The Epigenetics Revolution

Research in Arabidopsis thaliana has shown that plants use epigenetic modifications to regulate thousands of genes[282]. This regulation probably serves the same purposes as in animal cells. It helps cells to maintain appropriate but short-term responses to environmental stimuli, and it also locks differentiated cells in permanent patterns of specific gene expression. Because of epigenetic mechanisms we humans don’t have teeth in our eyeballs, and plants don’t have leaves growing out of their roots.

Flowering plants share a characteristic epigenetic phenomenon with mammals, and with no other members of the animal kingdom. Flowering plants are the only organisms we know of besides placental mammals in which genes are imprinted. Imprinting is the process we examined in Chapter 8, where the expression pattern of a gene is dependent on whether it was inherited from the mother or father.

At first glance, this similarity between flowering plants and mammals seems positively bizarre. But there’s an interesting parallel between us and our floral relations. In all higher mammals, the fertilised zygote is the source of both the embryo and the placenta. The placenta nourishes the developing embryo, but doesn’t ultimately form part of the new individual. Something rather similar happens when fertilisation occurs in flowering plants. The process is slightly more complicated, but the final fertilised seed contains the embryo and an accessory tissue called the endosperm, shown in Figure 15.2.

^{Figure 15.2 The major anatomical components of a seed. The relatively small embryo that will give rise to the new plant is nourished by the endosperm, in a manner somewhat analogous to the nourishment of mammalian embryos by the placenta.}

Just like the placenta in mammalian development, the endosperm nourishes the embryo. It promotes development and germination but it doesn’t contribute genetically to the next generation. The presence of any accessory tissues during development, be this a placenta or an endosperm, seems to favour the generation of imprinted control of the expression of a select group of genes.

In fact, something very sophisticated happens in the endosperm of seeds. Just like most animal genomes, the genomes of flowering plants contain retrotransposons. These are usually referred to as TEs – transposable elements. These are the repetitive elements that don’t encode proteins, but can cause havoc if they are activated. This is especially because they can move around in the genome and disrupt gene expression.

Normally such TEs are tightly repressed, but in the endosperm these sequences are switched on. The cells of the endosperm create small RNA molecules from these TEs. These small RNAs travel out from the endosperm into the embryo. They find the TEs in the embryo’s genome that have the same sequence as themselves. These TE small RNA molecules then seem to recruit the machinery that permanently inactivates these potentially dangerous genomic elements. The risk to the endosperm genome through re-activation of the TEs is high. But because the endosperm doesn’t contribute to the next generation genetically, it can undertake this suicide mission, for the greater good[283][284][285][286].

Although mammals and flowering plants both carry out imprinting, they seem to use slightly different mechanisms. Mammals inactivate the appropriate copy of the imprinted gene by using DNA methylation. In plants, the paternally-derived copy of the gene is always the one that carries the DNA methylation. However, it’s not always this methylated copy of the gene that is inactivated[287]. In plant imprinting, therefore, DNA methylation tells the cell how a gene was inherited, not how the gene should be expressed.

There are some fundamental aspects of DNA methylation that are quite similar between plants and animals. Plant genomes encode active DNA methyltransferase enzymes, and also proteins that can ‘read’ methylated DNA. Just like primordial germ cells in mammals, certain plant cells can actively remove methylation from DNA. In plants, we even know which enzymes carry out this reaction[288]. One is called DEMETER, after the mother of Persephone in Greek myths. Demeter was the goddess of the harvest and it was because of the deal that she struck with Hades, the god of the Underworld, that we have seasons.