The four-dimensional Cellome (4D Cellome) will be a new approach to elucidate the mechanism of how cellular functions are generated and regulated by the dynamic change of structure of intracellular functional elements such as organelles and supramolecular complexes. In addition to the comprehensive understanding of biochemical reaction paths and factors in cells (static information) obtained by molecular biology approach, 4D Cellome will require the measurement and the analysis as follows;

• - comprehensive acquisition of spatiotemporal information of biomolecules such as nucleic acids and proteins;
• - integration of the acquired information with structure (three-dimensional) and its dynamics (four-dimensional) of intracellular functional elements, whose level is between biomolecules and cells;

However, 4D Cellome is challenging to realize due to lack of comprehensiveness and quantitativity on the conventional measurement and analysis techniques. As a basis of 4D Cellome, innovative technology that enables comprehensive and quantitative acquisition and analysis of spatiotemporal information in single cell should be developed. Such Japanese-originated technology to be developed could become must-to-use technology in worldwide as a door opener to a new phase of life science research.

Molecular biology has been focusing on interactions and biochemical reactions of biomolecules. One-to-one correlation and causality of intracellular factors used to be the main scope of molecular biology in its early days. However, as systems biology approach being common, cell is regarded as the system where numerous intracellular factors interact in a complex manner. In structural biology field, development of the measurement techniques such as cryo-electron microscopy, X-ray crystallography and super-resolution microscopy enabled us to observe the native structure of intracellular functional elements under the actual intracellular environment. However, systems biology and structural biology to date don't consider the dynamics of structure and location of intracellular functional elements which could influence cellular function by localizing intracellular factors and regulating biochemical reactions. Therefore, the mechanism of neurodegenerative disease development, which is thought to be closely related to the structural transition of intracellular molecules and intracellular functional elements, and mechanism of the phenomena such as transition to cancer cells and aging of cells associated with degeneration of nuclei and mitochondria, are not thoroughly uncovered, and thus it is still challenging to develop an effective intervention for such disorders.

Although life is an open dynamic system where the multiple levels with different scales overlap, life science researchers have ought to focus on interactions between components at a single level. Thanks to advancing of the various techniques, a global major trend in life science field is being shifted to bridging of the different spatiotemporal levels to decipher the universal mechanism of biological system.

Brain Initiative (2013-) and Human Cell Atlas (HCA, 2017-), the world-leading big projects of basic research, are the examples of top-down approach to describe relationship between the levels of cell-tissue-organ from the upper level. Bottom-up approach from the lower level with smaller scale is also taken based on synthetic biology, which started from the fundamental question: what would differentiate between biomolecules as non-living material and cells as living organism? Sc2.0(Synthetic Yeast 2.0, 2012-) and GP-write (Genome Project Write, 2014-) are the examples of the ongoing projects. Their aim is to establish the technology for artificial genome design and synthesis. As the level of intracellular functional elements is between those the top-down and the bottom-up approach are focusing, dynamic structure and function of intracellular functional elements are consequently out of scope in both the approaches.

The factors bridging the multiple levels of organism are the interactions (chemical reactions) between various molecules such as proteins, nucleic acids, lipids, sugars, and the other small organic molecules. What is the latest state of cellular molecular biology focusing on those factors? From the basic intracellular system such as transcription, translation, folding, and transport, to the regulatory function by switching and feedback such as DNA repair, epigenome, ncRNA (non-coding RNA) / miRNA (micro-RNA), endoplasmic reticulum stress, degradation, most of the factors related to the important intracellular phenomena have been already identified. On the other hand, we don't still have thorough understanding of micro-environment on intracellular functional elements where intracellular interactions occur due to lack of comprehensiveness and quantitativity on the conventional measurement and analysis techniques. Moreover, recent discovery of the new intracellular phenomena such as ncRNA, intrinsically disordered proteins / region, membrane contact site between organelles, droplet formation by liquid-liquid phase separation (LLPS) etc. gives us a different view of intracellular function elements. Comprehensive and quantitative acquisition of location and dynamics(time) in single cell is essential to uncover the functionality of intracellular function elements.

Advancing of single cell transcriptome (RNA-seq) has brought the redefinition of life and disease: Cells in single tissue and single diseased part are not uniform but quite varied than thought. Therefore, information of quantity, location, dynamics in single cell is required to investigate cell as an independent system instead of the averaged picture of multiple cells.

Computational / digital methodology is more and more commonly applied to life science research at all the levels from molecule, cell to whole body, as throughput of data acquisition is getting higher. On the other hand, further advancing of measurement technology and mathematical modelling that enable to describe the complex micro-environment on intracellular functional elements are needed in prior to applying computational methodology to 4D Cellome. It is becoming more difficult to achieve a new discovery or to elucidate a new mechanism only by the conventional biochemistry and molecular biology approach, instead necessary to tackle under collaboration with mathematics, informatics, physics and chemistry. Therefore, it is desirable that the Society of Biophysics, the Society of Protein Science, the Society of Chemical Biology, the Society of Cell Biology, the Society of Systems Biology and others work together across disciplines.

The expected direct outcome from our proposal would be the newly developed techniques of real-time micro-visualization and manipulation to reveal the full picture of structure and dynamics of intracellular function elements. Even the direct quantitative counting of proteins and nucleic acids in single live cell could be realized.

From scientific aspect, comprehensive acquisition of spatiotemporal behavior of intracellular function elements would lead to deciphering the universal mechanism of how intracellular functions are generated at the level of intracellular function elements (non-living material) between molecules and cells (organism). This would deepen our insight of how the multiple levels in organism up to cell population, tissue, organ and whole body are connected / integrated.

From application aspect, the mechanism to cause neurodegeneration and aging of cell would be elucidated. Although they are the disorder and the phenomenon observed at the larger scale than cell, it is suggested that they would be triggered by the phenomena at the level of intracellular function elements such as mitochondrial dysfunction, autophagy dysfunction, protein aggregation. Thorough treatment for these disorders hasn't been established yet, but the uncovered mechanism by the innovative technology to be developed would guide us to an effective medicine of the new modality to regulate a phenomena at the level of intracellular function elements.