Science & Technology

Geneticists Searched the Dark Centers of Human Chromosomes and Found Neanderthal DNA

Often, artifacts thought lost to time are found in the hardest places to search, whether that's an ancient shipwreck or grandma's attic. When it comes to the human genome, geneticists have their own dark corners where no one has dared to venture. A research team from the University of California finally tried, and what they found was certainly historic: previously undiscovered Neanderthal DNA lurking in the chromosomes of modern humans.

X Marks the Split

To understand this discovery, you first have to understand chromosomes. Chromosomes are structures that exist in the nucleus of every cell in your body, which you've probably seen as X-shaped things in textbook diagrams and science articles. While that's not wrong, it's a little bit misleading; most of the time, chromosomes just hang out in the nucleus as a tangled mess of DNA. It's only when the cell is ready to divide that chromosomes shape up to look the way you've seen them in a textbook.

When a cell is ready to divide, those long strands of DNA coil into 46 separate chromosomes. These still aren't X shapes; they're more like I shapes. Those 46 chromosomes are technically 23 pairs of chromosomes since you've got one corresponding version from each of your parents, but these pairs aren't attached to each other.

Cell division spurs each of your 46 chromosomes to make a copy of itself, known as a chromatid, which it holds onto for safekeeping by attaching at a central region known as the centromere. That's where the X shape forms, with the centromere sitting at the intersection of that X. At this point, little fibers called microtubules stretch out from special organelles at each end of the nucleus and attach to the centromere of each X-shaped double chromosome. Finally, the microtubules pull the chromatids apart to either end of the nucleus as it divides. Those two chromatids then go their separate ways to each be a chromosome in a brand-new daughter cell.

That cell-division process is called mitosis. But for the body to produce egg cells or sperm cells, the process, known as meiosis, is a little different. In this case, each X-shaped double-chromosome lines up with its corresponding partner from the other parent. The chromatids from each X tangle up together and end up trading sections of DNA in a crossover process — like, I'll take your section for eye color and give you mine, you take my section for height and I'll take yours. From these four mixed-up chromatids form four egg or sperm cells. It's that mixing that allows for that genetic roll of the dice that gives offspring a particular blend of traits that differ from child to child.

Almost every gene you've ever heard about was found in the outer portion of the chromosome — the arms of the X, as it were. In this new study published in eLife, geneticists examined the centromere, or the intersection of the X. The DNA in that region is full of repeating sequences that make it really hard to properly map. "It's the heart of darkness of the genome, we warn students not to go there," said senior author Charles Langley in a press release.

Venturing into the Heart of Darkness

Identifying genes in the centromere is a big deal since the centromere doesn't participate in crossover during meiosis. That means that it could contain genes that have existed undisturbed for hundreds of thousands of years. The researchers figured that this would mean that there might be large groups of genes that have been inherited from generation to generation, called haplotypes, that extend over this region. To find them, the team looked for single gene mutations around the centromere that might let them identify common haplotypes. Sure enough, this led them to find centromeric haplotypes, both in fruit fly and in human DNA.

So what exactly did they find? In one chromosome, they found haplotypes that had been around for 500,000 years, just after humans left Africa. In another, they found Neanderthal DNA that had been around for 700,000 years, right around the time our human ancestors split from the ancestors of Neanderthals. (Those genes in particular are mostly associated with our sense of smell.) In yet another chromosome, they found an even older haplotype from a relative they can't identify.

This is just the beginning of the search for ancient DNA in this dark center of our chromosomes, but there's also a more modern application. If scientists can tell the difference between chromosomes based on their centromeres, they can figure out whether which centromere haplotype a person inherits from an egg or sperm cell makes a difference. It's possible that some haplotypes are inherited more readily or are more prone to errors than others. This is the first step in finding out.

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Intrigued by genetic inheritance? Get the whole story in the book named 2018's science book of the year by the Guardian, "She Has Her Mother's Laugh: The Powers, Perversions, and Potential of Heredity" by Carl Zimmer. The audiobook is free with an Audible trial. We handpick reading recommendations we think you may like. If you choose to make a purchase, Curiosity will get a share of the sale.

Written by Ashley Hamer July 12, 2019

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