The Epigenetics Revolution

But DNA methylation is also an aspect of epigenetics where there are clear differences in the way plants and higher animals use the same basic system. One of the most obvious differences is that plants don’t just methylate at CpG motifs (cytosine followed by a guanine). Although this is the most common sequence targeted by their DNA methyltransferases, plants will also methylate a cytosine followed by almost any other base[289].

A lot of DNA methylation in plants is focused around non-expressed repetitive elements, just like in mammals. But a big difference becomes apparent when we examine the pattern of DNA methylation in expressed genes. About 5 per cent of expressed plant genes have detectable DNA methylation at their promoters, but over 30 per cent are methylated in the regions that encode amino acids, in the so-called body of the genes. Genes with methylation in the body regions tend to be expressed in a wide range of tissues, and are expressed at moderate to high levels in these tissues[290].

The high levels of DNA methylation at repetitive elements in plants are very similar to the pattern at repetitive elements in the chromatin of higher animals such as mammals. By contrast, the methylation in the bodies of widely expressed genes is much more like that seen in honeybees (which don’t methylate their repetitive elements). This doesn’t mean that plants are some strange epigenetic hybrid of insects and mammals. Instead, it suggests that evolution has a limited set of raw materials, but isn’t too obsessive about how it uses them.

Chapter 16. The Ways Ahead

Prediction is very difficult, especially about the future.

Niels Bohr

One of the most exciting things about epigenetics is the fact that in some ways it’s very accessible to non-specialists. We can’t all have access to the latest experimental techniques, so not all of us will unravel the chromatin changes that underlie epigenetic events. But all of us can examine the world around us and make predictions. All we need to do is look to see if a phenomenon meets the two most essential criteria in epigenetics. By doing this, we can view the natural world, including humans, in a completely new light. These two criteria are the ones we have returned to over and over again throughout this book. A phenomenon is likely to be influenced by epigenetic alterations in DNA and its accompanying proteins if one or both of the following conditions are met:

Two things are genetically identical, but phenotypically variable;

An organism continues to be influenced by an event long after this initiating event has occurred.

We always have to apply a common sense filter, of course. If someone loses their leg in a motorbike accident, the fact that they are still minus a leg twenty years later doesn’t mean that we can invoke an epigenetic mechanism. On the other hand, that person may continue to have the sensation that they have both legs. This phantom limb syndrome might well be influenced by programmed gene expression patterns in the central nervous system that are maintained in part by epigenetic modifications.

We are sometimes so overwhelmed by the technologies used in modern biology that we forget how much we can learn just by looking thoughtfully. For example, we don’t always need sophisticated laboratory equipment to determine if two phenotypically different things are genetically identical. Here are a couple of examples with which we are all familiar. Maggots turn into flies and caterpillars turn into butterflies. An individual maggot and the adult fly into which it finally develops must have the same genetic code. It’s not as if a maggot can request a new genome as it metamorphoses. So, the maggot and the fly use the same genome in completely different ways. The painted lady caterpillar has interesting spikes all over its body and is fairly dull in colour. Like a maggot, it has no wings. The painted lady butterfly is a beautiful creature, with enormous wings coloured black and vivid orange, and it has no big spikes on its body. Once again, an individual caterpillar and the butterfly into which it develops must have the exact same DNA script. But the final productions from these scripts differ enormously. We can hypothesise that this is likely to involve epigenetic events.