical individuals are phenotypically different from one another, we would like to be able to do the following:
Analyse hundreds of identical individuals, not just pairs of them;
Manipulate their environments, in completely controlled ways;
Transfer embryos or babies from one mother to another, to investigate the effects of early nurture;
Take all sorts of samples from the different tissues of the body, at lots of different time points;
Control who mates with whom;
Carry out studies on four or five generations of genetically identical individuals.
Needless to say, this isn’t feasible for humans.
This is why experimental animals have been so useful in epigenetics. They allow scientists to address really complex questions, whilst controlling the environment as much as possible. The data that are generated in these animal studies produce insights from which we can then try to infer things about humans.
The match may not be perfect, but we can unravel a surprising amount of fundamental biology this way. Various comparative studies have shown that many systems have stayed broadly the same in different organisms over almost inconceivably long periods. The epigenetic machinery of yeast and humans, for example, share more similarities than differences and yet the common ancestor for the two species lies about one billion years in the past[33]. So, epigenetic processes are clearly fairly fundamental things, and using model systems can at least point us in a helpful direction for understanding the human condition.
In terms of the specific question we’ve been looking at in this chapter – why genetically identical twins often don’t seem to be identical – the animal that has been most useful is our close mammalian relative, the mouse. The mouse and human lineages separated a mere 75 million or so years ago[34]. 99 per cent of the genes found in mice can also be detected in humans, although they aren’t generally absolutely identical between the two species.
Scientists have been able to create strains of mice in which all the individuals are genetically identical to each other. These have been incredibly useful for investigating the roles of non-genetic factors in creating variation between individuals. Instead of just two genetically identical individuals, it’s possible to create hundreds, or thousands. The way this is done would have made even the Ptolemy dynasty of ancient Egypt blush. Scientists mate a pair of mice who are brother and sister. Then they mate a brother and sister from the resulting litter. They then mate a brother and sister from their litter and so on. When this is repeated for over twenty generations of brother-sister matings, all the genetic variation gets bred out, throughout the genome. All mice of the same sex from the strain are genetically identical. In a refinement of this, scientists can take these genetically identical mice and introduce just one change into their DNA. They may use such genetic engineering to create mice which are identical except for just one region of DNA that the experimenters are most interested in.
The most useful mouse model for exploring how epigenetic changes can lead to phenotypic differences between genetically identical individuals is called the agouti mouse. Normal mice have hair which is banded in colour. The hair is black at the tip, yellow in the middle and black again at the base. A gene called agouti is essential for creating the yellow bit in the middle, and is switched on as part of a normal cyclical mechanism in mice.
There is a mutated version of the agouti gene (called a) which never switches on. Mice that only have the a, mutant version of agouti have hair which is completely black. There is also a particular mutant mouse strain called Avy, which stands for agouti viable yellow. In Avy mice, the agouti gene is switched on permanently and the hair is yellow through its entire length. Mice have two copies of the agouti gene, one inherited from the mother and one from the father. The Avy version of the gene is dominant to the a version, which means that if one copy of the gene is Avy and one is a, the Avy will ‘overrule’ a and the hairs will be yellow throughout their length. This is all summarised in Figure 5.2.
Figure 5.2 Hair colour in mice is affected by the expression of the agouti gene. In normal mice, the agouti protein is expressed cyclically, leading to the characteristic brindled pattern of mouse fur. Disruption of this cyclical pattern of expression can lead to hairs which are either yellow or black throughout their length.
Scientists created a strain of mice that contained one copy of Avy and one copy of a in every cell. The nomenclature for this is Avy/a. Since Avy is dominant to a, you would predict that the mice would have completely yellow hair. Since all the mice in the strain are genetically identical, you would expect that they would all look the same. But they don’t. Some have the very yellow fur, some the classic mouse appearance caused by the banded fur, and some are all shades in-between, as shown in Figure 5.3.
Figure 5.3 Genetically identical mice showing the extent to which fur colour can vary, depending on expression of the agouti protein. Photo reproduced with the kind permission of Professor Emma Whitelaw.
This is really odd, since the mice are all genetically exactly the same. All the mice have the same DNA code. We could argue that perhaps the differences in coat colour are due to environment, but laboratory conditions are so standardised that this seems unlikely. It’s also unlikely because these differences can be seen in mice from the same litter. We would expect mice from a single litter to have very similar environments indeed.