The Gene
How can a cell “silence” an entire chromosome? This process must involve not just the activation or inactivation of one or two genes based on an environmental cue; here an entire chromosome—including all its genes—was being shut off for the lifetime of a cell. The most logical guess, proposed in the 1970s, was that cells had somehow appended a permanent chemical stamp—a molecular “cancellation sign”—to the DNA in that chromosome. Since the genes themselves were intact, such a mark had to be above genes—i.e., epigenetic, à la Waddington.
In the late 1970s, scientists working on gene-silencing discovered that the attachment of a small molecule—a methyl group—to DNA was correlated with a gene’s turning off. These methyl tags decorated the strands of DNA, like charms on a necklace, and they were recognized as shutdown signals. The production of RNA ceased and the expression of the gene was silenced. If a chromosome was heavily decorated by methyl tags, then perhaps the whole chromosome could be silenced.
Methyl tags were not the only charms hanging off the DNA necklace. In 1996, working at Rockefeller University in New York, a biochemist named David Allis found yet another system to etch permanent marks on genes.II Rather than stamping the marks directly on genes, this second system placed its marks on proteins, called histones, that act as the packaging material for genes.
Histones hang tightly to DNA and wrap it into coils and loops, forming scaffolds for the chromosome. When scaffolding changes, the activity of a gene can change—akin to altering the properties of a material by changing the way that it is packaged (a skein of silk packed into a ball has very different properties from that same skein stretched into a rope). A “molecular memory” is thus stamped on a gene—this time, indirectly, by attaching the signal to protein. When a cell divides, the marks can be copied into daughter cells, thereby recording the memory over several generations of cells. When sperm or eggs are generated, it is conceivable these marks are copied into these germ cells, thereby recording the memory over several generations of organisms. The heritability and stability of these histone marks, and the mechanism to ensure that the marks appear in the right genes at the right time, are still under investigation—but simple organisms, such as yeast and worms, can seemingly transmit these histone marks across several generations.
We now know that the silencing and activation of genes using various chemical tags and markers is a pervasive and potent mechanism of gene regulation. The transient turning on and off of genes had been known for decades. But this system of silencing and reactivation is not transient; it leaves a permanent chemical imprint on genes. The tags can be added, erased, amplified, diminished, and toggled on and off in response to cues from a cell or from its environment.
These marks function like notes written above a sentence, or like marginalia recorded in a book—pencil lines, underlined words, scratch marks, crossed-out letters, subscripts, and endnotes—that modify the context of the genome without changing the actual words. Every cell in an organism inherits the same book, but by scratching out particular sentences and appending others, by “silencing” and “activating” particular words, by emphasizing certain phrases, each cell can write a unique novel from the same basic script. We might visualize genes in the human genome, with their appended chemical marks, thus:
. . . This . . . . is . . . the . . . . . . , , , . . . . . . . struc . . . ture , . . . . . . of . . . Your . . . . . . Gen . . . ome . . .
As before, the words in the sentence correspond to the genes. The ellipses and punctuation marks denote the introns, the intergenic regions, and regulatory sequences. The boldface and capitalized letters and the underlined words are epigenetic marks appended to the genome to impose a final layer of meaning.
This was the reason that Gurdon, despite all his experimental ministrations, had rarely been able to coax an adult intestinal cell backward in developmental time to become an embryonic cell and then a full-fledged frog: the genome of the intestinal cell had been tagged with too many epigenetic “notes” for it to be easily erased and transformed into the genome of an embryo. Like human memories that persist despite attempts to alter them, the chemical scribbles overwritten on the genome can be changed—but not easily. These notes are designed to persist so that a cell can lock its identity into place. Only embryonic cells have genomes that are pliant enough to acquire many different kinds of identities—and can thus generate all the cell types in the body. Once the cells of the embryo have taken up fixed identities—turned into intestinal cells or blood cells or nerve cells, say—there is rarely any going back (hence Gurdon’s difficulty in making a tadpole out of a frog’s intestinal cell). An embryonic cell might be able to write a thousand novels from the same script. But Young Adult Fiction, once scripted, cannot easily be reformatted into Victorian Romance.
Epigenetics partially solves the riddle of a cell’s individuality—but perhaps it can also solve the more tenacious riddle of an individual’s individuality. “Why are twins different?” we had asked earlier. Well, because idiosyncratic events are recorded through idiosyncratic marks in their bodies. But “recorded” in what manner? Not in the actual sequence of genes: if you sequence the genomes of a pair of identical twins every decade for fifty years, you get the same sequence over and over again. But if you sequence the epigenomes of a pair of twins over the course of several decades, you find substantial differences: the pattern of methyl groups attached to the genomes of blood cells or neurons is virtually identical between the twins at the start of the experiment, begins to diverge slowly over the first decade, and becomes substantially different over fifty years.
Chance events—injuries, infections, infatuations; the haunting trill of that particular nocturne; the smell of that particular madeleine in Paris—impinge on one twin and not the other. Genes are turned “on” and “off” in response to these events, and epigenetic marks are gradually layered above genes.III Every genome acquires its own wounds, calluses, and freckles—but these wounds and calluses “exist” only because they have been written into genes. Even the environment signals its presence through the genome. If “nurture” exists, it is only by virtue of its reflection in “nature.” That idea inspires an unsettling philosophical quandary: If we erased their imprints from the genome, would those events of chance, environment, and nurture cease to exist, at least in any readable sense? Would identical twins become truly identical?
In his remarkable story “Funes the Memorious,” the Argentine writer Jorge Luis Borges described a young man who awakes from an accident to discover that he has acquired “perfect” memory. Funes remembers every detail of every moment in his life, every object, every encounter—the “shape of every cloud . . . the marble grain of a leather-bound book.” This extraordinary ability does not make Funes more powerful; it paralyzes him. He is inundated by memories that he cannot silence; the memories overwhelm him, like the constant noise from a crowd that he cannot silence. Borges finds Funes lying in a cot in the darkness, unable to contain the hideous influx of information and forced to shut the world out.
A cell without the capacity to selectively silence parts of its genome devolves into Funes the Memorious (or, as in the story, Funes the Incapacitated). The genome contains the memory to build every cell in every tissue in every organism—memory so overwhelmingly profuse and diverse that a cell devoid of a system of selective repression and reactivation would become overwhelmed by it. As with Funes, the capacity to use any memory functionally depends, paradoxically, on the ability to silence memory. An epigenetic system exists to allow the genome to function. Its ultimate purpose is to establish the individuality of cells. The individuality of organisms is, perhaps, an unintended consequence.
Perhaps the most startling demonstration of the power of epigenetics to reset cellular memory arises from an experiment performed by the Japanese stem-cell biologist Shinya Yamanaka in 2006. Like Gurdon, Yamanaka was intrigued by the idea that chemical marks attached to genes in a cell might function as a record of its cellular identity. What
if he could erase these marks? Would the adult cell revert to an original state—and turn into the cell of an embryo, reversing time, annihilating history, furling back toward innocence?
Like Gurdon, again, Yamanaka began his attempt to reverse a cell’s identity with a normal cell from an adult mouse—this one from a fully grown mouse’s skin. Gurdon’s experiment had proved that factors present in an egg—proteins and RNA—could erase the marks of an adult cell’s genome and thereby reverse the fate of a cell and produce a tadpole from a frog cell. Yamanaka wondered whether he could identify and isolate these factors from an egg cell, then use them as molecular “erasers” of cellular fate. After a decades-long hunt, Yamanaka narrowed the mysterious factors down to proteins encoded by just four genes. He then introduced the four genes into an adult mouse’s skin cell.
To Yamanaka’s astonishment, and to the subsequent amazement of scientists around the world, the introduction of these four genes into a mature skin cell caused a small fraction of the cells to transform into something resembling an embryonic stem cell. This stem cell could give rise to skin, of course, but also to muscle, bones, blood, intestines, and nerve cells. In fact, it could give rise to all cell types found in an entire organism. When Yamanaka and his colleagues analyzed the progression (or rather regression) of the skin cell to the embryo-like cell, they uncovered a cascade of events. Circuits of genes were activated or repressed. The metabolism of the cell was reset. Then, epigenetic marks were erased and rewritten. The cell changed shape and size. Its wrinkles unmarked, its stiffening joints made supple, its youth restored, the cell could now climb up Waddington’s slope. Yamanaka had expunged a cell’s memory, reversed biological time.
The story comes with a twist. One of the four genes used by Yamanaka to reverse cellular fate is called c-myc. Myc, the rejuvenation factor, is no ordinary gene: it is one of the most forceful regulators of cell growth and metabolism known in biology. Activated abnormally, it can certainly coax an adult cell back into an embryo-like state, thereby enabling Yamanaka’s cell-fate reversal experiment (this function requires the collaboration of the three other genes found by Yamanaka). But myc is also one of the most potent cancer-causing genes known in biology; it is also activated in leukemias and lymphomas, and in pancreatic, gastric, and uterine cancer. As in some ancient moral fable, the quest for eternal youthfulness appears to come at a terrifying collateral cost. The very genes that enable a cell to peel away mortality and age can also tip its fate toward malignant immortality, perpetual growth, and agelessness—the hallmarks of cancer.
We can now understand the Dutch Hongerwinter, and its multigenerational effects, in mechanistic terms that involve both genes and epigenes. The acute starvation of men and women during those brutal months in 1945 indubitably altered the expression of genes involved in metabolism and storage. The first changes were transient—no more, perhaps, than the turning on and turning off of genes that respond to nutrients in the environment.
But as the landscape of metabolism was frozen and reset by prolonged starvation—as transience hardened into permanence—more durable changes were imprinted in the genome. Hormones fanned out between organs, signaling the potential long-term deprivation of food and auguring a broader reformatting of gene expression. Proteins intercepted these messages within cells. Genes were shut down, one by one, then imprints were stamped on DNA to close them down further. Like houses shuttering against a storm, entire gene programs were barricaded shut. Methylation marks were added to genes. Histones may have been chemically modified to record the memory of starvation.
Cell by cell, and organ by organ, the body was reprogrammed for survival. Ultimately, even the germ cells—sperm and egg—were marked (we do not know how, or why, sperm and egg cells carry the memory of a starvation response; perhaps ancient pathways in human DNA record starvation or deprivation in germ cells). When children and grandchildren were born from these sperm and eggs, the embryos may have carried these marks, resulting in alterations in metabolism that remained etched in their genomes decades after the Hongerwinter. Historical memory was thus transformed into cellular memory.
A note of caution: epigenetics is also on the verge of transforming into a dangerous idea. Epigenetic modifications of genes can certainly superpose historical and environmental information on cells and genomes—but this capacity is limited, idiosyncratic, and unpredictable: a parent with an experience of starvation produces children with obesity and overnourishment, while a father with the experience of tuberculosis, say, does not produce a child with an altered response to tuberculosis. Most epigenetic “memories” are the consequence of ancient evolutionary pathways, and cannot be confused with our longing to affix desirable legacies on our children.
As with genetics in the early twentieth century, epigenetics is now being used to justify junk science and enforce stifling definitions of normalcy. Diets, exposures, memories, and therapies that purport to alter heredity are eerily reminiscent of Lysenko’s attempt to “re-educate” wheat using shock therapy. A child’s autism, the result of a genetic mutation, is being backtracked to the intrauterine exposures of his grandparents. Mothers are being asked to minimize anxiety during their pregnancy—lest they taint all their children, and their children, with traumatized mitochondria. Lamarck is being rehabilitated into the new Mendel.
These glib notions about epigenetics should invite skepticism. Environmental information can certainly be etched on the genome. But most of these imprints are recorded as “genetic memories” in the cells and genomes of individual organisms—not carried forward across generations. A man who loses a leg in an accident bears the imprint of that accident in his cells, wounds, and scars—but does not bear children with shortened legs. Nor has the uprooted life of my family seem to have burdened me, or my children, with any wrenching sense of estrangement.
Despite Menelaus’s admonitions, the blood of our fathers is lost in us—and so, fortunately, are their foibles and sins. It is an arrangement that we should celebrate more than rue. Genomes and epigenomes exist to record and transmit likeness, legacy, memory, and history across cells and generations. Mutations, the reassortment of genes, and the erasure of memories counterbalance these forces, enabling unlikeness, variation, monstrosity, genius, and reinvention—and the refulgent possibility of new beginnings, generation upon generation.
It is conceivable that an interplay of genes and epigenes coordinates human embryogenesis. Let us return, yet again, to Morgan’s problem: the creation of a multicellular organism from a one-celled embryo. Seconds after fertilization, a quickening begins in the embryo. Proteins reach into the nucleus of the cell and start flicking genetic switches on and off. A dormant spaceship comes to life. Genes are activated and repressed, and these genes, in turn, encode yet other proteins that activate and repress other genes. A single cell divides to form two, then four, and eight cells. An entire layer of cells forms, then hollows out into the outer skin of a ball. Genes that coordinate metabolism, motility, cell fate, and identity fire “on.” The boiler room warms up. The lights flicker on in the corridors. The intercom crackles alive.
Now a second code stirs to life to ensure that gene expression is locked into place in each cell, enabling each cell to acquire and fix an identity. Chemical marks are selectively added to certain genes and erased from others, modulating the expression of the genes in that cell alone. Methyl groups are inserted and erased, and histones are modified to repress or activate genes.
The embryo unfurls step by step. Primordial segments appear, and cells take their positions along various parts of the embryo. New genes are activated that command subroutines to grow limbs and organs, and more chemical marks are appended on the genomes of individual cells. Cells are added to create organs and structures—forelegs, hind legs, muscles, kidneys, bones, eyes. Some cells die a programmed death. Genes that maintain function, metabolism, and repair are turned on. An organism emerges from a cell.
Do not be lulled by that description. Do not, gentle
reader, be tempted to think—“My goodness, what a complicated recipe!”—and then rest assured that someone will not learn to understand or hack or manipulate that recipe in some deliberate manner.
When scientists underestimate complexity, they fall prey to the perils of unintended consequences. The parables of such scientific overreach are well-known: foreign animals, introduced to control pests, become pests in their own right; the raising of smokestacks, meant to alleviate urban pollution, releases particulate effluents higher in the air and exacerbates pollution; stimulating blood formation, meant to prevent heart attacks, thickens the blood and results in an increased risk of blood clots to the heart.
But when nonscientists overestimate complexity—“No one can possibly crack this code”—they fall into the trap of unanticipated consequences. In the early 1950s, a common trope among some biologists was that the genetic code would be so context dependent—so utterly determined by a particular cell in a particular organism and so horribly convoluted—that deciphering it would prove impossible. The truth turned out to be quite the opposite: just one molecule carries the code, and just one code pervades the biological world. If we know the code, we can intentionally alter it in organisms, and ultimately in humans. Similarly, in the 1960s, many doubted that gene-cloning technologies could so easily shuttle genes between species. By 1980, making a mammalian protein in a bacterial cell, or a bacterial protein in a mammalian cell, was not just feasible; it was, in Berg’s words, rather “ridiculously simple.” Species were specious. “Being natural” was “often just a pose.”
The genesis of a human from genetic instructions is indubitably complex, but nothing about it forbids or restricts manipulation or distortion. When a social scientist emphasizes that gene-environment interactions—not genes alone—determine form, function, and fate, he is underestimating the power of master-regulatory genes that act nonconditionally and autonomously to determine complex physiological and anatomical states. And when a human geneticist says, “Genetics cannot be used to manipulate complex states and behaviors because these are usually controlled by dozens of genes,” that geneticist is underestimating the capacity of one gene, such as a master regulator of genes, to “reset” entire states of being. If the activation of four genes can turn a skin cell into a pluripotent stem cell, if one drug can reverse the identity of a brain, and if a mutation in a single gene can switch sex and gender identity, then our genomes, and our selves, are much more pliable than we had imagined.