Category: Publications

Paper Published

New paper by Dr Soya Shinkai has been published.

Understanding how chromosomes move inside living cells requires quantitative models linking genome structure to chromatin dynamics. Here, using genome-wide live-cell imaging together with our PHi-C technology, a Hi-C data-constrained polymer modeling approach, we built an integrative, physics-based “digital twin” of the fission yeast genome that reproduces its spatiotemporal chromatin dynamics. The model captures known architectural features, reveals characteristic chromatin relaxation times, and shows that low-frequency forces generated outside the nucleus propagate through the spindle pole body and centromeres to drive genome-wide chromatin displacement. This work provides a physical framework for understanding how nuclear mechanics shapes genome dynamics and function.

Reference

S. Shinkai, T. Namba, T. Sugawara, S. Hagiwara, S. Onami, T. Haraguchi, Y. Hiraoka, A. Awazu, M. Ueno, & S. Tate, Integrative modeling of the genome structure and dynamics in fission yeast, Proc. Natl. Acad. Sci. U.S.A. 123 (37) e2612002123, (2026). doi: 10.1073/pnas.2612002123

236 GFP-tagged C. elegans strains from the Onami Lab released in WormTagDB

We have released information for 236 endogenously GFP-tagged Caenorhabditis elegans strains in WormTagDB, a community resource for endogenously tagged worm strains. With this contribution, our laboratory is now the second-largest contributor of tagged alleles in the database. Notably, approximately 150 of the genes in our collection had not previously been tagged, making this a substantial contribution toward expanding proteome-wide fluorescent tagging resources in C. elegans.


The strains were generated as part of our efforts to systematically visualize protein expression and localization during embryonic development. We plan to continue expanding the collection and developing associated imaging resources.


WormTagDB: https://wormtagdb.rc.duke.edu

SSBD:BFF Explorer Released

A new feature, SSBD:BFF Explorer, has been implemented in the SSBD database to facilitate the discovery, organization, filtering, and visualization of bioimaging datasets through metadata. The tool enables efficient exploration of large-scale bioimaging datasets in OME-Zarr format directly in a web browser and also supports links to datasets managed in OMERO, thereby promoting the reuse and accessibility of bioimaging data.

Read more: https://biosciencedbc.jp/news/20260622-01.html (In Japanese Only)

Reference

  • Meharry, S.L., Borensztejn, A., Gaudreault, N. et al. Search, organize, aggregate and share image data with BioFile Finder (BFF). Nat Methods (2026). doi: 10.1038/s41592-026-03130-w

[Press Release]Discovery of a new mechanism by which changes in the distance between genes regulate their expression

Drs Hiroaki Oishi, Hiroshi Ochiai, (Kyushu University, respectively) and Soya Shinkai et al. found a novel mechanism of gene expression regulation involving changes in the spatial distance between genes. Understanding the mechanisms of gene expression regulation is crucial not only for molecular biology but also for medical research, as it directly links to identifying disease causes and therapeutic targets.

Learn more about the study on Press Release by Kyushu University, RIKEN and JST. (In Japanese only)

Reference

Ohishi, H., Shinkai, S., Owada, H., Fujii, T., Hosoda, K., Onami, S., Yamamoto, T., Ohkawa, Y., Ochiai, H. (2024). Transcription-coupled changes in genomic region proximities during transcriptional bursting. Sci. Adv. 10, eadn0020. DOI:10.1126/sciadv.adn0020

[Press Release] Development of life sciences by sharing image data

Drs Koji Kyoda, Hitoya Itoga, Yuki Yamagata (RIKEN R-IH), et al. developed and published a public repository and high-value database that facilitates the sharing and re-using of image data in the life sciences. In this paper, we describe the international positioning and functions of the SSBD.

The SSBD is positioned as one of the core ecosystems of the international consortium ‘foundingGIDE’, which aims to promote the standardisation and sharing of FAIR image data, and is expected to enhance the transparency and reliability of science and contribute to the development of science throughout society through the advancement of open science. The project is expected to contribute to the development of science in society as a whole through the advancement of open science.

Learn more about the study on Press Release by RIKEN. (In Japanese only)

Reference

Kyoda, K., Itoga, H., Yamagata, Y., Fujisawa, E., Wang, F., Miranda-Miranda, M., Yamamoto, H., Nakano, Y., Tohsato, Y., Onami, S.(2024) SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data. Nucleic Acids Res. gkae860. https://doi.org/10.1093/nar/gkae860

Behind the Paper “Prototyping an Ontological Framework for Cellular Senescence Mechanisms: A Homeostasis Imbalance Perspective”

Dr. Yuki Yamagata (R-IH Life Science Data Sharing Unit) et al. published a paper in BMC Medical Informatics and Decision Making on the development of an otology related to COVID-19 infectious processes. We published a video to introduce our study on YouTube.

We developed the HoIP ontology to organize cellular senescence knowledge from a homeostasis disturbance perspective. HoIP was assessed, and relationships between cellular senescence, COVID-19, and diabetes were inferred. This framework elucidates mechanisms linking cellular and organismal aging. Lean more about the study at https://go.nature.com/3yLP0QO.

Reference

Yamagata, Y., Fukuyama, T., Onami, S. et al. Prototyping an Ontological Framework for Cellular Senescence Mechanisms: A Homeostasis Imbalance Perspective. Sci Data 11, 485 (2024). https://doi.org/10.1038/s41597-024-03331-y

[Press Release] Development and publication of the zebrafish brain gene expression database

Dr Towako Hiraki-Kajiyama(Assistant professor at Graduate School of Life Science, Tohoku University, former researcher at RIKEN CBS) and Yoshihiro Yoshihara (TL at Riken CBS) et al. with Drs Hiroya Itoga and Shuichi Onami established the database for scanned data of brain sections of zebrafish.

The database uses SSBD (https://ssbd.riken.jp/) and OMERO (https://openmicroscopy.org) as infrastructures.The database and anatomical findings will contribute to future neuroscience research using zebrafish.

Learn more about the study on Press Release from RIKEN. (In Japanese only)

Reference

Hiraki-Kajiyama, T., Miyasaka, N., Ando, R., Wakisaka, N., Itoga, H., Onami, H. I. S., & Yoshihara, Y. (2024). An atlas and database of neuropeptide gene expression in the adult zebrafish forebrain. Journal of Comparative Neurology, 532, e25619. https://doi.org/10.1002/cne.25619