X in a new light

New findings Scientists have enlisted colour coding in the effort to better understand X chromosomes, how they are shut down in certain cells, and what it all means for men and women, writes Carl Zimmer

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 labelled 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.

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.

Deeper look

A Japanese biologist, Susumu Ohno, first recognised 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 shrivelled 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.

British geneticist Mary F Lyon realised that she could learn more about X-chromosome inactivation by breeding mice, because some colour genes sit on the X. In 1961 she reported that female mice sported patches of hair with their mother’s colour 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 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.

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 colour-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 neighbour shut down the father’s.

Nathans hopes his coloured 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.

Making the choice

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 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.

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. 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. 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 labelled with an X.