Shiori Iida

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.

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/...

I launched my lab at UMass Amherst this fall. We study the mechanisms of meiotic homolog pairing using advanced live‑cell and super‑resolution imaging. Currently in budding yeast, with plans to expand to other eukaryotes. #Chromosome #Meiosis #Mitosis
www.umass.edu/biology/abou...

Welcome @shiori-iida.bsky.social , it’s great to have you in the lab! Excited about new directions in chromatin rheology and cell fate 🤓

I’ve recently joined @sarawickstrom.bsky.social lab at @mpi-muenster.bsky.social as a postdoc!
I’ll keep doing exciting science with joy and passion 🔬💫

Huge thanks to @kazu-maeshima.bsky.social lab for all the support during my PhD journey⛰️

I’ll start by tasting every single sausage here🇩🇪

Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells - Nature Cell Biology McCreery, Stubb et al. show that mechano-osmotic changes in the nucleus induce general transcriptional repression and prime chromatin for cell fate transitions by relieving repression of specific differentiation genes.

How do #stemcells integrate information to coordinate fate decisions? Delighted to finally see our work showing how growth factors regulate the mechano-osmotic state of the #nucleus and #chromatin to control #pluripotency exit out! www.nature.com/articles/s41... see 🧵 👇

Is euchromatin really “open”? Our new study @bioRxiv suggests otherwise. Using super-resolution imaging @shiori-iida.bsky.social‬ @masaashimazoe.bsky.social reveals: Euchromatin forms condensed domains in live cells. Cohesin constrains them and prevents domain mixing.
www.biorxiv.org/cgi/content/...

Euchromatin is mostly condensed⁉️

With @shiori-iida.bsky.social , We revealed the detailed structure of euchromatin using super-resolution imaging.

Cohesin regulates the function of euchromatin via chromatin dynamics!
(1/n)

Thank you, Amro! Grad to see you soon ☺️

You can see that the slower subpopulation localizes like heterochromatin, while the faster one resembles euchromatin.

One more movie!
Using the RL algorithm (from pnas.org/doi/10.1073/...),
@masaashimazoe.bsky.social analyzed our nucleosome tracking data and classified them by their mobility.
Hotter color = faster motion (Slow🔵→ 🟢 → 🟡 → 🟠 Fast)

Thank you! ☺️

I’m grateful to my supervisor
@kazu-maeshima.bsky.social
for leading this project, my amazing co–first author
@masaashimazoe.bsky.social
for putting this paper together, all coauthors, supporters, and lab members!

Check out our opinion article, too:

www.sciencedirect.com/science/arti...

Our new preprint is out!
We combined single-nucleosome imaging and 3D-SIM to reveal:
🔹 Euchromatin forms condensed domains, not open fibers
🔹Cohesin loss increases nucleosome mobility without decompaction
🔹Cohesin prevents neighboring domain mixing

Full story & movies👇

Conserved nucleocytoplasmic density homeostasis drives cellular organization across eukaryotes Nature Communications - Cells can regulate their mass density. Here, the authors demonstrate how eukaryotes establish and maintain a lower density in the nucleus than in the cytoplasm via pressure...

FINALLY! Challenging to publish but we believe it is an important discovery: rdcu.be/eATFz

💚 Thanks to the team ‪@biswashere.bsky.social‬, Omar Muñoz, ✨Q✨ C. Hoege, B. Lorton, R. Nikolay ‪@matthewkraushar.bsky.social‬ @dshechter.bsky.social @gucklab.bsky.social @vasilyzaburdaev.bsky.social‬ 💚

My #PhD defense work is on #Biorxiv!
Link: biorxiv.org/content/10.110…
Using single-molecule #imaging, we showed that liquid-like BRD4-NUT condensates locally constrain #chromatin via #bromodomain-dependent crosslinking.
I thank my supervisor, Prof. @kazu-maeshima.bsky.social, for his support!

Our new preprint 🧬🔗 www.biorxiv.org/content/10.1...
BRD4-NUT forms liquid-like condensates that locally constrain nucleosomes via BRD4-mediated crosslinking— physical control of #chromatin by #LLPS transcription condensates. @semeigazin.bsky.social @katsuminami.bsky.social @masaashimazoe.bsky.social

📢 NIG Postdoc Fellowship Call!
www.nig.ac.jp/nig/career-d...
🧬We’re seeking motivated postdocs to join our lab. 🔬We study chromatin behavior in living cells using advanced live-cell imaging and quantitative analysis:
www.science.org/doi/10.1126/...
doi.org/10.2183/pjab...
Interested? Please apply!

Check out this exciting preprint from @aznarbenitahlab.bsky.social discovering a new mode of crosstalk between YAP and the circadian regulator BMAL1. Congrats @juliabonjoch.bsky.social and @guiomarsolanas.bsky.social for fantastic work and thank you for the fun collaboration!

In developing embryos, cells move a lot! Plenty of that movement is random. Is random cell mixing a feature or bug for tissue patterning? Turns out, it’s both! Excited to share the 1st preprint from my postdoc w/ Sean Megason @seanemcgeary.bsky.social and Allon Klein. 1/20 doi.org/10.1101/2025...

Single-nucleosome imaging reveals steady-state motion of interphase chromatin in living human cells Local chromatin motion remains steady during interphase, allowing cells to conduct housekeeping tasks under similar environments.

🎥 Video: See chromatin in action — each dot is a single nucleosome, dynamically fluctuating in a living HeLa cell (TMR-labeled, 50 ms/frame).
🔬 Original paper: www.science.org/doi/full/10....

🧬My retrospective chromatin review is out @Proc Jpn Acad:
doi.org/10.2183/pjab...
The textbook view of #chromatin as 30-nm fibers is fading.
A new paradigm: chromatin forms #liquid-like domains—locally dynamic, yet globally stable at the chromosome level (viscoelastic)—supporting genome function. ✨

Our new paper is out@ScienceAdvances👇
www.science.org/doi/10.1126/...
🧬Our Repli-Histo labeling marks nucleosomes in euchromatin and heterochromatin in live human cells.
🔍 @katsuminami.bsky.social et al. have developed a chromatin behavior atlas within the nucleus. 1/2

On top of that, I’m honored to receive the SOKENDAI Award from my university for my PhD work!

I can't thank @kazu-maeshima.bsky.social, my labmates, and all the NIG members enough for their support.

This recognition gives me even more motivation for the journey ahead!

It took blood, sweat, tears, too much coffee☕️, and just the right amount of alcohol🍺—but I finally got my PhD!

Huge thanks to everyone supported me, especially my mentor @kazu-maeshima.bsky.social, labmates, friends, and family.

I’m excited to keep chasing big questions and growing as a scientist!

Our new preprint is out＠bioRxiv: www.biorxiv.org/content/10.1...
@masaashimazoe.bsky.social et al. reveal that linker histone H1 acts as a liquid-like glue to organize chromatin in living cells. 🎉 Fantastic collab with @rcollepardo.bsky.social @janhuemar.bsky.social and others—huge thanks! 🙌 1/

Our new review on how the #chromatin domain is formed in the cell is now available @Curr Opin Struct Biol.📄✨
We critically discuss the domain formation mechanism from a physical perspective, including #phase-separation and #condensation.
📥 Free-download link:
authors.elsevier.com/a/1keGn,LqAr...

Mature chromatin packing domains persist after RAD21 depletion in 3D RAD21 contributes to nascent packing domain formation, but maturation requires nucleosome posttranslational modifications.

Today in Science Advances: "Mature chromatin packing domains persist after RAD21 depletion in 3D". Researchers at CPGE integrated measurements of genome connectivity and physical structure to deepen our understanding of chromatin organization

#chromatin #genomics

www.science.org/doi/10.1126/...

Thanks🎅🏼🦌
Merry Christmas all.
@shiori-iida.bsky.social @dai.tsujino
#NIGchrismtmass

We are seeking a motivated postdoc to join our lab!  Our research focuses on live-cell imaging/analysis to reveal how chromatin behaves in living cells and how its behavior contributes to cellular functions.
www.nature.com/articles/s41...
www.science.org/doi/10.1126/...
Interested? Please DM me!