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Stowers researchers contribute to complete human Y chromosome sequence assembly

Will help better our understanding of chromosome structure, evolution, and disease

23 August 2023

These panels show an image of chromosome Y labeled by fluorescent in situ hybridization (FISH) using fluorescent DNA probes that recognize different sequences in the chromosome (centromere in magenta, Hsat3 in yellow, and Hsat1 in blue).

In 2022, researchers at the Stowers Institute for Medical Research helped fill the gaps in the human genome that remained after the landmark DNA sequencing efforts of the Human Genome Project two decades ago. About 8% of the total sequence needed to be filled to produce the first complete human genome sequence. Even then, however, something was still missing because that genome did not contain a Y chromosome.

Now, new research from the lab of Stowers Investigator Jennifer Gerton, Ph.D., has provided important contributions to a collaborative research effort resulting in the first complete assembly of the human Y chromosome, published online August 23, 2023, in Nature.

“Until now, about half of the Y chromosome sequence has been missing in the human reference genome,” said Gerton. “Overall, having the complete human reference genome is going to help us understand chromosome structure, evolution, and disease.”

Assembling the complete, end-to-end human genome — and now the complete Y chromosome — has been the goal of the international, multi-institutional Telomere-to-Telomere (T2T) consortium, which is co-chaired by Karen Miga, Ph.D., from the University of California, Santa Cruz, and Adam Phillippy, Ph.D., from the National Human Genome Research Institute of the National Institutes of Health. Gerton and Tamara Potapova, Ph.D., Research Specialist II in the Gerton Lab, have been active members of the T2T consortium since it was formed in 2017 and are coauthors of the study.

“Sequencing and assembling the human Y chromosome has been challenging because it contains various sequence repeats that are difficult to put together in the correct order,” said Potapova. “Previous assemblies of the Y chromosome were plagued by large gaps of unknown sequences.”

Y Chromsome animation. Credit: Ernesto del Aguila III, NHGRI.

Drawing upon her expertise in imaging chromosomes under the microscope, Potapova worked with Arang Rhie, Ph.D., from the Philippy Lab to validate the physical placement of the difficult-to-assemble repetitive sequences along the Y chromosome using fluorescent staining techniques.

“Having a complete human genome assembly that now includes the Y chromosome is considerably better for the field of genomics than previous assemblies,” said Potapova. “It will help the scientific community very broadly — any researcher may use this assembly in their studies.”

The assembly has also mapped genome sequence variants relevant to different populations and clinical settings. This work is a significant step towards completing genome assemblies from many individuals, a pangenome effort with contributions from the Gerton Lab.

“The impact on human health may be relatively distant, but the idea is to have enough genomes assembled to improve genomic analysis of populations and potentially provide help for medical conditions by enabling genome editing approaches and personalized medicine,” explained Gerton.

Learn more here from the National Human Genome Research Institute.

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