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...

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.

doi.org

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:

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/...

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.

science.org

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/...

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.

science.org

Yohsuke T. Fukai@fukaity.bsky.social · 2y ago

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...

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!

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 ...

napari.org

napari@napari.org · 9mo ago

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!

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.

Ulrike Endesfelder@uendesfelder.bsky.social · 11mo ago

Please share: The application for Les Houches is open (until Oct 31) fluorescenceleshouches.wordpress.com *This is for you, if you ever wanted to learn all about fluorescence markers & how to apply them for your biological research!* PS: no fees this year, you just need to get there, that's all!

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...

FY 2025 Call for RIKEN ECL Team / Unit Leaders

riken.jp

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

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...

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 ...

nature.com

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!

Kyogo Kawaguchi@kyogok.bsky.social · 2y ago

We can host Special Postdoctoral Researchers (SPDR) for FY 2026. This is one of the best postdoc positions you can find in Japan, comparable to departmental or institutional fellowships in the US or Europe. Feel free to reach out if you’re interested! www.riken.jp/en/careers/p...

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.

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...

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 ...

biorxiv.org

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”.

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

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

github.com

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...

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 ...

biorxiv.org

Kyogo Kawaguchi@kyogok.bsky.social · 2y ago

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...

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...