Biochemistry, Molecular Biology
Indiana University Bloomington
Dr. Pikaard is a Howard Hughes Medical Institute–Gordon and Betty Moore Foundation investigator. He is also Carlos O. Miller Professor of Plant Growth and Development at Indiana University Bloomington.
Mechanisms of Gene Silencing in Plants
When Craig Pikaard entered college, he wasn’t considering a scientific career that requires being cooped up in a lab all day. A lifelong nature lover, he majored in horticulture and hoped to start a home and garden business with his father after graduation.
His plans changed as soon as he took a few college-level science courses. "I was enthralled by biochemistry and physiology classes and just realized, ‘Wow, that’s so cool,’" recalls Pikaard.
That revelation turned out to be a boon for the field of plant genetics. He still gets to tend to plants—thousands of them, in fact—but he does it in his lab at Indiana University, where he is learning how plants control the activity of their genes.
Over the past two decades, Pikaard has made numerous discoveries about how plant cells silence gene expression. He focuses on epigenetics, inherited changes in gene activity that do not involve alterations in the primary DNA sequence. One way cells silence particular genes is by chemically attaching methyl groups to DNA. This process is fundamental to controlling growth and development in both plant and animal cells and is important in most cancers. For example, cancer cells silence tumor suppressor genes through DNA methylation, and uncontrolled growth results. "This gene silencing phenomenon happens in all sorts of different contexts, and we really don’t understand it very well," he says.
While in graduate school at Purdue University in the early 1980s, before he discovered the world of molecular biology, Pikaard spent three years studying how plants react to stress. As much as he enjoyed working on plants, Pikaard thought he could broaden his perspective by using his postdoctoral fellowship to study how gene regulation works in other organisms. Unfortunately, then as now, it was difficult for researchers to make that switch. "Not a lot of people would give me the time of day as a plant biologist applying to major biomedical labs," Pikaard says. "Traditionally there had been this division of plants versus every other organism."
Ron Reeder of the Fred Hutchinson Cancer Center in Seattle took a chance on Pikaard. Reeder was interested in nucleolar dominance, a mysterious genetic event that occurs in genetic hybrids in the plant and animal kingdoms. In hybrids, genes inherited from both parents are typically expressed, producing offspring with a range of phenotypes. However, sometimes the phenomenon of nucleolar dominance occurs. When this happens, offspring use only one parent's set of the genes that make the major RNAs of ribosomes, the cellular machines that pump out proteins.
In Reeder's lab, Pikaard studied how ribosomal RNA genes in frogs are switched on by stretches of DNA known as enhancers. At the time, prevailing wisdom said that nucleolar dominance occurred because one set of genes had more, or stronger, enhancers and was preferentially turned on. This turned out to be wrong, as Pikaard discovered later while doing experiments on plants in his own lab at Washington University in St. Louis. He showed that nucleolar dominance occurs when one set of parental genes is preferentially turned off.
Nucleolar dominance is one aspect of a system that helps cells maintain precise control over protein production. "Ribosomal genes are present in hundreds of copies in most organisms, and at certain points of development you need them all. But at other points, you’ve got more than you need," Pikaard explains. At those times, the cell "chooses" to shut down an entire set of ribosomal RNA genes. Understanding how that choice is actually made is a very important question in biology, he notes.
Working on Arabidopsis thaliana, a plant in the mustard family, Pikaard has since discovered several parts of the gene-silencing machinery. A decade ago, as part of the large team that analyzed the full sequence of Arabidopsis, he discovered two previously unknown enzymes—dubbed Pol IV and Pol V—that help transcribe DNA into RNA. A few years later, he showed that the pathway in which these enzymes work is also involved in nucleolar dominance: a pathway in which short RNAs direct the addition of methyl groups to DNA, which effectively tags genes that are to be silenced.
Still, some of the most fundamental questions about the gene silencing behind nucleolar dominance have not been answered. Why doesn't the cell just damp down both sets of genes equally? How does it tell the two sets apart? How and why does it choose one of them? "These are the things we're pursuing now," Pikaard says.
He moved to Indiana University in 2009 in large part because its cutting-edge technological facilities will help him answer these questions. For example, he plans to use a technique called cryoelectron microscopy—which zooms in to the level of a single atom—to visualize the molecular players involved in gene silencing.
His green thumb still comes in handy as he and his team grow indoors all the plants these experiments demand. "It's keeping the bugs down that’s the hard part," he says, laughing. "All the things we worry about in the garden happen in our growth room, too."