Researchers assemble the first complete sequence of a human Y chromosome

In a groundbreaking study, Arizona State University’s Biodesign Institute joins an international research team led by the Telomere-to-Telomere (T2T) Consortium, a group of researchers funded by the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health. The result is the first truly complete sequence of a human Y chromosome. The study provides fresh insights into the genetic factors underlying health and fertility.

Using advanced, long-read sequencing and assembly methods, the researchers generated a high-quality sequence spanning all 62.5 million DNA bases on chromosome Y. This completed assembly, named T2T-Y, adds over 30 million bases that were previously gaps in the reference genome.

The Y chromosome is the final human chromosome to be fully sequenced. The new sequence, which fills in gaps across more than 50% of the Y chromosome’s length, uncovers important genetic features with implications for fertility, such as factors in sperm production, according to the new study, which appeared today in the journal Nature.

The X and Y chromosomes are often discussed in the context of determining sex, and although they do play a central role, the factors involved in human sexual development are complex and spread across all chromosomes. Further, the X and Y chromosomes contain genes that are critical for many other biological processes, as recent work demonstrating how genes on the Y chromosome contribute to cancer risk and severity has shown.

“Y chromosomes have been ignored or dismissed for years,” says geneticist Melissa Wilson, a researcher in the Biodesign Center for Mechanisms of Evolution and associate professor with ASU’s School of Life Sciences and Center for Evolution and Medicine. “And despite playing critical roles in testis development, there is a whole other world we have to explore concerning the role of the Y chromosome in human health.”

Wilson is the ASU principal investigator for the new study and led the analysis of so-called pseudoautosomal regions of the Y chromosome. These are specific portions of the sex chromosomes (X and Y in mammals) that are homologous, meaning they share sequence similarity and can undergo pairing and DNA swapping, just like autosomal chromosomes.

Although the X and Y chromosomes are mostly distinct and carry different sets of genes, the pseudoautosomal regions allow the X and Y chromosomes to pair and recombine during the stage of cell division known as meiosis.  

Filling the gaps

When researchers completed the first human genome sequence 20 years ago, gaps were left in the sequences of every chromosome, and in the race to sequence the human genome, the Y chromosome got left in the dust. 

Of the 24 human chromosomes, the Y chromosome is unusually repetitive, making it particularly difficult to sequence. Unlike the small gaps sprinkled across the rest of the genome sequence — gaps that the T2T Consortium filled in last year — over half of the Y chromosome’s sequence remained a mystery.

Previously, the T2T Consortium finished the first gapless genome sequence of the first 23 human chromosomes, with only the enigmatic Y chromosome remaining to be sequenced, according to Adam M. Phillippy, a senior investigator at NHGRI and corresponding author of the new study.

The how and the Y

To tackle these most repetitive pieces of the genome, the T2T Consortium applied new DNA sequencing technologies and sequence assembly methods, as well as knowledge gained from generating the first gapless human genome sequence.

To the researchers’ surprise, the repeating sequences filling the previously missing sections were highly organized, rather than chaotic, as might have been expected. Approximately half of the chromosome is represented by alternating blocks of specific repeating sequences, known as satellite DNAs. Two different satellite DNA sequences alternate for millions and millions of letters in a very tidy pattern.

By filling in the large sequencing gaps, the researchers have begun to explore new protein-coding genes, characterize complex gene families, and reveal the underlying satellite repeat structure of the Y chromosome for the first time.

The study has already unveiled 42 additional protein-coding genes, mostly extra copies of the TSPY gene family, which are critical for sperm production. While TSPY was known to exist as many repeating copies, the number of copies and their organization was previously unknown. As the researchers analyzed this region in the complete Y chromosome sequence, they found that different individuals contained between 10 and 40 copies of TSPY.

One section of the Y chromosome, known as the azoospermia factor region, is a stretch of DNA containing several genes known to be involved in sperm production, embedded within a series of palindromic sequences. One of these gene families, known as DAZ, is vital for germ cell development and spermatogenesis. It is believed to play a role in maintaining the stem cell population of germ cells, which are precursor cells that give rise to sperm.

Charting fertility

Deletions of the DAZ genes are a common genetic cause of spermatogenic failure. Such deletions can lead to conditions like azoospermia (complete lack of sperm in ejaculate) or severe oligospermia (very low sperm count).

With a complete Y chromosome sequence, researchers can now more precisely analyze these deletions and their effects on sperm production.

“One of the most exciting aspects of this work,” says Wilson, “ is how it now makes it possible to comprehensively incorporate the Y chromosome into our studies of human health.”

The new gapless Y chromosome sequence complements the gapless human genome sequence released by the T2T Consortium in 2022, as well as the “pangenome” released in May of this year by the NHGRI-funded Human Pangenome Reference Consortium. Through these achievements, scientists have access to an abundance of new genomics resources to unravel human biology and pave the way for the future of genomic medicine.

This comprehensive human reference genome will allow more accurate interpretation of genetic factors underlying reproductive health, infertility and heritable diseases. It may also help better characterize cancer risk and advance the understanding of human origins and diversity.