Shiori Iida
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shiori-iida.bsky.social
Shiori Iida
@shiori-iida.bsky.social
Postdoc at @sarawickstrom.bsky.social 🇩🇪/ PhD at Maeshima Lab 🇯🇵/ Cell differentiation, Nuclear mechanics, Chromatin / 🧡🔬

https://linktr.ee/shiori_iida
Pinned
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)
Reposted by 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/...
November 20, 2025 at 2:24 AM
Reposted by Shiori Iida
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.
www.science.org
November 20, 2025 at 7:46 AM
Reposted by Shiori Iida
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...
November 13, 2025 at 12:13 PM
Reposted by Shiori Iida
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🇩🇪
October 20, 2025 at 7:24 PM
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🇩🇪
October 20, 2025 at 6:43 PM
Reposted by Shiori Iida
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 🧵 👇
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.
www.nature.com
September 29, 2025 at 4:45 PM
Reposted by Shiori Iida
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/...
August 28, 2025 at 4:18 AM
Reposted by Shiori Iida
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)
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/...
August 28, 2025 at 8:43 AM
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)
August 29, 2025 at 12:36 AM
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👇
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/...
August 28, 2025 at 3:11 PM
Reposted by Shiori Iida
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 💚
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...
rdcu.be
August 15, 2025 at 11:54 AM
Reposted by Shiori Iida
My #PhD defense work is on #Biorxiv!
Link: biorxiv.org/content/10.110…
Using single-molecul#imagingng, we showed that liquid-like BRD4-NUT condensates locally constrai#chromatinin vi#bromodomain-dependentnt crosslinking.
I thank my supervisor, Prof. @kazu-maeshima.bsky.social, for his support!
July 16, 2025 at 2:21 PM
Reposted by Shiori Iida
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
July 10, 2025 at 4:21 AM
Reposted by Shiori Iida
📢 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!
April 30, 2025 at 3:27 PM
Reposted by Shiori Iida
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!
Hi Bluesky community:)

Our new manuscript is now available as a preprint!⛅️
biorxiv.org/content/10.1...

1/ Here, we describe a novel BMAL1-YAP complex in epidermal cells, which is hijacked during ageing to control the expression of up-regulated inflammation genes through enhancer binding.🧵
BMAL1 and YAP cooperate to hijack enhancers and promote inflammation in the aged epidermis
Ageing is characterised by persistent low-grade inflammation that is linked to impaired tissue homeostasis and functionality. However, the molecular mechanisms driving age-associated inflammation rema...
biorxiv.org
April 23, 2025 at 7:32 PM
Reposted by Shiori Iida
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...
April 24, 2025 at 1:19 PM
Reposted by Shiori Iida
🎥 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....
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.
www.science.org
April 25, 2025 at 12:24 AM
Reposted by Shiori Iida
🧬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. ✨
April 25, 2025 at 12:24 AM
Reposted by Shiori Iida
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
March 29, 2025 at 1:06 AM
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!
March 27, 2025 at 2:34 AM
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!
March 27, 2025 at 2:19 AM
Reposted by Shiori Iida
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/
March 7, 2025 at 12:37 AM
Reposted by Shiori Iida
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...
February 20, 2025 at 11:15 AM
Reposted by Shiori Iida
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/...
Mature chromatin packing domains persist after RAD21 depletion in 3D
RAD21 contributes to nascent packing domain formation, but maturation requires nucleosome posttranslational modifications.
www.science.org
January 24, 2025 at 10:32 PM
Reposted by Shiori Iida
Thanks🎅🏼🦌
Merry Christmas all.
@shiori-iida.bsky.social @dai.tsujino
#NIGchrismtmass
December 24, 2024 at 12:04 PM