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Planting the seeds of defense

Joe Ecker and Hong Qiao

Salk researchers Joe Ecker and Hong Qiao infected two lines of plants with bacteria to determine whether methylation, a type of epigenetic chemical modification to DNA, plays a role in a plant's response to stress. Image: Courtesy of Robert H. Dowen

It was long thought that methylation, a crucial part of normal organism development, was a static modification of DNA that could not be altered by environmental conditions. New findings by Joseph Ecker, however, suggest that the DNA of organisms exposed to stress undergoes changes in DNA methylation patterns that alter how genes are regulated.

Ecker and his team found that exposure to a pathogenic bacterium caused widespread changes in a plant's epigenetic code, an extra layer of biochemical instructions in DNA that help control gene expression. The epigenetic changes were linked to the activity of genes responsible for coordinating a plant's response to stress, suggesting that the epigenome may help organisms develop resistance to pathogens and other environmental stressors.

"This means the epigenome may not just be a static set of instructions, but also a way of rewriting those instructions based on experience," says Joseph Ecker. "Our findings, combined with other researchers' findings, build the case that life experiences leave an imprint on our DNA."

In the study, published in the Proceedings of the National Academy of Sciences, Ecker and his colleagues explored how DNA methylation regulates the immune system of Arabidopsis thaliana, a flowering plant in the mustard family. Methylation is a biochemical process that, among other things, suppresses the expression of "jumping genes," called transposons, that have been incorporated into the genome over time. Using genome-wide sequencing technologies, the researchers found a wide range of methylation changes in the plant's response to a bacterial infection and performed a variety of analyses to determine how these methylation changes alter gene expression.

The findings may have broad implications for agriculture, including engineering the DNA methylation patterns of plants to generate pathogenresistant crops and minimize pesticide exposure. These application technologies are of intense interest, as more than 30 to 40 percent of annual crops are lost to pathogens each year, at a cost of some $500 billion.