Kazunari Kaizu

Whole-cell modeling of a bacterial cell from genomic sequence

Researcher

Kazunari Kaizu

Outline

A whole-cell simulation is one of the essential tools to design genomic DNA from scratch. This project aims to develop a novel platform for automated bottom-up modeling of a bacterial cell, Escherichia coli, to predict phenotypes from its genomic sequence. This approach provides a sustainable way of modeling and quantitative simulation based on huge amounts of knowledge from databases. The simulation results provide “in silico omics” data quantitatively comparable with wet omics experiments such as transcriptome, proteome, and metabolome. The computational evaluation of genomes synthesized in silico will reveal how a genomic sequence is optimized and what principles genomes are designed by.

Andres Canela

Role of DNA topology in genome organization

Researcher

Andres Canela

Outline

In all organisms the genome is folded to fit inside of the cell that is thousands of times smaller. Correct folding of the DNA is essential for gene expression and understanding this process is crucial for optimal synthetic DNA design. In mammalian interphase cells, DNA is folded into loops by a ring-shaped complex cohesin that entraps DNA. I found that Topoisomerase (TOP2), that releases torsions in the DNA, acts at cohesin sites. However, the source of the torsional stress and role of TOP2 are unknown. I aim to elucidate how topoisomerase 2 regulates loop formation to better understand how the genome is spatially organized.

Tsuyoshi Terakawa

DNA curtain assay of epigenome inheritance at single molecule level

Researcher

Tsuyoshi Terakawa

Outline

To design a genomic sequence based on the principle of genome function and to create an artificial cell, we need to understand the regulation of gene expression by acquired chemical modification to biomolecules (epigenetic modifications). Considering that the artificial cells multiply by cell division, it is crucial to understand the mechanism of the inheritance of the epigenetic modifications. In this study, I will reveal the molecular mechanism of epigenetic inheritance using a DNA curtain assay, one of the single-molecule fluorescent microscopic techniques.

Tomoko Nishiyama

Hub structure connecting higher-order chromatin architecture and genome function

Researcher

Tomoko Nishiyama

Outline

Numerous recent genome-wide sequencing studies are revealing higher order chromatin architecture in the nucleus, which includes chromatin domains, topologically associated domains, compartments, and so on. These chromatin architectures are thought to be tightly related to genomic functions such as transcription, replication and formation of chromosomal territories. However, the molecular mechanisms of how these architectures are constructed and fine-tuned to regulate genomic functions are still unclear. This study aims to uncover the molecular mechanisms organizing higher-order chromatin architecture, especially in single molecule resolution, and to reconstitute the architecture for regulating genomic machinery in vitro.

Shingo Nozaki

Generation of synthetic bacteria by ship in a bottle method

Researcher

Shingo Nozaki

Outline

In this research, I aim to generate synthetic bacteria by introducing fragmented artificial genomes into bacterial cells and assembling them into complete large genomes inside the cells, like a ship in a bottle, which is produced by building a model ship inside an empty bottle. The technology to create synthetic bacteria with flexibly designed artificial genomes is useful not only for production of materials but also for determining the essential factors of life, and is expected to greatly approach the answer to the question of what life is.

Gosuke Hayashi

in vitro reconstitution of epigenetically modified nucleosomes powered by organic chemistry

Researcher

Gosuke Hayashi

Outline

In this project, I develop a technology for reconstitution of epigenetically modified nucleosomes and their arrays on naturally-occurring DNA sequences by utilizing precise molecular manipulation techniques of organic chemistry. In particular, I prepare DNA and nuclear proteins such as histone proteins with site-specific modifications by total chemical synthesis, and create real nucleosomes that reflect intranuclear environment in terms of epigenetic modifications and DNA sequences. This technology will contribute not only to chromatin molecular biology but also to chromatin synthetic biology, which is aimed at this PRESTO and CREST research group.

Akihito Harada

Development of reconstruction technology for tissue-specific genomic structures

Researcher

Akihito Harada

Outline

The formation of an adult somatic cell from genomic DNA requires a tissue-specific genomic structure which selects a set of relevant genes for expression. In this project, I propose to identify tissue-specific transcription factors and higher-order genomic structures necessary for functional expression, and finally reconstruct such structures. For this purpose, I will advance the development of a novel regulatory technology which simultaneously allows the elucidation and reconstruction of the tissue-specific genomic organization.

Masatoshi Maeki

Development of transfection method for long-chain DNA using artificial exosomes

Researcher

Masatoshi Maeki

Outline

Lipid nanoparticles and exosomes have demonstrated excellent performance targeting organs, and high transfection efficiency. However, the transfection ability of exosomes is not understood in detail. It is expected that the unique characteristics of exosomes can be applied to develop an efficient transfection method. The aim of this project is to elucidate important factors regarding exosomes for transfection and develop a transfection method for long-chain DNA using artificial exosomes.

Yoshiaki Masaki

Long DNA synthesis using chemically stable nucleotide analogues

Researcher

Yoshiaki Masaki

Outline

It is known that various kinds of side-products form during the chemical synthesis of DNA. These side products are known to significantly influence the accuracy of synthesized genes and genomes. This project aims to develop a new technology to surpass the current technological limit of genome synthesis through the development of chemically stable nucleotide analogues and renovate phosphoramidite chemistry to specialize in genome synthesis.

Ryo Mizuuchi

Development of a genome expansion technology inspired by the early evolution of life

Researcher

Ryo Mizuuchi

Outline

Using knowledge of the early evolution of life, I will develop an artificial cell-based technology of evolutionary engineering to spontaneously integrate gene fragments into a long genome that efficiently replicates and functions. This technology allows us to construct a genome encoding arbitrary genes and evolve them by means of artificial cell systems.

Yasuto Murayama

Controlling DNA entanglements to ensure efficient DNA replication and recombination

Researcher

Yasuto Murayama

Outline

As genomic DNA is much longer than the cells in which it is stored, its replication is often associated with “DNA entanglements”, higher-order DNA structures that arise during DNA metabolism. This research aims to elucidate the mechanism whereby these higher-order DNA structures are resolved, with a particular focus on the role of SMC (Structural Maintenance of Chromosomes) proteins. By isolating and reconstituting this resolving activity, I aim to develop an in vitro system that enables chromosomal duplication in a test tube using purified eukaryotic proteins.