Scientists finally uncover complete Y-chromosome sequence

Scientists have cracked the Y chromosome mystery, providing a full genetic map of the male sex chromosome. This breakthrough will help us decode conditions ranging from infertility to cancer.
Rupendra Brahambhatt
digital image of Y chromosome
The mystery of the Y chromosome uncovered


For the last five years, more than a hundred researchers around the globe have been trying to solve a mystery linked to Y, the male sex chromosome that comprises nearly 60 million base pairs (units or building blocks that make up the DNA).

Scientists were already aware of the 30 million base pairs in the Y-chromosome but they were not able to decode the remaining half because of its complex molecular structure. 

However, they have now decoded the entire Y chromosome, and thanks to their hard work and commitment, others will be able to study human diseases, reproduction, evolution, and fertility with more clarity than ever using the newly discovered end-to-end genetic sequence of the Y-chromosome.

“Now that we have this 100% complete sequence of the Y chromosome, we can identify and explore numerous genetic variations that could be impacting human traits and disease in a way that we weren’t able to do before,” said Dylan Taylor, one of the researchers and a geneticist at Johns Hopkins University.

Decoding the Y-chromosome was challenging   

The researchers at the Telomere-to-Telomere (T2T) consortium sequenced the complete X chromosome in 2020. 

However, it took them an additional three years to do the same for the Y chromosome due to its ever-changing nature and repetitive palindromic DNA sequences. The former can be well understood from the fact that among apes and humans, the Y-chromosome is the most frequently changing chromosome. 

For instance, according to the researchers, it is even possible that the Y chromosome in two men can have a different number of copies of the same gene.

Another challenge was the palindromic sequences that may extend up to millions of base pairs and have the same structure when seen from forward and backward directions. Plus, a significant portion of the Y chromosome consists of satellite DNA. 

These are extensive regions of non-coding DNA characterized by high repetition. Within the Y chromosome, two satellites are intricately connected to each other, adding an extra layer of complexity to the sequencing procedure.

The researchers were able to overcome all these complications by employing the most advanced sequencing and computational technologies. They not only found the remaining 30 million base pairs for the Y chromosome reference but also came across 41 new genes.

Why does decoding the entire Y chromosome matter?

Although the Y chromosome is found in human males, it also influences the study of other genders that may have the chromosome, bacteria, and other microorganisms. 

For instance, previously, scientists were not able to clearly examine bacterial DNA because the samples often contained human DNA due to collection from human skin swabs. 

They relied on the human genome reference to distinguish and remove human contamination, which they didn’t have until now. 

Since the Y chromosome reference is now complete, scientists can better study the bacterial genome. During the current study, the researchers also identified 5,000 bacterial genomes that were previously mistaken as parts of the human Y chromosome due to contamination.

However, this is just one of the many benefits of knowing the entire Y chromosome reference. According to the researchers, here is a list of many other revolutionary changes their discovery could bring:

  • The newly established Y chromosome reference offers improved opportunities to study the evolution of sex-chromosome genes in men. This could further help us enhance the in vitro fertilization process and reveal valuable insights into infertility.

  • Generally, scientists analyze an individual's genome by comparing it to a standard reference to identify variations. The complete Y chromosome data will improve our understanding of such variations and related diseases. 

  • Since the Y chromosome passes from one generation to the next, the data from the complete sequence can help scientists study and predict the changes occurring in different sets of human populations over time in a more detailed manner and with greater accuracy.

  • Scientists can better understand the cause of numerous Y-chromosome-linked medical conditions like Swyer syndrome, Jacob’s syndrome, oligozoospermia (low sperm count), etc. This will allow them to come up with effective treatment strategies.

These findings could also shed light on how specific Y-chromosome genes shape male behavior and reproductive health. 

Interestingly, some recent studies link aging-related changes in Y chromosomes with cancer growth. The authors of the current study believe that scientists can now understand such mechanisms in depth using the complete reference sequence.   

More importantly, “We also aim to make these data widely accessible. By creating and sharing these important catalogs of genetic differences on the Y chromosome, we can expand genetic studies of human disease and provide new insights into basic biology,” said Karen Miga, one of the researchers and a professor of molecular biology at the University of California, Santa Cruz.

You can read the research papers here.

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