Mathematical Model Captures DNA Dynamics In Living Human Cells

Surprisingly, the genome as a whole is actually an active molecule that moves around and changes shape; researchers have now attempted to describe this movement.

AsianScientist (Oct. 31, 2016) – An interdisciplinary research team in Japan has used mathematical analysis to develop a formula that can describe the movement of DNA inside living human cells. Their work was published in PLOS Computational Biology.

DNA is often envisaged as a stable and static code, but the genome as a whole is actually an active molecule that moves around and changes shape. Currently, scientists can sequence the entire basic code of DNA, but knowing the larger-scale 3D architecture of the genome would reveal more information about how cells use the code.

Previous techniques of studying the human genome’s architecture have relied on methods that require killing the cells. The researchers from Hiroshima University, National Institute of Genetics, Keio University, and Sokendai Graduate University for Advanced Studies, employed alternative molecular and cell biology techniques to keep the cells alive and collect data about the natural movement of DNA. Using these calculations, researchers may be able to reveal the 3D architecture of the human genome.

“Our calculations consider the fractal dimensions of the DNA, which shows how densely the DNA is packed inside the cell. The way the DNA is packed may indicate how the cell uses certain genes,” said Dr. Soya Shinkai, assistant professor at Hiroshima University and first author of the research paper.

Before a cell can use a gene, the DNA must be completely unwound. Areas of chromatin containing frequently-used genes are less tightly wrapped than areas of chromatin with infrequently used genes. A model to visualize how chromatin is packed within the cell could allow researchers to understand which genes are accessed most or least often and how the genome is physically organized.

“Our calculations are relevant to local chromatin structures, but this method could also be extended to whole chromosomes,” said Dr. Yuichi Togashi, associate professor at Hiroshima University and last author of the research paper.

The article can be found at: Shinkai et al. (2016) Dynamic Nucleosome Movement Provides Structural Information of Topological Chromatin Domains in Living Human Cells.

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Source: Hiroshima Univesity; Photo: Shutterstock.
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