‘Waistbands’ of our chromosomes marked by unusual X-shaped DNA

Human Y chromosome’s center more ‘monkey-like’ than other human chromosomes, study finds
An illustration showing two chromosomes in cross stitch, with their centers marked in different colors, on a fabric background with a needle on the side.
A new study has found that the midpoints of chromosomes may be marked by unusually shaped DNA, like a tiny row of cross stitches. Illustration by Kim Carney / Fred Hutch News Service

For much of biologist Dr. Steve Henikoff’s career, a scientific conundrum has plagued him.

The centromere, the midpoint of our chromosomes that’s essential for cell division — and thus for the very essence of life — remains largely mysterious. Until recently, we didn’t even know what DNA sequences made up centromeres.

And scientists who study these chromosomal waistbands, as Henikoff does in his Fred Hutchinson Cancer Research Center laboratory, don’t fully agree on what defines a centromere.

Some think it’s the region’s DNA sequence, that the centromere bears a genetic ID tag. But most in the field are convinced that DNA has little to do with it, Henikoff said. The prevailing scientific dogma is that our centromeres are defined by something outside of genetics, a phenomenon known as epigenetics.

Henikoff and Sivakanthan Kasinathan, a Fred Hutch and University of Washington graduate student, have come up with a third theory, which they describe in a study published last week in the journal Molecular Biology and Evolution: DNA gives centromeres their identity, but it’s not the precise sequence of letters of the DNA that counts. It’s the shape they make.

Their study presents evidence that DNA at the centromere does not form the standard double helix twist, but rather kinks into a series of small, repeated X-shapes — like a row of cross-stitches.

They also saw that the centromere of the human Y chromosome — the chromosome responsible for determining the male sex — is different from all the other human chromosomes.

The Y chromosome looks a lot like a monkey chromosome,” Henikoff said — at least in terms of the DNA shape at its centromere.

Revisiting a scientific dogma

Researchers have been trying to figure out what makes a centromere a centromere long before they understood what DNA was, Kasinathan said.

“The fact that centromeres are specific spots on chromosomes is a really old idea. It’s almost 150 years old,” he said. “In that sense the fact that centromeres are spots on chromosomes predates genetics itself.” The dogma that centromere identity has nothing to do with DNA is only about a decade old.

Photo of Steve Henikoff
Fred Hutch molecular biologist Dr. Steve Henikoff Fred Hutch file photo

But that theory never sat right with Henikoff. Previous studies, including some from his own lab, had suggested that the DNA sequence does have a role to play.

To get a grasp on whether DNA features might play a significant role at the centromere after all, the researchers surveyed the genetic sequences of centromeres — which were only very recently captured in a way scientists could analyze them — from a variety of different living creatures, from humans to monkeys to mice to microscopic budding yeast. Using a computer algorithm that predicts DNA shape, they saw evidence for this strangely bent DNA at centromeres across evolutionary history.

Animals and other living things seem to have evolved two different ways to get their DNA into these weird twists, the researchers found. Either the DNA letters are strung in an order that naturally tends toward kinks, as in certain monkeys and the human Y chromosome, or the creatures rely on a protein known as CENP-B that helps the DNA bend — which is how mice and humans (other than the human Y) manage their centromeres.

Researchers hadn’t previously understood what CENP-B is doing at the centromere. This study provides an intriguing theory, that maybe the protein is bending the DNA into a new shape.

This was “a totally different way of looking at the problem,” Henikoff said.

Why the Y is different

Researchers had previously noted that the human Y chromosome didn’t have DNA sequences where CENP-B is known to bind, unlike the rest of our chromosomes, but they didn’t have a good explanation for that, Kasinathan said. Their study provides a possible rationale: Maybe the Y chromosome doesn’t need CENP-B.

The Y chromosome’s weirdness is not limited to its centromere. It’s also much smaller than the rest of our chromosomes, including the X, our other sex-defining chromosome. It’s got far fewer genes — only about 50, as compared to the X chromosome’s 1,600. It’s even slowly shrinking.

But even if the similarities between the male-defining Y chromosome and monkey DNA might make for a fun cocktail party conversation, this computational prediction actually makes sense when viewed through the lens of chromosome evolution, said Dr. Ben Black, a biochemist at the University of Pennsylvania who studies centromeres.

“It’s been framed that the Y lost the CENP-B protein and that makes it weaker,” said Black, who was not involved in the Fred Hutch study. “This proposal would say the Y is a little stronger than we thought before, because it’s compensated by getting more monkey-like.”

Possible gene therapy advances — but first more tests

If their theory holds up, it could lead to improvements in making human artificial chromosomes, laboratory-made chromosomes that could be used in gene therapy. Scientists have succeeded at making artificial chromosomes from simpler species such as bacteria and yeast. Mammalian versions have proven a tougher nut to crack, and that’s mainly due to the size and complexity of our centromeres, Kasinathan said.

A more streamlined centromere could lead to better, more efficient human artificial chromosomes, although Kasinathan and Henikoff pointed out that more basic experiments need to be conducted first.

So far, much of their theory of centromere identity is based on computational predictions of how the DNA is likely to bend. But a few recent studies from other groups lend credence to their theory that the DNA is oddly shaped at centromeres.

The studies used a laboratory technique to identify and quantify all the DNA in mouse and human cells not twisted into a double helix. Those datasets backed up the Hutch researchers’ theory, Henikoff said.

“It turned out when Siva looked, half of their signal in humans — half of it! — was from centromeres,” he said.

Those studies don’t prove that the centromeres are marked by little X-shaped DNA. But they strongly suggest that at least for mice and humans, DNA bends into unusual forms at these regions. Henikoff is hoping other centromere scientists will be inspired to start testing the model he and his colleagues have introduced.

Black agrees that the study offers an appealing theory — but more experiments need to be done to shore it up.

“It’s definitely a provocative proposal,” he said. “It opens up the idea for myriad molecular tests that will support or deny the model. It does what a lot of great science does and opens up the door for that.”

The study was funded by the ARCS Foundation and the Howard Hughes Medical Institute.

Rachel Tompa is a former staff writer at Fred Hutchinson Cancer Center. She has a Ph.D. in molecular biology from the University of California, San Francisco and a certificate in science writing from the University of California, Santa Cruz. Follow her on Twitter @Rachel_Tompa.

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