So far, we could be forgiven for thinking that honeybees and higher organisms, including us and our mammalian relatives, all use DNA methylation in the same way. It’s certainly true that changes in DNA methylation are associated with alterations in developmental processes in both humans and honeybees. It’s also true that mammals and honeybees both use DNA methylation in the brain during memory processing.
But oddly enough, honeybees and mammals use DNA methylation in very different ways. A carpenter has a saw in his toolbox and uses it to build a book case. An orthopaedic surgeon has a saw on his operating trolley and uses it to amputate a leg. Sometimes, the same bit of kit can be used in very different ways. Mammals and honeybees both use DNA methylation as a tool, but during the course of evolution they’ve employed it very differently.
When mammals methylate DNA, they usually methylate the promoter regions of genes, and not the parts that code for amino acids. Mammals also methylate repetitive DNA elements and transposons, as we saw in Emma Whitelaw’s work in Chapter 5. DNA methylation in mammals tends to be associated with switching off gene expression and shutting down dangerous elements like transposons that might otherwise cause problems in our genomes.
Honeybees use DNA methylation in a completely different way. They don’t methylate repetitive regions or transposons, so they presumably have other ways of controlling these potentially troublesome elements. They methylate CpG motifs in the stretches of genes that encode amino acids, rather than in the promoter regions of genes. Honeybees don’t use DNA methylation to switch off genes. In honeybees, DNA methylation is found on genes that are expressed in all tissues, and also on genes that tend to be expressed by many different insect species. DNA methylation acts as a fine-tuning mechanism in honeybee tissues. It modulates the activity of genes, turning the volume slightly up or down, rather than acting as an on-off switch[270]. Patterns of DNA methylation are also strongly correlated with control of mRNA splicing in honeybee tissues. However, we don’t yet know how this epigenetic modification actually influences the way in which a message is processed[271].
We’re really only just beginning to unravel the subtleties of epigenetic regulation in honeybees. For example, there are 10,000,000 CpG sites in the honeybee genome, but less than 1 per cent of these are methylated in any given tissue. Unfortunately, this low degree of methylation makes analysing the effects of this epigenetic modification very challenging. The effects of Dnmt3 knockdown show that DNA methylation is very important in honeybee development. But, given that DNA methylation is a fine-tuning mechanism in this species, it’s likely that Dnmt3 knockdown results in a number of individually minor changes in a relatively large number of genes, rather than dramatic changes in a few. These types of subtle alterations are the most difficult to analyse, and to investigate experimentally.
Honeybees aren’t the only insect species that has developed a complex society with differing forms and functions for genetically identical individuals. This model has evolved independently several times, including in different species of wasps, termites, bees and ants. We don’t yet know if the same epigenetic processes are used in all these cases. Shelley Berger from the University of Pennsylvania, whose work on ageing we encountered in Chapter 13, is involved in a large collaboration focusing on ant genetics and epigenetics. This work has already shown that at least two species of ants also can methylate the DNA in their genomes. The expression of different epigenetic enzymes varies between different social groups in the colonies[272]. These data tentatively suggest that epigenetic control of colony members may prove to be a mechanism that has evolved more than once in the social insects.
For now, however, most interest in the world outside epigenetics labs focuses on royal jelly, as this has a long history as a health supplement. It’s worth pointing out that there’s very little hard evidence to support this having any major effects in humans. The 10HDA, that Mark Bedford and his colleagues showed was a histone deacetylase inhibitor, can affect the growth of blood vessel cells[273]. Theoretically, this could be useful in cancer, as tumours rely on a good blood supply for continuing growth. However, we’re a very long way from showing that royal jelly can really fight off cancer, or aid human health in any other way. If there’s one thing we do already know, it’s that bees and humans are not the same epigenetically. Which is just as well, unless you’re a really big fan of the monarchy …
Chapter 15. The Green Revolution
To see a world in a Grain of Sand,
And a Heaven in a Wild Flower,
Hold Infinity in the palm of your hand,
And eternity in an hour.
Probably all of us are familiar with the guessing game ‘animal, vegetable or mineral’. The implicit assumption in the name of this game is that plants and animals are completely different from one another. True, they are both living organisms, but that’s where we feel the similarity ends. We may be able to get on board with the idea that somewhere back in the murky evolutionary past, humans and microscopic worms have a shared ancestor. But how often do we ever wonder about the biological heritage we share with plants? When do we ever think of carnations as our cousins?
Yet animals and plants are surprisingly similar in many ways. This is especially the case when we consider the most advanced of our green relatives, the flowering plants. These include the grasses and cereals that we rely on for so much of our basic food intake, and the broad-leaved plants, from cabbages to oak trees and from rhododendrons to cress.
Animals and the flowering plants are each made up of lots of cells; they are multi-cellular organisms. Many of these cells are specialised for particular functions. In the flowering plants these include cells that transport water or sugars around the plant, the photosynthesising cells of the leaves and the food storing cells of the roots. Like animals, plants have specialised cells which are responsible for sexual reproduction. The sperm nuclei are carried in pollen and fertilise a large egg cell, which ultimately gives rise to a zygote and a new individual plant.
The similarities between plants and animals are more fundamental than these visible features. There are many genes in plants which have equivalents in animals. Crucially, for our topic, plants also have a highly developed epigenetic system. They can modify histone proteins and DNA, just like animal cells can, and in many cases use very similar epigenetic enzymes to those used by animals, including humans.
These genetic and epigenetic similarities all suggest that animals and plants have common ancestors. Because of our common ancestry, we’ve inherited similar genetic and epigenetic tool kits.
Of course, there are also really important differences between plants and animals. Plants can create their own food, but animals can’t do this. Plants take in basic chemicals in the environment, especially water and carbon dioxide. Using energy from sunlight, plants can convert these simple chemicals into complex sugars such as glucose. Nearly all life on planet earth is dependent directly or indirectly on this amazing process of photosynthesis.
There are two other ways in which plants and animals are very different. Most gardeners know that you can take a cutting from a growing plant – maybe just a small shoot – and create an entire new plant from this. There are very few animals where this is possible, and certainly no advanced ones. True, if certain species of lizard lose their tail, the animal can grow a new one. But they can’t do this the other way around. We can’t grow a new lizard from a discarded bit of tail.