AGU RESEARCH

Topics that shape the future
- Closer look at research results -

Aoyama Gakuin University faculty members:
He is an uncompromising researcher.
Aiming for a prosperous society,
We are always conducting cutting-edge research.
We will explore the research results of our faculty members who are shaping the future.

  • Faculty of Science and Engineering, Department of Physical Sciences
  • Posted on 2023/06/16
  • Discovering the mathematical formula that describes the movement of chromosomes within cells
    ~Unraveling the mysteries of life from a physical perspective~
  • Professor Takahiro Sakaue
  • Faculty of Science and Engineering, Department of Physical Sciences
  • Posted on 2023/06/16
  • Discovering the mathematical formula that describes the movement of chromosomes within cells
    ~Unraveling the mysteries of life from a physical perspective~
  • Professor Takahiro Sakaue

TOPIC

Collaborative research involving Professor Takahiro Sakaue (Faculty of Science and Engineering) achieves great results

Key points of the research

We discovered that the movement of chromosomes within living cells, where complex conditions are thought to be intertwined, can be expressed by a physically simple mathematical formula based on Brownian motion. The paper was published in "Physical Review Letters," the express edition of "Physical Review," an American scientific journal said to be the most authoritative journal in the field of physics, and has attracted a great deal of attention not only from researchers in the fields of physics but also from researchers in the fields of biology.

イラスト:矢印

Explore the topic with your teacher

Takahiro SakaueProfessor

Faculty of Science and Engineering, Department of Physical Sciences

He graduated from the Department of Basic Sciences, Faculty of Integrated Human Studies, Kyoto University. He completed his doctoral studies at the Department of Physics and Astrophysics, Graduate School of Science, Kyoto University. He holds a PhD in Science from Kyoto University. His fields of expertise are statistical physics and polymer physics. He has long had a strong interest in the world of biophysics, which explores the physical laws inside cells, and responded to a call from his co-researcher, Professor Kimura Akira of the National Institute of Genetics, to participate in the joint research project. He has utilized his expertise to achieve great results together with biology experts.

Within the cell, organelles and proteins are moving vigorously, and chromosomes (chromatin) are also moving.

Based on data obtained by observing the movement of chromosomes, the mathematical formula for the physical laws governing their movement was discovered.

Using the concept of Brownian motion to elucidate intracellular movements, a biological field, from a physics perspective

Could you please tell us how you got involved in this research and what its objectives are?

From 2017 to 2022, a new academic research project called "Chromatin potential as the basis of gene regulation" (*) was carried out. As part of this project, Professor Akira Kimura of the National Institute of Genetics, Information and Systems Research Organization, who studies cell architecture, is conducting research to elucidate the movement of chromatin that decreases during animal embryo development. He asked me to cooperate from the perspective of polymer physics in interpreting the observation results, which prompted me to participate in the joint research project.
Although I originally specialized in theoretical physics, I had always wanted to try researching living organisms, which I have always been interested in. However, I thought that working with living organisms would be difficult, as it is not my specialty, so I feel that this was a very good opportunity, and I hope to continue to conduct collaborative research that transcends fields of expertise.

*A type of Grant-in-Aid for Scientific Research aimed at developing new research areas that will lead to the improvement and strengthening of academic standards in Japan through joint research, training of research personnel, sharing of facilities, etc. The title of this research project is "Understanding chromatin potential through physical measurements and theoretical model construction."

What does the decline in chromatin dynamics during embryonic development mean?

Inside cells, various organelles such as mitochondria and proteins are actively moving. Chromosomes, which carry genetic information, are made up of condensed string-like molecules called chromatin, which is a complex of DNA and proteins, and it has been found that this chromatin also moves in a similar way. Recent research has shown that when looking at cells in the early stages of development, the movement of chromatin also decreases as embryonic cell division progresses from the 2-cell stage to the 4-cell stage to the 8-cell stage.
As the cell divides, the size of the cell nucleus that contains the chromosomes decreases. Therefore, it has been speculated that the movement of the chromosomes becomes slower as they are confined in a small space, like the inside of a crowded train. It is also easy to imagine this if you think of the thickening polysaccharides used in foods, but as the concentration of chromatin, a long, string-like polymer, increases, it becomes more viscous, and the movement becomes slower.
The theme of this research is to elucidate the movement of chromatin within cells and its laws, which have until now only been speculated upon.

Professor Sakagami, please tell us about the physical law you discovered this time.

Professor Kimura's research has demonstrated that chromatin moves (diffuses) within the cell nucleus, and has also been able to quantify and evaluate its motility. The results of this research have taken that result one step further, discovering whether there are universal (qualitative) rules for chromatin motility.
First, I will talk about the quantitative observation of movement. When we looked at the movement observed inside the cell nucleus, it looked like the Brownian motion of particles. Brownian motion is the irregular movement of particles caused by collisions with surrounding molecules that are moving thermally. Although the movement of chromatin looks like Brownian motion, careful analysis of the data also revealed behavior that differs from normal Brownian motion.

Quantifying chromatin movement within cells

How did you derive the rules from that?

The observation of chromatin movement in the cell nucleus that I just mentioned was carried out by fluorescently staining a part of the chromatin, the DNA part (gene locus) that contains genetic information. Therefore, the visualized part looks like a Brownian particle at first glance, but in fact we are only looking at a part of a huge string-like molecule (polymer) called chromatin. Therefore, we thought that the extremely long string-like part might have some effect on the observed gene locus. Going back to the analogy of a crowded train, it is like being influenced by the passengers around you, but not being unable to move, but rather like many passengers are connected to each other by a long string. Even if you can move freely to a certain extent in the nearby parts, if you try to move a long distance, you will have to move with the passengers around you because of the string restraints, in other words, you cannot move as easily as a normal Brownian particle. This is why the movement of chromatin is qualitatively different from normal Brownian motion.

A model showing chromatin as a long, string-like molecule

So why does motility decrease with development? Earlier, we talked about viscosity, and it is true that the viscosity increases inside the cell nucleus, which contains a high concentration of chromatin, a polymer. However, this is a macroscopic (nuclear) issue. Looking at the details, the inside of the cell nucleus is like a mesh made of chromatin, and the inside of this mesh is relatively smooth. Therefore, when considering the movement of chromatin, we need to distinguish between movement on a scale smaller than the mesh that occurs in a short period of time, and movement on a scale larger than the mesh that occurs over a long period of time. The size of the mesh becomes smaller as the size of the cell nucleus decreases with the progression of embryonic development. A decrease in the size of the cell nucleus means an increase in the concentration of chromatin, so taking this into account, it is intuitive to understand why the mesh size becomes smaller.
To summarize the argument, as embryo development progresses, the size of the cell nucleus decreases, and the mesh size that characterizes the spatial structure of chromatin within the cell nucleus also becomes smaller. Furthermore, the chromatin movement properties change qualitatively at the mesh size boundary. At this point, it naturally follows that in order to appropriately compare chromatin movement in cells at different developmental stages, the idea of re-measuring the distance traveled by the movement using the mesh size as a "ruler" is reached.

Could you please tell me about the analysis results?

When the chromatin movement data obtained from nuclei of different sizes was normalized using the mesh size as a "ruler," the data converged beautifully onto a single line.
At first glance, the chromatin movement characteristics appear to differ for each developmental stage, but by observing the phenomenon using the mesh size, a fundamental length scale, as a "ruler," it has become clear that they in fact follow the same laws. The laws revealed experimentally in this way were indeed predicted by polymer physics analysis. We believe that we have been able to elucidate universal aspects hidden in chromatin movement occurring in living cells from the perspective of polymer physics.

Steps leading to formulation of intracellular chromosome movement

Could you please tell me about publishing in “Physical Review Letters”?

Which scientific journal to publish a paper in is one of the points that researchers must consider, but this time I chose "Physical Review Letters" which has a high impact factor because I wanted more scientists, especially biology researchers, to know that we have been able to reduce the movement of chromatin in a complex living organism to such a simplified mathematical formula. I had several exchanges with the reviewers asking "Can it really be explained so simply?" and had them confirm it over and over again. As a result, it was deemed persuasive enough and was published.
Our research team would like to promote this result to as many people as possible, so we continue to introduce it at academic conferences and other occasions when we have the chance, and people have shown a great deal of interest in it.

What are your future goals for this research?

We believe that this research has only shown one possibility. Since the formula was only applied to the early developmental embryo of nematodes, we would like to develop the theory together with the professors who collaborated with us this time, such as what happens in cells that have progressed in differentiation under more complex environments, and further applying it to other developmental stages or cells of complex organisms. Another area of great interest is how the movement of gene loci is related to biological functions, such as the transcriptional activity of genetic information.

What significance has this research had for your career?

Physicists are always trying to find universals in phenomena. It was a truly valuable experience for me to take on the big challenge of finding universality in the extremely complex existence of living organisms. Furthermore, in a broader sense, this research is related to Brownian motion theory, which has always interested me. I would like to continue researching Brownian motion, and also explore the phenomenon of life from the perspective of statistical physics and soft matter physics.

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