Combination of switches turns off excess X chromosome just at the right time

Two X chromosomes are actually one too many. So female mammalian cells turn off one of them – but only when the cells start to specialize in tissue. A Berlin research team has now discovered how cells “count” their chromosomes and at the same time detect what stage of development they are in.

Female mammalian cells have a problem with dosing because they have twice as many X chromosomes as are needed in the body. Therefore, one of them is randomly selected and deactivated early in embryonic development. the Xist gene wakes up and produces hundreds of RNA molecules, locking up an X chromosome and causing it to shrink into a tiny piece.

But how does the cell know how to deactivate a chromosome at any given time, but only if there are two? A research team led by Edda Schulz, head of the Lise Meitner group at the Max Planck Institute for Molecular Genetics (MPIMG), found the answer to this decades-old puzzle in mouse stem cells and published their findings in review Molecular cell.

A new genetic circuit

Scientists in Berlin have identified a genetic circuit that receives information about the developmental stage of the cell and passes it on to the Xist uncomfortable. “We found the regulatory region that detects whether the cell has left its stem cell state,” says Edda Schulz.

The newly discovered genetic switch, dubbed “Xert“, is part of the family of regulatory” enhancer “sequences. It is not enough on its own to trigger the deactivation program. Xist will respond to developmental signals only if it is freely accessible and not blocked by other factors, which is the case when two X chromosomes are present in the cell. Only when both conditions are met, Xist can silence the “surplus” X chromosome.

DNA elements around Xist process information from different sources, almost like a computer, explains Schulz: “A cell has programs that can be started and stopped. But unlike a machine made of wires and silicon, its circuits are made up of molecules that stick together or are created by chemical reactions. “

Obtain insight by disturbance

“Our goal was to trace the genetic circuits without knowing the patterns,” explains Rutger Gjaltema, scientist at Schulz’s laboratory and first author of the article. “In the end, we got a pretty complete picture of Xist’s regulatory landscape.”

In a first screening experiment, the scientists determined 138 DNA segments on the X chromosome that appeared to be involved in some way in signaling around the Xist gene. For each of the segments, they designed a DNA extract that could individually target and turn off potential genetic switches. The researchers placed the extracts into virus-like particles, infected cells with them, and observed in which cases Xist RNA production was either increased or impaired.

“We have found many Xist regulators that we already knew, which was a good sign as it confirmed that our approach was working, ”says Till Schwämmle, another scientist on Schulz’s team and also the paper’s first author. “More exciting, of course, was that a number of completely unknown sequences appeared in the analyzes.”

Division of labor in space

To study the function of the new sequences, Gjaltema and Schwämmle compared their activity in stem cells, developing cells, and cells with two or only one X chromosome. They noticed that there appears to be a division of labor between them. genetic switches and a striking spatial separation.

The first switch is located in the immediate vicinity of Xist and its startup sequence. It only switches when a double dose of encoded X-linked enzymes is present. These enzymes appear to mediate the breakdown of factors that block nearby sections Xist. Once there are enough enzymes, the gene becomes accessible to signals from the Xert enhancer. However, with just one X chromosome there is too little of it and Xist gets stuck and unable to do its job.

The second switch is not located nearby XistSchulz explains: “Similar to other developmental genes, the activator is relatively far from its target gene. The DNA has to fold into a loop to come into contact with the gene, ”explains the scientist. With Stefan Mundlos’ research group at MPIMG, his team studied the three-dimensional structure of DNA around the Xist uncomfortable. “We show that far apart signals on the DNA strand are integrated.”

“The two signaling pathways are related,” says Schulz. “The region near Xist arms the mechanism, acting as an on-off switch. Then the amplifier can pull the trigger when the cell has grown sufficiently. “

A model for other developmental genes

The new findings provide clues for years of further study to fully elucidate X chromosome inactivation, says Schulz. However, while the process controlled by Xist is unique in the animal kingdom, the mechanisms of genetic control are not. Schulz thinks that Xist Regulation can also be used to better understand other developmental genes: “The inactivation of X is a fascinating system in itself, but above all, it is a very valuable model for better understanding the regulatory relationships in our genome.

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