The Epigenetics Revolution

The scientists who have been investigating the behavioural responses in the different rodent systems counter this by arguing that molecular biologists are too used to quite artificial experimental models, where they can study extensive molecular changes with very on-or-off read-outs. The behaviourists suspect that this has left molecular biologists relatively inexperienced at interpreting real-world experiments, where the read-outs tend to be more ‘fuzzy’ and prone to greater experimental variation.

The second reason for scepticism lies in the very localised nature of the epigenetic changes. Infant stress affects specific regions of the brain, such as the nucleus accumbens, and not other areas. Epigenetic marks are only altered at some genes and not others. This seems less of a reason for scepticism. Although we refer to ‘the brain’, there are lots of highly specialised centres and regions within this organ, the product of hundreds of millions of years of evolution. Somehow, all these separate regions are generated and maintained during development and beyond, and thus are clearly able to respond differently to stimuli. This is also the case for all our genes, in all our tissues. It’s true that we don’t really know how epigenetic modifications can be targeted so precisely, or how the signalling from chemicals like neurotransmitters leads to this targeting. But we know that similarly specific events occur during normal development – so why not during abnormal periods of stress or other environmental disturbances? Just because we don’t know the mechanism for something, it doesn’t mean it doesn’t happen. After all, John Gurdon didn’t know how adult nuclei were reprogrammed by the cytoplasm of eggs, but that didn’t mean his experimental findings were invalid.

The third reason for scepticism is possibly the most important and it relates to DNA methylation itself. DNA methylation at the target genes in the brain is established very early, possibly pre-natally but certainly within one day of birth, in rodents. What this means is that the baby mice or baby rats in the experiments all started life with a certain baseline pattern of DNA methylation at their cortisol receptor gene in the hippocampus. The DNA methylation levels at this promoter alter in the first week of life, depending on the amount of licking and grooming the rats receive. As we saw, the DNA methylation levels are higher in the neglected mice than in the loved ones. But that’s not because the DNA methylation has gone up in the neglected mice. It’s because DNA methylation has gone down in the ones that were licked and groomed the most. The same is also true at the arginine vasopressin gene in the baby mice removed from their mothers. It’s also true for the corticotrophin-releasing hormone gene in the adult mice that were susceptible to social defeat.

So, in every case, what the scientists observed was decreased DNA methylation in response to a stimulus. And that’s where, molecularly, the problem lies, because no-one knows how this happens. In Chapter 4 we saw how copying of methylated DNA results in one strand that contains methyl groups and one that doesn’t. The DNMT1 enzyme moves along the newly synthesised strand and adds methyl groups to restore the methylation pattern, using the original strand as a template. We could speculate that in our experimental animals, there was less DNMT1 enzyme present and so the methylation levels at the gene dropped. This is referred to as passive DNA demethylation.

The problem is that this can’t work in neurons. Neurons are terminally differentiated – they are right at the bottom of Waddington’s landscape, and cannot divide. Because they don’t divide, neurons don’t copy their DNA. There’s no reason for them to do so. As a result, they can’t lose their DNA methylation by the method described in Chapter 4.

One possibility is that maybe neurons simply remove the methyl group from DNA. After all, histone deacetylases remove acetyl groups from histones. But the methyl group on DNA is different. In chemical terms, histone acetylation is a bit like adding a small Lego brick onto a larger Lego brick. It’s pretty easy to take the two bricks apart again. DNA methylation isn’t like that. It’s more like having two Lego bricks and using superglue to stick them together.

The chemical bond between a methyl group and the cytosine in DNA is so strong that for many years it was considered completely irreversible. In 2000, a group from the Max Planck Institute in Berlin demonstrated that this couldn’t be the case. They showed that in mammals the paternal genome undergoes extensive DNA demethylation, during very early development. We came across this in Chapters 7 and 8. What we glossed over at the time was that this demethylation happens before the zygote starts to divide. In other words, the DNA methylation was removed without any DNA replication[222]. This is referred to as active DNA demethylation.