With so many similarities in the environment and genetic makeup of these two plants, how can their many differences be explained?

Photo by David Kilper

(From left) Barbara Kunkel, Ph.D., assistant professor of biology in Arts & Sciences; graduate student Trevor Stokes; and Eric Richards, Ph.D., associate professor of biology, investigate differences in plants due to factors above and beyond their gene sequence.

Graduate student Trevor Stokes and his mentor, Eric Richards, Ph.D., associate professor of biology in Arts & Sciences, aimed to understand what was wrong with the dwarf plant. They found that a dwarfed plant, called "bal" because of its shape, constantly perceives a pathogen attack even though it has the exact same DNA sequence of a non-paranoid plant.

The researchers found that the differences between the two plants are not due to changes in the DNA sequence; rather, the differences are due to factors above and beyond the gene sequence. Moreover, such factors, like genes, can be inherited.

Stokes and Richards published their findings in a recent issue of Genes and Development with co-author Barbara Kunkel, Ph.D., assistant professor of biology, who studies plant-pathogen interactions.

The Richards lab specializes in epigenetics, a biological field that deals with information stored "above and beyond the gene," referring to the Greek meaning of the term. The researchers found that the bal dwarf is caused by increasing activation of a single gene, which is otherwise identical in its basic chemical sequence compared to the gene in normal-looking plants.

"So you've got something that looks like a mutation and behaves like a mutation, but it's actually caused by the packaging of the DNA and not by the DNA sequence itself," Richards said.

The gene affected in the bal variant is involved in disease resistance and is called an R-gene. The research shows that there is a cost of resistance in plants. In the bal plant, the R-gene is more active, and consequently the plant's defense system becomes hyperactivated, constantly fighting off disease even when no pathogens are present to pose a threat. The resulting dwarfed plant is more resistant to bacterial infection.

So why should a plant so well prepared against infection appear so sickly? Stokes and Richards explain that the bal dwarf provides evidence that there is a cost to resistance in these plants.

"They (bal) don't set a lot of seed, they're dwarfed, their leaves are obviously really damaged by this constitutive activation, so there's definitely a cost to being so resistant," Stokes said.

The precise molecular change leading to the increased R-gene activation is not clear. But the group suspects changes in DNA methylation, a chemical modification of cytosine, one of the four chemical subunits of DNA.

Without proper DNA methylation, higher organisms from plants to humans have a host of developmental problems, from dwarfing in plants to certain death in mice.

But methylation is just one type of DNA modification studied in epigenetics. There are several others.

The next level of gene regulation studied in epigenetics is DNA packaging. DNA is wrapped around proteins similar to the way that thread is wrapped around a spool.

Loosely wrapped DNA is more readily accessible and therefore more easily expressed than tightly wrapped DNA, allowing another mechanism for regulation of gene expression. The location of DNA within the nucleus also influences gene expression.

Stokes made the comparison to a landscape.

"There are some parts of the nucleus that are like deserts where not much is happening," he said. "And others are like lush forests where a lot of activity happens."

Genes in a desert region will have a much lower rate of gene activation than those found in the lush forests.

Epigenetic changes, like traditional genetic changes, can be inherited. The phenotype of an organism -- that is, the sum of all its physical characteristics -- depends on much more than just its DNA sequence.

"Genes do not just come in one type," Stokes said. "Genes can be modified, they can be packaged, they can be pushed and pulled around, and that alters how they are interpreted and how they are used."

The finding that these levels of epigenetic regulation can be inherited has added to a growing interest in this field, once considered only a side note to the realm of traditional genetics.

"People have known about this sort of thing (epigenetics) for a long time, but it was relegated to the bin of weird genetics," Richards said. "Some people liked to study it as an oddity. But now it's becoming more appreciated."

Today, research in epigenetics is providing insight into a broad range of study areas. Molecular biologists working to introduce foreign genes into organisms, such as the introduction of resistance genes into crops, often face the problem of "gene silencing," whereby the gene is properly inserted into the host genome, but it never gets turned on and thus the desired gene product is not produced.

An epigenetic perspective suggests that the source of this silencing can be found in incorrect modification, packaging or location of the inserted gene inside the nucleus. In this example, that means no resistant crops, but understanding gene silencing is of interest to more than just plant biologists.

Evidence suggests epigenetic mutations may also be involved in cancer.