Supercomputers are beneficial for the development of modern-day technologies, as they could measure, analyze, and simulate the possibilities of a subject without the need for extensive supporting studies. In new genetic research, a supercomputer-powered model was developed to manipulate a chromosome in mammalian embryos.

The technology was made possible through experimental data and allowed experts to turn off one X chromosome found in a female mammal embryo cell. Through this approach, biology researchers will have more information about the role of RNA, and the inactive X chromosome plays in gene expression. Among the expected contribution of the findings from the chromosome inactivation process are drug solutions and other treatments for gene-based disorders.

Molecular Biology Meets Computational Approach

RNA particles swarm an X chromosome from a mouse in a new visualization of X chromosome inactivation.
(Photo: Los Alamos National Laboratory)

Harvard's Department of Molecular Biology, Los Alamos National Laboratory, and Massachusetts General Hospital expert Anna Lappala said that the novel approach is the first model to sort all of the RNA surrounding a chromosome and inactivate it. The first author of the study noted that a whole chromosome, along with its detail, cannot be observed with a simple 2D and static perspective.

Lappala added that the overall gene expression and regulation were examined thoroughly with the supercomputer modeling simulation. Although the comprehensive modeling is intensive, the information was based on the initial 2D experimental information previously gathered from both Harvard and the Massachusetts General Hospital.

The gene-capture model is a better version of the variant available today. Compared to the 2D modeling, the study was able to manage a 4D imaging technique that is powered by Los Alamos supercomputers. Most of the genome collections in the database of the model were obtained from experimental data gathered through the approach called 4DHiC.

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X Chromosome Shut Down in a Supercomputer Method

According to the study, the visualization showed how the RNA molecules scattered across the X chromosome. The RNA materials had a strand-like structure that tangled the chromosome surface's depths and eventually deactivated it. Harvard Medical School genetics expert and Massachusetts General Hospital molecular biology researcher Jeannie Lee said in a PhysOrg report that the new approach allowed their team to view a clear and interactive illustration of the epigenetic process between the RNA and the X Choromose works. In addition, the model could also be manipulated in an unconstricted way, making it user-friendly even for individuals who are not fond of computational complexities. Lee compared the similarities of using the model to how the Google Earth application works. The interactive feature of the genetic model allows users to see the comprehensive detail in one place, zoom in to a specific chromosome, and observe the surrounding genes.

The Google Earth-like visually dimensional model allows the experts to have a grasp of the genomic data. One of the examinations was an embryo of a female mammalian conceived with two X chromosomes inherited from both parents. The experts believe that shutting down one of the X chromosomes will be a gateway to a funnel of pharmacological solutions that could treat developmental disorders. The study was published in the journal bioRxiv, titled "4D chromosome reconstruction elucidates the spatial reorganization of the mammalian X-chromosome."

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