mouse brain
© Hao Wu and Jeremy Nathans/Cell Press
In a female mouse’s brain, a left-to-right pattern in the silencing of the X chromosome. These patterns may influence how individual brains function
The term "X chromosome" has an air of mystery to it, and rightly so. It got its name in 1891 from a baffled biologist named Hermann Henking. To investigate the nature of chromosomes, Henking examined cells under a simple microscope. All the chromosomes in the cells came in pairs.

All except one.

Henking labeled this outlier chromosome the "X element." No one knows for sure what he meant by the letter. Maybe he saw it as an extra chromosome. Or perhaps he thought it was an ex-chromosome. Maybe he used X the way mathematicians do, to refer to something unknown.

Today, scientists know the X chromosome much better. It's part of the system that determines whether we become male or female. If an egg inherits an X chromosome from both parents, it becomes female. If it gets an X from its mother and a Y from its father, it becomes male.

But the X chromosome remains mysterious. For one thing, females shut down an X chromosome in every cell, leaving only one active. That's a drastic step to take, given that the X chromosome has more than 1,000 genes.

x chromosome
© Hao Wu and Jeremy Nathans/Cell Press
Cells silence X chromosomes in different patterns, sometimes skewing entire organs toward one parent. Clockwise from top left, a mouse’s cornea, skin, cartilage and inner ear. Dr. Jeremy Nathans hopes his colored maps serve as an atlas for the effects of X-chromosome inactivation on women
In some cells, the father's goes dormant, and in others, the mother's does. While scientists have known about this so-called X-chromosome inactivation for more than five decades, they still know little about the rules it follows, or even how it evolved.

In the journal Neuron, a team of scientists has unveiled an unprecedented view of X-chromosome inactivation in the body. They found a remarkable complexity to the pattern in which the chromosomes were switched on and off.

At the same time, each copy of the X chromosome contains versions of genes not found on its partner. So having two X chromosomes gives females more genetic diversity than males, with their single X chromosome. Because of that, females have a genetic complexity that scientists are only starting to understand.

"Females simply have access to realms of biology that males do not have," said Huntington F. Willard, the director of Duke University's Institute for Genome Sciences & Policy, who was not involved in the research.

But while the additional genes provided by their second X chromosome may in some cases provide females with a genetic advantage, X chromosomes also have a dark side. Their peculiar biology can lead to genetic disorders in males and, new research suggests, create a special risk of cancer in females. Understanding X-chromosome inactivation can also shed light on the use of stem cells in therapies.

A Japanese biologist, Susumu Ohno, first recognized X-chromosome inactivation in the late 1950s. In every female cell that he and his colleagues studied, they found that one of the two X chromosomes had shriveled into a dormant clump. Scientists would later find that almost no proteins were being produced from the clump, indicating that it had been shut down.

The British geneticist Mary F. Lyon realized that she could learn more about X-chromosome inactivation by breeding mice, because some color genes sit on the X. In 1961 she reported that female mice sported patches of hair with their mother's color and others with their father's.

Getting a deeper look at how females shut down their X chromosomes has remained a challenge in the decades since Dr. Lyon's discovery. In recent years, Dr. Jeremy Nathans, a Howard Hughes Medical Institute investigator at Johns Hopkins University, and colleagues have developed a way to make X chromosomes from different parents light up. They inserted a set of genes into the X chromosomes of mice. The genes produced a green fluorescent protein, but only if their X chromosome was active and they were exposed to a particular chemical trigger.

Dr. Nathans and his colleagues engineered other mice to produce a red protein from active X chromosomes in response to a different chemical. The researchers bred the altered mice to produce female pups. The pups inherited a green X from one parent and a red one from the other.

The scientists then added both of their color-triggering chemicals to the mouse cells. The cells lit up in a dazzling mosaic of reds and greens. One cell might shut down the mother's X, while its neighbor shut down the father's.

In recent years, scientists have increasingly appreciated that our cells can vary genetically - a phenomenon called mosaicism. And X-chromosome inactivation, Dr. Nathans's pictures show, creates a genetic diversity that's particularly dramatic. Two cells side by side may be using different versions of many different genes. "But there is also much larger-scale diversity," Dr. Nathans said.

In some brains, for example, a mother's X chromosome was seen dominating the left side, while the father's dominated the right. Entire organs can be skewed toward one parent. Dr. Nathans and his colleagues found that in some mice, one eye was dominated by the father and the other by the mother. The diversity even extended to the entire mouse. In some animals, almost all the X chromosomes from one parent were shut; in others, the opposite was true.

© Hao Wu and Jeremy Nathans/Cell Press
To learn more about how females shut down their X chromosomes, researchers developed a way to make X chromosomes from different parents light up as green or red in mice. A mouse’s left and right retinas
"It's incredibly important," said Dr. Willard, the Duke geneticist. "This is the most stunning display of what Mary Lyon said 50 years ago."

Dr. Nathans hopes his colored maps can serve as an atlas for the effects of X-chromosome inactivation on women's bodies. Because each X chromosome carries different variants of the same genes, father-dominated tissues may behave differently from mother-dominated ones.

How one cell ends up silencing its mother's or father's X chromosome is still not entirely clear. Scientists are just starting to decipher some of the key steps in the process. "The knowledge of this is exploding," said Dr. Jeannie T. Lee, a Howard Hughes Medical Institute investigator at Harvard Medical School.

Scientists don't know how a cell chooses one chromosome or another to silence. But they've identified a number of the molecules that do the silencing. The leader of this molecular team is known as Xist.

Ever since it was discovered in the 1990s, scientists have debated how Xist managed to shut down an entire chromosome. Some researchers suggested that one Xist molecule landed on one spot on the X chromosome and then others attached to it, spreading along its length. But recent studies by Dr. Lee and colleagues show that Xist molecules envelop the X chromosome like a swarm of bees. "It's going to all the genes all at once," she said.

Once Xist latches on, it lures other types of molecules. Together they enshroud the X chromosome. When a cell divides, new copies of the molecules silence the same chromosome in its descendants.

Why women's cells should bother with such an elaborate dance has also intrigued scientists. While scientists have proposed a number of explanations ever since X-chromosome inactivation was discovered, Gabriel A.B. Marais, an evolutionary biologist at the University of Lyons in France, said that none fit the current evidence very well. "The situation is very confusing," he confessed.

It's possible, for example, that males have to increase the production of proteins from their X chromosome because they have only one copy of its genes. But this creates a quandary for females, because they may overdose themselves. They shut down one of the hyperactive X chromosomes to regain a balance of their own.

Females might have evolved to choose randomly between their parents' chromosomes because it gave them more genetic versatility. Sometimes a gene on one X chromosome is defective. Cells that use the healthy copy of the X chromosome can compensate. Males, by contrast, are far more prone to genetic disorders linked to the X chromosome, such as color blindness. With only one X chromosome in their cells, they have no backup.

Dr. Nathans speculates that using chromosomes from both parents is especially useful in the nervous system. It could create more ways to process information. "Diversity in the brain is the name of the game," he said.

But the X chromosome may also pose a risk to women. Dr. Lee and her colleagues have found that when they shut down Xist in female mice, the animals were more likely to develop cancer. She suspects that when a cell stops making Xist, its inactivated X chromosome wakes up. The extra proteins it makes can drive a cell to grow uncontrollably.

"That has bearing on stem cell therapy," she added. When stem cells are reared in the lab, they sometimes stop making Xist as well. Dr. Lee is concerned that female stem cells may rouse sleeping X chromosomes, with devastating consequences.

Before stem cells can be safely used in medical treatments, we may finally need to solve the mystery that Henking originally labeled with an X.