The Epigenetics Revolution

Eggs and sperm are highly specialised cells – they are at the bottom of one of Waddington’s troughs. The egg and the sperm will never be anything other than an egg and a sperm. Unless they fuse. Once they fuse, these two highly specialised cells form one cell which is so unspecialised it is totipotent and gives rise to every cell in the human body, and the placenta. This is the zygote, at the very top of Waddington’s epigenetic landscape. As this zygote divides, the cells become more and more specialised, forming all the tissues of our bodies. Some of these tissues ultimately give rise to eggs or sperm (depending on our sex, obviously) and the whole cycle is ready to start again. There’s effectively a never-ending circle in developmental biology.

The chromosomes in the pro-nuclei of sperm and eggs carry large numbers of epigenetic modifications. This is part of what keeps these gametes behaving as gametes, and not turning into other cell types. But these gametes can’t be passing on their epigenetic patterns, because if they did the fertilised zygote would be some sort of half-egg, half-sperm hybrid when it clearly isn’t this at all. It’s a completely different totipotent cell that will give rise to an entirely new individual. Somehow the modifications on eggs and sperm get changed to a different set of modifications, to drive the fertilised egg into a different cell state, at a different position in Waddington’s epigenetic landscape. This is part of normal development.

Re-installing the operating system

Almost immediately after the sperm has penetrated the egg, something very dramatic happens to it. Pretty much all the methylation on the male pronucleus DNA (i.e. from the sperm) gets stripped off, incredibly quickly. The same thing happens to the DNA on the female pronucleus, albeit a lot more slowly. This means that a lot of the epigenetic memory gets wiped off the genome. This is vital for putting the zygote at the top of Waddington’s epigenetic landscape. The zygote starts dividing and soon creates the blastocyst – the golf ball inside the tennis ball from Chapter 2. The cells in the golf ball – the inner cell mass, or ICM – are the pluripotent cells, the ones that give rise to embryonic stem cells in the laboratory.

The cells of the ICM soon differentiate and start giving rise to the different cell types of our bodies. This happens through very tightly regulated expression of a few key genes. One specific protein, for example OCT4, switches on another set of genes, which results in a further cascade of gene expression, and so on. We have met OCT4 before – it is the most critical of all the genes that Professor Yamanaka used to reprogram somatic cells. These cascades of gene expression are associated with epigenetic modification of the genome, changing the DNA and histone marks so that certain genes stay switched on or get switched off appropriately. Here’s the sequence of epigenetic events in very early development:

The male and female pronuclei (from the sperm and the egg respectively) are carrying epigenetic modifications;

The epigenetic modifications get taken off (in the immediate post-fertilisation zygote);

New epigenetic modifications get put on (as the cells begin to specialise).

This is a bit of a simplification. It’s certainly true that researchers can detect huge swathes of DNA demethylation during stage 2 from this list. However, it’s actually more complicated than this, particularly in respect of histone modifications. Whilst some histone modifications are being removed, others are becoming established. At the same time as the repressive DNA methylation is removed, certain histone marks which repress gene expression are also erased. Other histone modifications which increase gene expression may take their place. It’s therefore too naïve to refer to the epigenetic changes as just being about putting on or taking off epigenetic modifications. In reality, the epigenome is being reprogrammed.

Reprogramming is what John Gurdon demonstrated in his ground-breaking work when he transferred the nuclei from adult toads into toad eggs. It’s what happened when Keith Campbell and Ian Wilmut cloned Dolly the Sheep by putting the nucleus from a mammary gland cell into an egg. It’s what Yamanaka achieved when he treated somatic cells with four key genes, all of which code for proteins highly expressed naturally during this reprogramming phase.