Contemporary geneticists devote much of their time to trying to understand the invisible, but Robert Martienssen found his inspiration from their predecessors, who defined the discipline with studies of the observable. His research at Cold Spring Harbor Laboratory builds directly on the findings of two towering figures in plant genetics: Gregor Mendel, whose colored flowers and pea-pod shapes helped him describe the rules of inheritance in the mid-1800s, and Nobelist Barbara McClintock, who discovered an important exception to Mendel’s rules a century later by tracking variance in maize-kernel colors.

McClintock, also a Cold Spring Harbor biologist, showed that the speckled, spattered, and striated patterns of corn kernels arise not as a result of classic gene inheritance patterns but instead are caused when bits of DNA physically move from one chromosome to another. As these bits of DNA hop around the genome they can alter gene function, creating extra copies of a gene or interrupting the native DNA sequence when they land. McClintock was the first to recognize these movable genetic elements, now known as transposons. She called them “controlling elements,” and her discovery captivated Martienssen.

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Martienssen began investigating the molecular underpinnings of maize transposons during his postdoctoral work at the University of California, Berkeley, in the mid-1980s. There, he discovered why, when a transposon settles into the regulatory region of DNA near a particular gene, it sometimes turns that gene off—but not always. By studying mutant plants that are impaired in their ability to attach chemical methyl groups to DNA, he discovered that transposons regulate genes by acquiring methyl groups. Methylated transposons also lose their ability to move within the genome and are considered inactive.

“I found a methylation-based regulatory mechanism that controlled genes in just the way Barbara had predicted,” Martienssen says. Evolutionarily, it makes sense that organisms would have the ability to silence transposons: their constant movement around the genome poses a threat to genetic integrity, Martienssen explains. “Plants and animals have evolved these mechanisms to prevent them from moving around,” he says.

He took a faculty position at Cold Spring Harbor Laboratory in 1989 and began digging deeper into the transposon story, working alongside McClintock for the first few years. His studies into the forces that shut down transposons have implications for another kind of gene silencing as well: the cell-specific silencing of sets of genes that allows different cell types to take on their own identities and carry out specialized functions. A plant's cells all share the same genetic material, but the silencing of different genes in different cells—for example by methylation—ensures that all the descendents of that cell activate the genes appropriate for them. This type of inheritance is often called “epigenetic” to distinguish it from inherited changes in DNA sequence.

A major discovery came when Martienssen began investigating Arabidopsis plants that lacked a gene called Argonaute. Without the gene, leaves seem to have trouble knowing which direction is up. Martienssen had reason to suspect this lack of direction had something to do with impaired gene silencing. Scientists had recently discovered RNA interference (RNAi)—a biological process that uses small bits of RNA to selectively shut off certain genes. This process depends on Argonaute. Martienssen noticed that plants without Argonaute looked very similar to plants that could not produce certain small pieces of RNA and soon determined that Argonaute helped get the regulatory RNAs to the right cells. Without Argonaute’s guidance, the small RNAs shut off genes in the wrong cells. The resulting confusion caused the leaf defects Martienssen had observed.

Plants call on 10 different versions of Argonaute to keep their regulatory RNAs under control, and the proteins’ overlapping functions can make it tricky to figure out exactly what they are doing. So Martienssen followed up these studies in the much simpler research model of single-celled yeast, where he found that small RNAs guided the addition of methyl groups to DNA-packaging proteins in transposon-rich regions of the genome. This chemical modification causes the chromosome to adopt a compacted form, blocking access for the enzymes that turn genes on.

Martienssen was the first to link RNAi to this tightly wrapped, inactive form of chromosomal DNA known as heterochromatin. “That has made people really think about how RNAi silences genes and transposons,” Martienssen says—so much so that Science magazine proclaimed his research part of their 2002 “Breakthrough of the Year.” Soon after his discovery, other researchers discovered that this kind of gene silencing also occurs in animal cells.

Transposon silencing is preserved from one generation to the next, which is remarkable because most methylation marks are stripped off DNA in reproductive cells during a process known as genetic reprogramming. Reprogramming clears the genetic slate for the sperm and egg, so that genes can be silenced only in the appropriate cells after pollination takes place and a new plant begins to grow. But reactivating transposons during this process could be dangerous.

Martienssen discovered new regulatory RNAs in germline cells that help reinstate transposon silencing after reprogramming occurs. Not only did those RNAs explain how transposon silencing is regulated in the germ line, they also appeared to regulate germ cell fate. That discovery has opened up a new line of research in Martienssen’s lab. By manipulating the way these RNAs and their target genes are regulated in sperm and egg cells, Martienssen thinks it may be possible to create plants that can reproduce without pollination. Plants that can grow from an egg cell with no fertilization would allow breeders to produce seeds that are an exact clone of the parent—a long-sought goal. Martienssen isn’t there yet, but he’s working on it.

“We’re explaining how reprogramming can, through transposons, really influence inheritance in such a fundamental way. We can’t explain how, yet, but just being able to say that this is true is amazing to me,” Martienssen says. “Genetics can abstract a seemingly huge, complex idea into simple components, such as genes. It explains heredity, and evolution, and all this wonderful stuff, and it was plants that led the way.”

Robert Martienssen is a Professor at Cold Spring Harbor Laboratory. He earned a M.A. in Natural Sciences from Cambridge University and a Ph.D. in plant molecular genetics from the Plant Breeding Institute and Cambridge University. He is a fellow of the Royal Society and an Associate Member of the European Molecular Biology Organization, and a recipient of the Newcomb-Cleveland Prize from the American Association for the Advancement of Science.