This is the website of the Division of Gene Expression Dynamics, Medical Research Center Initiative for High Depth Omics, Medical Institute of Bioregulation, Kyushu University.

Using mouse embryonic stem (ES) cells as a model, we aim to elucidate the regulatory mechanism of a phenomenon called transcriptional bursting using a novel experimental approach that combines genome editing technology, live imaging, and cell biology. We are also working on elucidating the molecular mechanism of cell-to-cell heterogeneity in gene expression levels in mouse ES cells.

We are currently recruiting undergraduate, graduate students, and postdocs. If you would like to know more about our research and educational policies, please contact Ochiai.


NEWS

  • A joint research paper with Kyushu University’s Institute of Medical Science, Ohkawa Laboratory, on the spatial omics technology “PECAb” has been published in Nature Communications!
    The Ohkawa Laboratory at the Medical Institute of Bioregulation, Kyushu University, has developed PECAbs (Precise Emission Canceling Antibodies) with cleavable fluorescent labels. PECAbs enable high-specificity sequential imaging using hundreds of antibodies, allowing for the reconstruction of spatiotemporal dynamics of signal transduction pathways. Furthermore, by combining this approach with continuous single-molecule RNA-FISH, it is possible to effectively classify cells within human tissues and identify their signal activation states. The PECAb system functions as a comprehensive platform for analyzing complex cellular processes. This content has been published in the journal Nature Communications. Title: Precise immunofluorescence canceling for highly multiplexed imaging to capture specific cell states Authors: Kosuke Tomimatsu, Takeru Fujii, Ryoma Bise, Kazufumi Hosoda, Yosuke Taniguchi, Hiroshi Ochiai, Hiroaki Ohishi, Kanta Ando, Ryoma Minami, Kaori Tanaka, Taro Tachibana, Seiichi Mori, Akihito Harada, Kazumitsu Maehara, Masao Nagasaki, Seiichi Uchida, Hiroshi Kimura, Masashi Narita & Yasuyuki Ohkawa Nature Communications, 15, 3657 (2024) https://www.nature.com/articles/s41467-024-47989-9
  • Our lab has just released a new preprint!
    Our lab has published a new preprint! It has been observed that in the state of transcriptional activation, distinctive higher-order genomic structures and protein aggregates are formed, furthermore, the viscosity around genes increases, and the interaction time between enhancers and promoters is prolonged. This research was conducted in collaboration with Drs. Hiroaki Ohishi (in our lab), Soya Shinkai (RIKEN), Shuichi Onami (RIKEN), Kazufumi Hosoda (Ansanga Labs), and Yasuyuki Ohkawa (MIB, Kyushu U.)! https://www.biorxiv.org/content/10.1101/2023.11.27.568629v1 Recent imaging analyses have revealed that transcription is a dynamic process that switches between an active state, where genes are continuously transcribed by RNA Polymerase II, and an inactive state where transcription does not occur. This is known as transcriptional bursting and is a universal phenomenon observed across many species and cell types. It has been shown that this transition involves the interaction between enhancers and promoters, as well as the assembly of transcriptional regulatory factors. 転写因子は、遺伝子のプロモーター領域や、転写を調節するエンハンサーに結合します。これにより、RNAポリTranscription […]
  • We have been selected for JST CREST (Bio-DX)!
    We have been selected for the JST CREST, “Innovation of Life Science through Digital Transformation Focused on Data-Driven and AI-Driven Technologies” (Bio-DX, Research Director: Professor Yasushi Okada). https://www.jst.go.jp/kisoken/crest/application/2023/230919/230919crest.pdf Research Project Title: Understanding the Mammalian Cell Fate Regulation Framework through Multimodal Spatiotemporal Integrated Omics Analysis. The lead researcher is Ochiai from Kyushu University. Main collaborators include Takuya Funatomi (Nara Institute of Science and Technology), Kazumitsu Maehara (Kyushu University Institute of Biodefense Medicine), and Soya Shinkai (RIKEN Center for Life Science Technologies). Research Overview: The process of mammalian development involves numerous stochastic elements and unknown factors, making a detailed understanding of the cell fate regulation mechanism challenging. In this research, we will target the early developmental stages of mice and organoids to analyze the heterogeneity in gene expression between cells, the epigenomic elements that regulate it, and intercellular interactions in a data-driven, multimodal, and spatiotemporal manner, elucidating the cell fate regulation mechanism. […]
  • A review article was published in CURRENT OPINION IN STRUCTURAL BIOLOGY
    A review article titled “Organization of transcription and 3D genome as revealed by live-cell imaging,” written with Hiroshi Kimura and Yuko Sato of Tokyo Institute of Technology, has been published in CURRENT OPINION IN STRUCTURAL CURRENT OPINION IN STRUCTURAL BIOLOGY.https://doi.org/10.1016/j.sbi.2023.102615It summarizes the relationship between higher-order genomic structure and gene transcription as revealed by live cell imaging.
  • Moved to the High Depth Omics Center, MIB, Kyushu Univ.
    Our laboratory moved from Hiroshima University to the Division of Gene Expression Dynamics, Medical Research Center Initiative for High Depth Omics, Medical Institute of Bioregulation, Kyushu University on March 1, 2023.