CATEGORY

news

  • 2024年5月9日
  • 2024年5月9日

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

Read more
  • 2023年11月29日
  • 2023年12月22日

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 […]

Read more
  • 2023年9月20日
  • 2023年9月20日

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. […]

Read more
  • 2023年6月2日
  • 2023年6月2日

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.

Read more
  • 2022年12月21日
  • 2024年3月28日

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.

Read more
  • 2022年12月11日

Review article was published in Gene and Genome Editing

Ochiai’s review article titled “Facilitating genome function understanding using genome editing dependent bioimaging techniques” was published in Gene and Genome Editing. https://www.sciencedirect.com/science/article/pii/S2666388022000120?via%3Dihub

Read more