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
- 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.)! 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 factors […] - 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. - Our paper on the “STREAMING-Tag” system for real-time detection of gene activation was published in Nature Communications.
A paper on the “STREAMING-Tag” system, a joint research project led by researcher Ohishi-san and the groups of Prof. Hiroshi Kimura at the Tokyo Institute of Technology and Prof. Yasuyuki Ohkawa at the Medical Institute of Bioregulation, Kyushu University, has been published in Nature Communications.https://www.nature.com/articles/s41467-022-35286-2 In this paper, we established the Spliced TetO REpeAt, MS2 repeat, and INtein sandwiched reporter Gene tag (STREAMING-tag) system that enables highly precise quantification of transcriptional activity and nuclear localization of specific endogenous genes. Using this system and fluorescent protein knock-in to transcription-related factors, we have revealed that specific transcription-related factors form clusters around genes in a transcriptional activity state-dependent manner. This system is expected to contribute to the elucidation of detailed transcriptional regulation mechanisms.
