Norikazu Ichihashi

Development of a self-regenerative artificial genome replication-transcription-translation system

Research Director

Norikazu Ichihashi

Collaborator

Kazuhiro Maeda

Associate Professor Faculty of Computer Science and Systems Engineering Kyushu Institute of Technology

Outline

We develop a self-regenerative artificial DNA genome replication, transcription, and translation system in this project. For this purpose, we have developed a simplified DNA replication system and the evolutionary optimizing method of genome sequence. A self-reproducing artificial cell will be within reach after this project.

Jun Kitano

Genomic basis of speciation

Research Director

Jun Kitano

Collaborator

Satoshi Ansai	Professor Faculty of Environmental, Life, Natural Science and Technology Okayama University
Toshiya Ando	Project-specific Associate Proffessor the Hakubi Center for Advanced Research Kyoto University
Kazunori Yamahira	Professor Tropical Biosphere Research Center University of the Ryukyus

Outline

Speciation is a continuous process by which reproductive isolation is being established. Using natural populations, we investigate whether chromosomal structural changes that reduce recombination rates promote speciation. We also aim at establishing genome-editing tools for manipulating chromosomal structures.

Yasubumi Sakakibara

Genomic-style feature extraction and de novo design and synthesis of DNA sequence using deep learning

Research Director

Yasubumi Sakakibara

Collaborator

Masakazu Kataoka	Associate Professor Graduate School of Science and Technology Shinshu University
Yoshiaki Masaki	Associate Professor School of Life Science and Technology Tokyo Institute of Technology
Kenji Miyamoto	Professor Faculty of Science and Technology Keio University

Outline

We develop a method for designing and generating a primary DNA sequence using deep learning technology, synthesize and transform the DNA into cells, and verify its functional expression. We propose a novel sequence feature, called genomic style, inspired by image classification and develop a method to convert the style of DNA while retaining the genetic information. Next, we establish a DNA synthesis platform using Bacillus subtilis and apply the DNA design and synthesis to functional modifications such as heat resistance and stability, targeting gene clusters of PET degrading enzymes and their metabolic pathways.

Shino Suzuki

Insight into ancient life: Lessons from metabolic and genetic functions in early Earth analgue sites.

Research Director

Shino Suzuki

Collaborator

Yoshihiro Shimizu

Team Leader Center for Biosystems Dynamics Research RIKEN

Outline

What were the features of ancient life? This project aims to illustrate the view of ancient life by synthesizing the energy metabolism and genetic systems that were seen in the microbial life living at the early Earth analog sites. Knowledge gained through the combinational studies of systems biology and synthetic biology should expand our understanding of ancient life and the early evolution, and will further contribute to construing artificial cells in the future.

Ichiro Hiratani

Deciphering the design principles of the genome through the analysis of its potential instability

Research Director

Ichiro Hiratani

Collaborator

Hirohisa Kyogoku	Assistant Professor Graduate School of Agricultural Science Kobe University
Shu Kondo	Assocate Professor Faculty of Advanced Engineering Tokyo University of Science
Atsuko Shirai	Research Scientist Cluster for Pioneering Research RIKEN
Takashi Sumikama	Assistant Professor Nano Life Science Institute Kanazawa University
Shin-ichiro Takebayashi	Professor graduate school of bioresources Mie University

Outline

This study aims to reveal the basis for the dynamic regulation of chromosomes, with a focus on understanding the sources of potential instability of the mammalian chromosomes. We will conduct a comprehensive screening for factors involved in regulating the nuclear compartments, clarify the developmental and cell-cycle dynamics of TADs and nuclear compartments, and attempt to artificially reconstitute nuclear compartments. We will also explore the molecular mechanisms that suppress chromosome aneuploidy, identify difficult-to-replicate genomic regions, and explore their relationship to aneuploidy. In parallel, we aim to improve the resolution of our single-cell genome-wide sequencing technology and pave the way for single-cell multi-omics analysis.

Sachihiro Matsunaga

Innovation of artificial photosynthetic animal cells

Research Director

Sachihiro Matsunaga

Collaborator

Akihisa Osakabe	Project Assistant Professor Graduate School of Science The University of Tokyo
Keishi Osakabe	Professor Graduate School of Technology, Industrial and Social Sciences Tokushima University
Yuuko Satou	Assistant Professor Institute of Innovative Research Tokyo Institute of Technology
Hidenori Nishihara	Associate Professor Faculty of Agriculture Kindai University

Outline

We will establish animal cell lines to stably maintain the plant genome through the genome transfer using cell engineering techniques. We will investigate the dynamics of the transferred genome and try to express the photosynthesis-related genes. Innovating the knock-in technique of long DNA and light-specific gene regulation, we will aim to activate the photosynthesis in animal cells.