Division of Gene Expression Dynamics,
Medical Institute of Bioregulation,
Kyushu University

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

Our laboratory employs advanced techniques such as live imaging, multimodal spatial omics, genome editing, molecular cell biology, and biophysics using mouse early embryos, adult, and embryonic stem (ES) cells as models to:

NEWS

  • Diagram comparing the classical open-loop view with condensed euchromatin domains separated by cohesin, and local domain mixing after cohesin loss.
    Our collaborative study with the Maeshima lab at the National Institute of Genetics has been published in Nature Genetics!
    Our collaborative study with Professor Kazuhiro Maeshima’s laboratory at the National Institute of Genetics was published in Nature Genetics on September 8, 2026. Using imaging approaches in living human cells, the study revealed that transcriptionally active euchromatin forms condensed domains. It further showed that cohesin constrains chromatin motion within these domains and prevents neighboring domains from mixing. From our laboratory, Assistant Professor Yoshiaki Kobayashi and Professor Hiroshi Ochiai contributed to visualizing nascent RNA and analyzing simultaneous transcription of spatially proximal genes using intron-seqFISH. This analysis showed that cohesin depletion increased the frequency of simultaneous transcription between nearby genes. These findings suggest that the structure and dynamics of chromatin domains help maintain transcriptional independence between genes. Read the paper／Press release from the National Institute of Genetics／Press release from Kyushu University (in Japanese) Image credit: Shiori Iida, Sachiko Tamura, Kazuhiro Maeshima, National Institute of Genetics, ROIS. Source: EurekAlert!
  • New bioRxiv preprint: Minute-scale coupling of chromatin marks and transcriptional bursts
    We have posted a new preprint on bioRxiv: “Minute-scale coupling of chromatin marks and transcriptional bursts” (https://www.biorxiv.org/cgi/content/short/2026.02.08.704500v1). In this study, we combine single-gene live-cell imaging at endogenous loci with fluorescent probes for histone modifications (mintbody/ChromID) to capture transcriptional bursting together with locus-centered chromatin-mark dynamics in mouse embryonic stem cells. We find that activating chromatin marks (H3K27ac/H3K4me3) increase during transcriptionally Active episodes and decrease during Inactive episodes, whereas a Polycomb-associated repressive mark (H3K27me3) shows the opposite tendency. We further show that acetylation-related regulators, including selected deacetylase modules, co-accumulate at Active loci, and that HDAC inhibition reshapes Active/Inactive dwell times, supporting a model in which opposing enzymatic activities tune state transitions on minute timescales. This work was led by graduate students Xiohui Gao and Chaebeen Ko, and was conducted in collaboration with Prof. Yasuyuki Ohkawa lab and Prof. Akihito Harada lab (Kyushu University), and Prof. Hiroshi Kimura (Tokyo Institute of Science). We […]
  • Our New Paper is Published in Science Advances!
    We are excited to announce that our latest research has been published in Science Advances! This study uncovers a novel mechanism by which changes in genomic proximity regulate gene expression dynamics. By utilizing advanced seq-DNA/RNA/IF-FISH technology and polymer dynamics simulations, we revealed how higher-order genome structures behave during transcriptional activation. These findings offer potential applications in gene therapy and drug discovery. Paper Title:“Transcription-coupled changes in genomic region proximities during transcriptional bursting”Journal: Science AdvancesPublication Date: December 6, 2024 Read more about our research here. Please see the press release here.
  • A protocol for DNA/RNA/IF-seqFISH image analysis has been published in Methods Mol. Biol.!
    The image analysis protocol for DNA/RNA/IF-seqFISH has been published in Methods Mol. Biol. (Computational Methods for 3D Genome Analysis, edited by Ryuichi Nakato)! https://link.springer.com/protocol/10.1007/978-1-0716-4136-1_24#DOI Image Analysis Protocol for DNA/RNA/Immunofluorescence (IF)-seqFISH DataHiroaki Ohishi & Hiroshi Ochiai AbstractImaging-based spatial multi-omics technologies enable the analysis of higher-order genomic structures, gene transcription, and the localization of proteins and posttranslational modifications (PTMs) at the single-allele level. This allows for detailed observation of biological phenomena, including transcription machinery within cells and tissues. This chapter provides an in-depth explanation of the principles behind these technologies, focusing on DNA/RNA/immunofluorescence (IF) sequential fluorescence in situ hybridization (seqFISH). The chapter also offers a comprehensive, step-by-step image analysis protocol, covering aspects such as image preprocessing, spot detection, and data visualization. For practical use, complete Jupyter Notebook codes are available on GitHub (https://github.com/Ochiai-Lab/seqFISH_analysis).
  • A collaborative study with the Mat Francois lab (Centenary Institute, The University of Sydney) has been published on bioRxiv!
    This research focuses on the complex molecular mechanisms required for stem cells to self-renew, shedding light on the dynamics of the SOX2 transcription factor. Using single-molecule tracking technology combined with the STREAMING-tag transcriptional reporter system, we visualized in real-time how SOX2 clusters form at the Nanog gene locus and their relationship to transcription bursts in embryonic stem cells. The study reveals that SOX2 clustering occurs at different timings from transcription bursts, highlighting distinct roles for SOX2 at various stages of the transcription cycle. https://www.biorxiv.org/content/10.1101/2024.09.10.612363v1 Anti-phase clustering of regulatory factors shapes gene bursting Bitong Li, Yew Yan Wong, Neftali Flores-Rodriguez, Tara Davidson, Matthew S Graus, Valeriia Smialkovska, Hiroaki Ohishi, Angelika Feldmann, Hiroshi Ochiai, Mathias Francois AbstractThe ability of stem cells to divide and self-renew depends on a complex choreography of molecular events that maintain the transcriptional oscillation of pluripotency genes. Only a handful of transcription factors (TFs) are necessary to preserve […]