Hidden layer of genome unveils how plants may adapt
"We expected variation in methylation patterns among groups of plants from around the globe," says co-lead author Robert J. Schmitz, a postdoctoral researcher in Ecker's lab. "The amount, however, was far greater than we ever anticipated."
By analyzing these patterns, Ecker's team was able to chart their effects on the activity of genes in the plants' genome. Scientists know that methylation can inactivate genes, but in contrast to DNA mutations, methylation patterns are reversible, giving the plants the ability to temporarily activate genes. The identification of genes that are epigenetically regulated has greatly narrowed the potential candidates important for environmental adaptation.
Methylation silencing also occurs in humans-and that has implications for treating cancer, a hallmark of which is the silencing of tumor suppressor genes. "If these genes are turned off by the epigenome, they could potentially be turned back on by removing the DNA methylation," says study co-lead author Matthew Schultz, a graduate student in Ecker's lab. Understanding how these methylation variants form in the wild will help toward better engineering of epigenomes.
Ecker's team will next study how methylation variations affect the traits of plants. They will examine stress-induced epigenomic changes and how they might provide clues as to which alterations are most important for the plants.
Other researchers on the study were Mark A. Urich, Joseph R. Nery, Mattia Pelizzola, Andrew Alix, Richard B. McCosh, and Huaming Chen, from the Salk Institute; and Ondrej Libiger and Nicholas J. Schork of The Scripps Research Institute.
About the Salk Institute for Biological Studies:
The Salk Institute for Biological Studies is one of the world's preeminent basic research institutions, where internationally renowned faculty probe fundamental life science questions in a unique, collaborative, and creative environment. Focused both on discovery and on mentoring future generations of researchers, Salk scientists make groundbreaking contributions to our understanding of cancer, aging, Alzheimer's, diabetes and infectious diseases by studying neuroscience, genetics, cell and plant biology, and related disciplines.
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