Yohsuke T. Fukai

Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture Reconstituting 20-kb chromatin shows that tuning acetylation alone reshapes its folding, dynamics, and contact domain formation.

Yohsuke T. Fukai, Kyogo Kawaguchi, et al. reconstituted gene-scale #chromatin arrays with controlled #histone modification patterns in vitro and showed that heterogeneous #acetylation alone can drive pattern-dependent changes in chromatin architecture and dynamics.
doi.org/10.1126/scia...

We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.

It ships many new features, detailed below, but that are articulated around the following:

Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture Reconstituting 20-kb chromatin shows that tuning acetylation alone reshapes its folding, dynamics, and contact domain formation.

To probe gene-scale chromatin physics, we built 96-mer (20 kb) arrays with defined histone marks. Combining single-molecule tracking, AFM imaging, and developing in vitro Hi-C, we saw how specific modifications dictate chromatin structure and dynamics. www.science.org/doi/10.1126/...

遺伝子スケールのクロマチンを設計し再構成する 理研らの共同研究グループは、真核生物の持つゲノム構造「クロマチン」を、設計したヒストン修飾パターンの下、試験管内で再構成する技術を開発し、約2万塩基対のDNAに対応する遺伝子スケール（一遺伝子座スケール）の長さを持つ再構成クロマチンの構造・動態の解析に成功しました。

日本語でプレスリリースも出していただきました！
www.riken.jp/press/2025/2...

Published in Science Advances! Looking forward to discussing the implications of our results and their applications with many researchers.
www.science.org/doi/10.1126/...

Community There are several different ways to be a part of the napari community. From being a code or documentation contributor, to creating educational content or examples, you are welcome to help develop and ...

Community information is here napari.org/stable/commu...

I truly appreciate the organizers, core contributors, and all attendees for this wonderful opportunity! I enjoyed learning and working on napari in a welcoming environment.
Those interested in talking about and contributing to napari, let’s join the regular community meeting together!

napari core team members coding with community members at the GloBIAS 2025 hackathon at RIKEN BDR in Kobe, Japan.

napari core team members and community members in a discussion at the GloBIAS 2025 hackathon at RIKEN BDR in Kobe, Japan.

napari core team members coding with community members at the GloBIAS 2025 hackathon at RIKEN BDR in Kobe, Japan.

napari core team members and community members posing together for a group photo on a staircase at the GloBIAS 2025 hackathon at RIKEN BDR in Kobe, Japan.

Longer wrap-up to come, but in the meantime: we had a fantastic and productive time at the napari hackathon at @globias.bsky.social 2025 conference! Thanks to all the participants and to the GloBIAS team for hosting us!

Last call for Les Houches! Apply now or never! ;) (ok, in 2 years again then) and share with your friends.

FY 2025 Call for RIKEN ECL Team / Unit Leaders

Call for RIKEN ECL Team / Unit Leaders. In my (biased) opinion, this is probably the best option if you are seeking an independent position in Japan. I will be happy to chat/answer questions via email. www.riken.jp/en/careers/p...

Excited to share our preprint on the molecular architecture of heterochromatin in human cells 🧬🔬w/ @jpkreysing.bsky.social, @johannesbetz.bsky.social,
@marinalusic.bsky.social, Turoňová lab, @hummerlab.bsky.social @becklab.bsky.social @mpibp.bsky.social

🔗 Preprint here tinyurl.com/3a74uanv

Integer topological defects offer a methodology to quantify and classify active cell monolayers - Nature Communications The orientation of elongated cells often rotates once around the center in tissue. Such structures are called +1 topological defects and play some roles in biological development. By inducing various ...

Congratulations to Zihui, Sano-san, and the team on this interesting work! They found that +1 topological defects attract neural progenitors—an observation that seems at odds with expectations for an extensile active nematic. www.nature.com/articles/s41...

I feel like this post is becoming even more relevant for our early-career researcher friends in the US—unless it’s already too late. It doesn’t have to be our lab or RIKEN; if you’re interested in coming to Japan, I’m always happy to chat!

Starting in April 2025, our RIKEN Hakubi Lab will transition to a Chief Scientist Lab, and we plan to move to Wako in 2026. My affiliation with the IPI, Department of Physics at The University of Tokyo, will continue as before.

Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture Chromatin organization plays a crucial role in gene regulation [[1][1], [2][2], [3][3]], but disentangling the contributions of various epigenetic components to gene-scale chromatin structure remains ...

In vitro synthesis of up to 96 nucleosomes. Amazing platform to study chromatin folding!!

Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture | BioRxiv

#chromatin #nucleosome #3Dchromatin #preprint

www.biorxiv.org/content/10.1...

GitHub - yfukai/laptrack: Particle tracking by solving linear assignment problem. Particle tracking by solving linear assignment problem. - yfukai/laptrack

Re-posting from my twitter:
LapTrack ( github.com/yfukai/laptr... ) provides you the linear-assignment based robust tracking algorithm, aware of splitting and merging particles, in a simple, Pythonic and flexible API. Installable with “pip install laptrack”.

We’re entering an exciting era of gene-scale chromatin reconstitution with precise modification patterns🚀 We hope this work will stimulate further studies to understand how different histone modifications and solution environment control chromatin architecture and function. 5/5

We developed an in vitro Hi-C method to map nucleosome interactions and found how the acetylation reduces the nucleosome interaction frequency. For the ligated arrays (12-96-mer mixture), we found that the acetylation patterns directly control the long-range contact patterns. 4/5

We observed arrays with different H4 hyperacetylation patterns, and found that higher acetylation density makes the array larger. There's an interesting relationship between the size and fluctuation timescales which agrees with the prediction of a simple polymer model. 3/5

How do histone modifications affect large-scale chromatin structure? We tackled this question in vitro by reconstituting gene-scale chromatin arrays with precise histone modification patterns and analyzing them using single-molecule fluorescence imaging and in vitro Hi-C. 2/5

Thrilled to share our latest preprint on bioRxiv! 🎉 This collaboration with @kyogok.bsky.social and lab members,
Kurumizaka lab(Kujirai-san in particular!) and Umehara lab sheds new light on how histone modification shapes chromatin architecture. 1/5
biorxiv.org/content/10.1...

And our new preprint! "Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture", biorxiv (2024). Led by Yohsuke T Fukai, in collaboration with Kurumizaka lab (U Tokyo) and Umehara lab (RIKEN BDR).

www.biorxiv.org/content/10.1...