New research confirms location of pseudoautosomal region border between two sex chromosomes

In the 1980s, scientists knew little about the X and Y chromosomes. What they did understand was that each cell in the body contains 23 pairs of chromosomes. Each of these pairs is similar, except one. While women typically have two X chromosomes, men have one

At first, the X and Y sex chromosomes seemed like an unlikely pair. But then researchers, including Whitehead Institute fellow David Page, began finding clues suggesting the opposite: identical DNA sequences on the X and Y chromosomes.

Soon it became clear that the ends of the X and Y chromosomes come together in a tight embrace, exchanging their genetic material in the process of producing sperm from immature male germ cells. This limited area of ​​genetic exchange between the two sex chromosomes is called the pseudoautosomal region (PAR).

But science is an iterative process – a continuous cycle of questioning, testing and revising knowledge. Last fall, what had long been considered well-established in genetics was called into question when new research suggested that the PAR limit may be half a million base pairs away from the accepted location. Given that a typical human gene is approximately tens of thousands of base pairs, this length could potentially span multiple genes on the X and Y chromosomes, raising serious concerns about the accuracy and validity decades of scientific literature.

Fortunately, new work by Page, researcher Daniel Winston Bellott and colleagues, published in The American Journal of Human Genetics-provides clarity. In this study, the group reexamines PAR size using sequencing data presented by external researchers in their 2023 work, as well as decades of genomic resources and single-cell sequencing of human sperm. Their results confirm that the location of the PAR boundary, as identified by scientists in 1989, is still valid.

“If we want to understand sex differences in health and disease, the boundary of the pseudoautosomal region is arguably the most fundamental landmark in the genome,” says Page, also a professor of biology at the Massachusetts Institute of Technology and researcher. with the Howard Hughes Medical Institute. “If this boundary had been altered by multiple genes, the field would have been shaken to its foundations.”

Dance of chromosomes

The X and Y chromosomes evolved from an ancestral pair of structurally identical chromosomes. Over time, the Y chromosome degenerated dramatically, losing hundreds of functional genes. Despite their differences, the X and Y chromosomes come together during a special type of cell division called male meiosis, which produces sperm.

This process begins with the ends of the sex chromosomes lining up side by side like two strands of rope. When the X and Y chromosomes kiss, enzymes create breaks in the DNA. These breaks are repaired using the opposite chromosome as a template, connecting the X and Y together. About half the time, an entire segment of DNA, which often contains several genes, passes to the opposite chromosome.

The genetic exchange, called recombination, ends with the X and Y chromosomes separating at opposite ends of the dividing cell, ensuring that each chromosome ends up in a different daughter cell.

“This complex dance of the X and Y chromosomes is essential for a sperm to get either an

This way, when the sperm, bearing either an X or a Y, fuses with the egg, bearing an parents.

But that’s not all. The exchange of DNA during recombination also allows chromosomes to have the same genes but with slight variations. These unique combinations of genetic material on sex chromosomes are essential to genetic diversity within a species, allowing it to survive, adapt and reproduce successfully.

Beyond the recombination region, the Y chromosome contains genes important for sex determination, sperm production, and general cellular function. The main sex-defining gene, SRY, which triggers the development of an embryo into a male, is located just 10,000 bases from the PAR boundary.

Moving forward together

To determine whether the location of this critical boundary on human sex chromosomes—where they stop crossing over during meiosis and become X or Y specific—had been misidentified for more than three decades, the researchers began by comparing publicly available DNA sequences from the X and Y chromosomes of seven primate species: humans, chimpanzees, gorillas, orangutans, siamangs, rhesus macaques and colobus monkeys.

Based on the crossover patterns between the X and Y chromosomes of these species, the researchers constructed an evolutionary tree. By analyzing how DNA sequences near and far from the PAR boundary cluster together across species, researchers discovered a substitution mutation – in which one letter in a long string of letters is replaced by another – in the DNA of human X and Y. chromosomes. This change was also present in the chimpanzee Y chromosome, suggesting that the mutation originally occurred in the last common ancestor of humans and chimpanzees and was later transferred to the human X chromosome.

“These alignments between different primates allowed us to observe where the X and Y chromosomes retained their identity over millions of years and where they diverged,” says Bellott. “This (pseudoautosomal) boundary has remained unchanged for 25 million years.”

Next, the group studied crossover events in living humans using a large single-cell sequencing dataset of sperm samples. They found 795 sperm with a clear exchange of genetic material somewhere between the originally proposed PAR limit and the newly proposed limit for 2023.

Once these analyzes confirmed that the initial location of the PAR boundary remained valid, Page and his team turned their attention to data from the 2023 study that challenged this 1989 conclusion. The researchers focused on 10 male genomes assembled by the outgroup, which contained contiguous PAR sequences.

Since substitutions on the Y chromosome usually occur at a constant rate – but in PAR, changes on the X chromosome can be transferred to the Y chromosome through recombination – the researchers compared the DNA sequences of the ten genomes to determine whether they followed the expected evolution. constant rate of change or whether they varied.

The team found that near the originally proposed PAR boundary, DNA sequences changed at a constant rate. But farther from the boundary, the rate of change varied, suggesting that crossover events likely occurred in this region. Additionally, the group identified several common genetic differences between the X and Y chromosomes of these genomes, demonstrating that recombination occurred even closer to the PAR boundary than scientists had observed in 1989.

“Ironically, instead of contradicting the original boundary, the 2023 work helped us refine the location of the transition to an even narrower area near the boundary,” says Page.

Thanks to the efforts of Page’s group at the Whitehead Institute, our understanding of PAR is clearer than ever and business can continue as usual for researchers studying gender differences in health and disease.