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Biological Chemistry

Genes Take A Back Seat

Epigenetics, the molecular framework that controls genes’ expression, takes its cues from both nature and nurture

by Ivan Amato
March 31, 2009 | A version of this story appeared in Volume 87, Issue 14

Famine’s Lasting Signs
Credit: U.S. Archives
A U.S. bomber drops food in the Netherlands at the end of World War II in response to a German blockade of the region. The resulting famine left permanent epigenetic marks in fetuses conceived at the time.
Credit: U.S. Archives
A U.S. bomber drops food in the Netherlands at the end of World War II in response to a German blockade of the region. The resulting famine left permanent epigenetic marks in fetuses conceived at the time.

IN THE WINTER MONTHS of 1944-45, the Nazis imposed an embargo on the western part of the Netherlands, fomenting a seven-month famine that had a clear beginning and end. During this time, Dutch officials maintained detailed health care registries and food-rationing documentation.

Unfortunate as the circumstances were, to those now pushing into an emerging research arena called environmental epigenetics, the Dutch Hunger Winter, as this wartime episode is known, has provided rare opportunities to study how environmental conditions reach inside fetal cells and influence the genetic program of human beings throughout their lives. It’s a set of conditions for a human study that could only be realized by accident, natural disaster, or human evil.

Molecular epidemiologist Bastiaan T. Heijmans of Leiden University Medical Center, in the Netherlands, and colleagues there and at Emory University, Columbia University, and New York State Psychiatric Institute, hypothesized that those 60-plus-year-olds still alive today who were fetuses in their hungry mothers’ wombs during the famine might still carry a molecular record of those conditions in their cells: the amount and pattern of methyl groups attached to specific cytosine nucleotides (those directly followed by a guanine nucleotide) in their DNA.

DNA methylation is one of the two primary types of so-called epigenetic modifications on chromosomes that control which genes can be expressed and which ones remain silent. In the wrong place or at the wrong time, epigenetic modifications, which leave genes’ sequences unchanged, can have deleterious effects indistinguishable from genetic mutations that cause cancer and other diseases. Epigenetic mechanisms also could alter genetic expression patterns to ones that favor the survivability of fetuses whose mothers are exposed to, say, molecular cues in their diets that correlate with trying times.

Heijmans’ group conjectured that during the Dutch Hunger Winter, the relative absence in the diets of pregnant women of foods rich in folate and other methyl-donating vitamins would have resulted in decreased DNA methylation in the genomes of their developing fetuses compared with fetuses that were not deprived of methyl-donating nutrients. The researchers compared methylation patterns along the chromosomal location of the gene insulin-like growth factor II, or IGF2, of those conceived during the famine with those of their same-sex siblings whose gestations occurred in better times. IGF2’s protein product is a key factor in growth and development. Using all of those intact wartime records in the Netherlands, Heijmans’ team located close to 1,000 living adults in their sixties who were fetuses just before, during, and after the Dutch Hunger Winter and got blood samples from them.

In the end, the result sounds modest. The scientists found that individuals alive today who were prenatally exposed to famine conditions had 5% less methylation along the IGF2 gene compared with their siblings who were not so exposed. “Our study provides the first evidence that transient environmental conditions early in human gestation can be recorded as persistent changes in epigenetic information,” the researchers write in their paper (Proc. Natl. Acad. Sci. USA 2008, 105, 17046).

THAT 5% DIFFERENCE is profound to epigenetics researchers—like Randy L. Jirtle of Duke University—who are convinced that genes themselves have enjoyed an overblown place in biology’s explanatory framework. To Jirtle, epigenetics is like the software that runs the genetic hardware.

As for the Dutch Hunger Winter study, Jirtle says, “what we are really talking about here is fetal origins of disease susceptibility.” There always has been a widespread intuition that we come into this world with in-born propensities and vulnerabilities, and Jirtle is betting that gene-controlling epigenetic mechanisms such as DNA methylation are big parts of the scientific explanation for that baggage. Jirtle’s animal studies show how different levels of methyl-donating nutrients such as folate in the diets of pregnant mice effectively dial in the fur color and size of their pups. His studies have become among the clearest and most famous demonstrations of an environmental cue’s epigenetic consequences.

Still to come from the Dutch Hunger Winter study is a report on whether and how the altered methylation levels relate to health patterns in the later lives of those who were fetuses during the famine. “This is the million-dollar question,” says Lambert H. Lumey, a Columbia University epidemiologist who collaborated on the project. “Everyone is waiting for this,” he says, unwilling to divulge details until he and his colleagues publish their findings.

Methyl Mice
Credit: Randy Jirtle/Duke U
Adding methyl-donating nutrients such as folic acid to the diet of pregnant Agouti mice alters the offspring’s gene-controlling epigenome and results in smaller, leaner, darker progeny compared with the larger, plumper, yellow mouse that a normal diet yields. Despite their appearances, the two mice are genetically identical.
Credit: Randy Jirtle/Duke U
Adding methyl-donating nutrients such as folic acid to the diet of pregnant Agouti mice alters the offspring’s gene-controlling epigenome and results in smaller, leaner, darker progeny compared with the larger, plumper, yellow mouse that a normal diet yields. Despite their appearances, the two mice are genetically identical.

To those researchers uncovering the molecular biology of epigenetics, there is a conceptual shift, potentially Copernican in scale, in the offing. “The epigenetics bombshell” is the metaphor that enzymologist Norbert O. Reich of the University of California, Santa Barbara, summons when describing the emerging epigenetics framework for understanding biology. Just as the Copernican solar system jerked Earth away from the system’s center, epigenetics researchers are dethroning the gene as biology’s center of the universe. “Genes are no longer the center of everything,” says Reich, who studies methyltransferase enzymes that insert methyl groups into bacterial DNA, an investigative path that he says could lead to new antibiotics.

Ushering in a broader conceptual framework based on both genes and epigenetics, Reich and others say, will elicit a far deeper molecular understanding of what underlies the similarities and differences among individuals and why different people respond differently to drugs, nutrients, and other environmental exposures.

Dethroning genes is verging on sacrilege. For decades, it has seemed that the whole point, if you’re into biology, has been to explain what is going on by way of genes that get translated into proteins that carry out the molecular actions of life. The genotype, mutations and all, begets the phenotype, healthy or diseased. That has been the mantra. Many who participated in the Human Genome Project in the 1990s knew that the result of their project—a fully sequenced human genome—would at first amount to a catalog of essentially hieroglyphic DNA sequences whose biological, evolutionary, and medical meanings would be far from obvious. But the multi-billion-dollar project could not have been more emblematic of the gene-centricity of modern biology.

“WE HAVE BEEN BLINDED,” says molecular and human geneticist Arthur L. Beaudet of Baylor College of Medicine, in Houston. Genes are crucial parts of the story, but it’s the epigenetic program that determines their activity, says Beaudet, who scours the chromosomal landscapes in brain cells from cadavers for epigenetic markings—perhaps ones acquired during gestation—that influence genetic programs associated with autism and schizophrenia. “Epigenetics is mediating between genotype and phenotype,” he says.

For a growing number of scientists, genes are getting downright blasé. Not that the 25,000 genes or so that occupy about 2% of the human genome are not vitally important. After all, a single mutation in just one genetic letter (nucleotide) of a gene that is thousands of letters long can mean, say, a life with sickle cell anemia or a much greater risk of developing cancer. But with so much of the genetic lettering the same between any two human beings, it has to be the orchestration of the activity or silence of the genes that makes up much of our personal differences.

Lights On Methylation
Credit: Christoph Bock
The crystal structure of this 12-base-pair stretch of DNA includes cytosine-guanine motifs that are primary sites of methylation (bright spots). The presence of many such marks in a given stretch of DNA can shut down gene expression.
Credit: Christoph Bock
The crystal structure of this 12-base-pair stretch of DNA includes cytosine-guanine motifs that are primary sites of methylation (bright spots). The presence of many such marks in a given stretch of DNA can shut down gene expression.

That’s where the other 98% of the genome—and the big-cast molecular opera that plays out on and along it—comes in. And it is looking more and more like the thing that matters most: It’s what activates and silences genes in different tissues at different times. It is the great decider behind the molecular unfolding of life, from a fertilized cell to a fully formed newborn, and throughout a lifetime in illness and in health, until death stills it all. Without that other 98% of the genome and its molecular context, genes might be nothing but unremarkable and impotent stretches of DNA.

Way more than the mere sequence of nucleotides that make up the DNA, this larger context also encompasses the millions of histone protein-DNA spools, called nucleosomes, that enable 6 feet worth of DNA to coil, bend, and otherwise condense until it fits inside a nucleus that fits inside a cell that can only be seen in a microscope. It is this DNA-protein stuff, chromatin, that is the macromolecular stage on which cues from the inside and from the outside worlds influence genetic expression. It is where nature and nurture mingle and wrestle via chemical rules that remodel chromatin—by way of DNA methylation patterns or an operatic orchestration of modifications on the histone proteins of nucleosomes—into a landscape with chemical signs that say the equivalent of such things as “No gene expression zone ahead” and “Gene transcription machinery welcome here.”

What’s more, all of this epigenetic signage, which does nothing to any gene’s signature sequence of nucleotides, is heritable, at least to a degree. In development, this is the type of heritability that ensures, for example, that liver cells beget only liver cells and not brain cells once in a while. It is a form of cellular memory. And evidence is mounting that epigenetic markings on egg or sperm cells and those acquired as a result of some sort of toxic exposure or hardship can be inherited for several generations, Jirtle says. This means that how well your mother ate and whether your father smoked when you were conceived could affect the health of your own children.

TO EPIGENETICS researchers such as Moshe Szyf of McGill University, in Montreal, the epigenome is where feast and famine, toxin and medicine, wealth and poverty, and love and neglect ultimately come into causal, molecule-mediated contact with a cell’s nucleus. Either directly by way of a chemical poison or nutrient or indirectly—say, by way of biomolecule-releasing stress conditions—environmental, behavioral, and psychological cues join the seemingly quixotic and capricious molecular negotiations by which a neighbor on the right lives to be 100 while the neighbor on the left dies young of a brain tumor.

Szyf is one of the more evangelical of epigenetics researchers. Talk to him and he’ll try to convince you, using a combination of polemics and data, that the time is approaching when epigeneticists will have in hand an explanatory framework that goes way beyond the gene-centric stories that have dominated the discussion of nature versus nurture. Szyf goes so far as to say that the epigenetics framework will open the path to explanatory stories detailing how this or that dietary input, this or that exposure to a pollutant, or even this or that social condition such as lack of parental affection elicits particular physical traits or health conditions in you or me throughout our lives. And at the bottom, he says, “it’s all chemistry. What is most provocative here is the realization that the social environment can affect methylation patterns.”

As much as anyone studying epigenetics, Szyf has been arguing that epigenetic mechanisms are the bridges by which even psychological and social conditions, especially in prenatal and early postnatal periods, elicit epigenetic interventions in genetic expression that, in turn, can have behavioral and psychological consequences throughout life. “Now I can talk to social scientists who look at poverty-and-diseases connections,” Szyf tells C&EN.

For the most part, conjectures about epigenetic mechanisms by which social conditions might influence health derive from animal studies. Szyf says the most complete example starts with just how much rat moms lick and groom their little pups.

“When rats maternally care for their offspring, it turns on reward systems in the pups’ brains, which work mostly through serotonin,” Szyf says, before chronicling a veritable biochemical Rube Goldberg machine. The neurotransmitter binds to receptors in the pups’ brain cells, initiating a sequence of chemical events and signaling pathways that activate production of a DNA-binding transcription factor in the brain’s hippocampal tissue. That transcription factor binds to a gene promoter region associated with expression of glucocorticoid receptor (GR) proteins, which are part of the stress response system. In that location, the transcription factor teams up with a histone acetyltransferase enzyme, which epigenetically alters histone proteins in nucleosomes of the well-licked pups’ chromatin. That, in turn, launches another cascade of events that demethylates the GR-associated DNA region, thereby unzipping the DNA and making gene expression there possible.

The behavioral consequence of a nurturing, tongue-lapping rat mom comes down to this: calmer rat progeny that grow up to be less ruffled in stressful situations than sibling rats who, as wee ones, are less doted over by their moms (Reprod. Toxicol. 2007, 24, 9). Taking the leap from this, Szyf says, “you can envisage how all of this happens in kids.”

How well your mother ate and whether your father smoked when you were conceived could affect the health of your own children.

NOT EVERYONE is ready to make the extrapolations to people from cell and animal studies that Szyf does, but most researchers who know about epigenetics at all predict it is ascending to prominence in biology and medicine. It is a framework, they say, that finally can provide scientific moorings for intuitions about nature-nurture connections.

With scientific promise of that sort, the epigenetics buzz has been getting louder. Funding agencies, academic departments, journal editors, life sciences research companies, and scientists collectively have been building up momentum to uncover and map the epigenetic and epigenomic (genome-scale) landscapes of health and disease.

This past September, for example, the National Institutes of Health announced the initial $18 million of grants of a five-year, $190 million epigenomics initiative. That’s some serious money and reflects the giant health research center’s take on epigenetics.


“The initiative includes genomewide studies to look at normal and diseased cells or environmentally exposed cells,” notes John Satterlee, program director for epigenetics, model organism genetics, and functional genomics for NIH’s National Institute on Drug Abuse. And he points out that the program will support research in “any diseases NIH would be interested in,” among them obesity, infectious diseases, psychiatric disorders, cardiovascular disorders, and autoimmune conditions.

The program has several major components. It is funding four centers that will profile the DNA methylation and histone modification patterns of a variety of diseased and healthy cells, among them embryonic stem cells. To manage the vast streams of data expected from this and other so-called reference epigenome work, the initiative also is funding an Epigenomics Data Analysis & Coordination Center at Baylor College of Medicine (Beaudet is a codirector of the center). And to help speed up the pace, efficiency, and thoroughness of epigenomic and epigenetic analyses, the initiative is supporting a bevy of projects to develop profiling methods and imaging techniques that can show epigenetic changes in cells and tissues. Another thrust is supporting searches for novel epigenetic marks beyond the DNA methylation and histone modifications that are already known.

“Understanding these processes has far-reaching implications, from reprogramming of adult cells to treat disease to learning how environmental exposures during pregnancy increases a child’s risk of developing chronic diseases, such as diabetes and cardiovascular disease,” says Griffin P. Rodgers, director NIH’s National Institute of Diabetes & Digestive & Kidney Diseases.

The science of epigenetics couldn’t be more thrilling, compelling, and powerful, Duke’s Jirtle says, but he notes that for those same reasons it is likely to have a double edge to it. As epigenetic storytelling by scientists and physicians becomes more detailed and backed by data, he says, expecting parents might feel an extra weight of responsibility or guilt about what they eat, where they go, what sorts of environmental exposures they are subject to, and whether they had nice or grumpy dispositions when their children were newborns. But it’s the flip side of that same body of knowledge that Jirtle and others in the epigenetics community have their eyes on most. The epigenetic stratum of molecular biology they now are excavating might sweep away the fatalism that comes with the traditional, gene-centric way of thinking.

“When you have a mutation in a gene, you are stuck. You feel like you have a death sentence. There is no way of treating that unless you do gene therapy,” which has had very few medical successes to date, Jirtle says. The epigenetic basis of health and disease might open up other routes of intervention. “You might develop drugs that target the epigenome to prevent or reduce susceptibility” to disease, Jirtle says. In some cases, he says, you might even leave drugs behind and “treat yourself simply by varying your diet or the way you live.”


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