Doing maize genetics, according to one geneticist, is “really cool.” It is exactly this kind of enthusiasm that fuels Karen Cone, Professor of Biological Sciences at MU, who specializes in plant genetics. Asked to summarize what researchers in her field actually do, Cone laughs and responds, “Geneticists make mutants…a geneticist learns about the way something works in real life by screwing it up, trying to figure out what’s wrong with the mutant, and then inferring what is normal when the mutant isn’t there.” The mutants that Cone makes involve corn and purple pigmentation.
“Why study maize?” I ask Cone, to which she replies: “Maize is considered to be a model genetic organism because what we learn in this organism is translatable to others.” Because it is a plant, she explains, there is the added advantage of seeds that can go dormant, then be stored for years until one wants to run make some additional crosses with them. Maize has other positive attributes as well; for example, it has separate male and female parts, and every kernel is a baby. With just one cross producing 300 to 800 progeny on each ear, Cone finds maize to be an ideal organism with which to do genetic research.
One of Cone’s earlier research projects on corn genetics was the Maize Mapping Project. Funded by the National Science Foundation as part of the Plant Genome Research Program, this project involved a collaboration of investigators at MU, the University of Arizona, and the University of Georgia. Of the four-year effort that was completed in 2002, Cone explains that “our goal was to make a map of the maize genome.” Using molecular methods and a genetic population tailored specifically for the project, Cone’s research team set about placing DNA "landmarks" onto the chromosomes: “When we finally finished the map, there were over 10,000 landmarks on it!”
Elaborating on this metaphor, Cone says, “I like to think of it as a road map. The chromosomes are like highways. The landmarks–DNA segments corresponding to genes–are like towns along the highway. For maize, the genetic map tells us the order of genes on each of the ten chromosomes–just like a road map tells you the order of towns along a highway. The next step is to pick apart the genes, sort of like you would go exploring a new town, to discover what is there. As a geneticist, my ultimate goal is to discover how genes function in the plant."
More specifically, Cone seeks to understand a group of genes that function to package DNA into chromatin, “the complex of DNA and protein, which allows us as humans–or plants like corn–to pack a lot of DNA into the tiny nucleus of a cell.” The DNA duplex for both corn plants and humans is huge, explains Cone. “We have about the same size genome, about three billion base pairs, and it is really long. We pack about six feet of DNA into every cell,” which is only five microns across, she reports. Using a food analogy to illustrate the proportions, Cone suggests that if you took a box of spaghetti (448 pieces) and laid them end-to-end, human DNA would be the length of 600 boxes of the spaghetti (about 268,800 pieces). That is how much DNA would go into the tiny nucleus were it the size of a basketball.
“That’s a heck of a lot of DNA,” remarks Cone. How does all of it fit inside the nucleus? “We’re smart,” she observes, adding that “corn and humans do it the same way.” In fact, every organism with a nucleus packages its DNA the same way. Starting out with a little ball of proteins, the DNA is wrapped around the ball twice, creating a link, and then around another ball, continuing in this way until all of the balls of protein have been wrapped. Then all of the balls coil around and associate with one another, compacting even more. “Eventually,” Cone summarizes, “you can take those 600 boxes of spaghetti and fit them inside a basketball through this DNA packaging. Chromatin is this association of DNA and proteins that serves to pack this really long molecule into a very small space.” It is a sort of microscopic compression system.
Cone recounts that when she first began researching this process, her big question concerned how, with this DNA so tightly wrapped up, the genes manage to leave their sequestered space to get turned on. We have to be able to turn on genes at a particular place and time. Interested in the implications for this DNA packaging, she has been investigating how a gene gets turned on just when it needs to be. In order to figure out how DNA gets packaged into the nucleus of the corn plant, to take one example, Cone creates mutants of genes that she suspects might play a role. By “knocking out a gene” – ergo, disrupting its function – Cone can observe the result. For instance, if disrupting the function of a particular gene makes the corn plant flower later than usual, she can conclude that the gene's normal function is to control when flowering occurs.
This research on DNA packaging is applicable to every organism because “from yeast, to mice, to humans, to plants—we all wrap up our DNA basically the same way.” Using the example of a calico cat, Cone explains: “Tortoise-shell and calico cats have orange and black fur patches on their body. That is due to a DNA packaging phenomenon.” As it turns out, the fur color gene is on the X chromosome. Just as human females have two X chromosomes, so do these calico cats, which are almost always female. In fact, they have one X with an orange-fur gene and one X with a black-fur gene; “so back when that little calico cat, with her different X chromosomes, was a 16 or a 32-cell embryo, in each cell one of the X chromosomes got really tightly packaged, so tightly that the genes on that chromosome weren’t expressed.” If the X with the orange-fur gene is packaged, Cone continues, then the X with the black-fur gene remains active. As the cell continues to divide in the embryo, it will eventually give rise to a black patch of fur. The orange patches, of course, derive from the fact that in another cell the X with the orange-fur gene was the one left active, while the black one was balled up too tightly to be expressed.
That is one concrete example of how DNA packaging influences whether or not a gene is turned on. Cone offers another instance of this remarkable process, one that involves not felines but rather humans and a phenomenon called imprinting. For the most part, we inherit half of our genes from mom and half from dad. In most cases, therefore, we express both, turning them on at different points during development. Experiments done years ago suggested that you have to have both a mom’s version and dad’s version of genes for successful development in an embryo. “But for some other genes,” Cone goes on, “we only express mom’s copy or we only express dad’s copy, but not both.” Hence, imprinting means that we don’t express both copies of the genes we inherited from our two parents.
Consider two human diseases, Angleman’s Syndrome and Prader-Willi Syndrome, both of which result from failing to inherit one parent’s copy of genes on chromosome 15 in the human genome. When the transmission of these genes is disrupted, one of these diseases results. Specifically, people will develop Angleman’s Syndrome if they didn’t get the mother’s copy, or Prader-Willi Syndrome if they didn’t get the father’s version. “Imprinting is all about DNA packaging,” Cone explains, “so when you’re supposed to express mom’s version, mom’s version is accessible for expression and dad’s version remains tightly packed.”
The genes, essentially, are opening and closing, clarifies Cone, “and that sort of imprint that comes from mom or from dad is imposed way back when the eggs were developing in mom and the sperm was developing in dad.” By the time we are born, our cells recognize which chromosomes came from which parent and when they should be expressed. Moreover, this process—the ability to differentiate imprints—“is remembered throughout the lifetime of the organism.” The imprints are finally erased when we ourselves make eggs or sperm, so that they can be re-imprinted. “So when I make eggs, the imprints that came from my dad and my mom are both erased from my chromosomes, so that my female-specific imprint can be put in the eggs.” When we have kids, in other words, their cells will “know” which copies of their chromosomes came from which parent—“and that is all DNA packaging.”
“Cool, huh?” Cone comments in response to my awed reaction. “I know, it’s amazing. It’s just amazing.” “It’s not something we understand very well,” she admits, but researchers are actively working to comprehend the mechanisms behind this process. “It is interesting to think about how and why imprinting happens. It happens in plants, too, so imprinting is not strictly just a mammalian phenomenon.” When it occurs in plant genes, Cone notes, it almost always affects those genes that contribute to the part of the seed that nourishes the little seedling before it can get above ground to photosynthesize and make its own food. If researchers can better understand how this chromatin packaging occurs, they might eventually be able to control the process to their advantage. According to Cone, “being able to understand that process might give us a chance down the road to manipulate that process, turning on certain genes in order to potentially improve features of the plant for crop production.”
The University of Missouri is a great place to study maize genetics, concludes Cone, who joined MU nearly two decades ago. During her first year, she recalls, “I jumped into this group that was fabulous for doing maize genetics, and they had a cornfield. I had colleagues out in the field, so when I found something cool, I could say, ‘Hey Ed, come on over, look at my corn, tell me what you think about this.’ And we would sit and talk about these things. It’s such a great collegial kind of atmosphere doing plant genetics here at MU.”