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Masa A. Shimazoe

@masaashimazoe.bsky.social
136 followers 120 following 24 posts

Ph. D. Student in Maeshima lab in NIG @kazu-maeshima.bsky.social Biophysics, Chromatin / Kyoto Uni. → NIG sites.google.com/view/masa-a-shimaz…

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Reposted by Masa A. Shimazoe
Kazuhiro Maeshima @kazu-maeshima.bsky.social · 26/09/2026
🧬 Highly related @natgenet.nature.com paper from @binzmit.bsky.social group, using nucleosome-resolution chromatin modeling: Euchromatin forms condensed domains with short active regions on the surface www.nature.com/articles/s41... Congratulations! 🎉
nature.com
Euchromatin forms condensed domains with short active regions on the surface - Nature Genetics
Simulations integrating micro-C and imaging data provide a coherent view of chromatin organization from nucleosomes to clutches to domains, revealing that most regions form compact domains but short r...
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Reposted by Masa A. Shimazoe
Fena Ochs @fenaochs.bsky.social · 25/09/2026
Happy to share our new software SIMworks out today in Nature Protocols (1/3) SIMworks is a software suite built on our previous tools SIMCheck, Chromagnon, ChaiN and SIMinspector and enables data augmentation, quantitative processing and analysis. Link to publication: www.nature.com/articles/s41...
nature.com
SIMworks—an integrated software suite for quality-controlled augmented quantitative structured illumination microscopy
Nature Protocols - SIMworks is an integrated software suite for quality-controlled augmented quantitative structured illumination microscopy (SIM), enabling both new learners and experienced users...
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Masa A. Shimazoe @masaashimazoe.bsky.social · 17/09/2026
Our new review paper on mitotic chromosomes is now out! Take a look!
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Shiori Iida @shiori-iida.bsky.social · 08/09/2026
Happy to share that this paper is now published in Nature Genetics! Grateful to everyone who supported this work throughout this long journey. I’m proud to see it out! www.nature.com/articles/s41...
nature.com
Cohesin prevents local mixing of condensed euchromatic domains in living human cells - Nature Genetics
Single-nucleosome imaging/tracking and super-resolution three-dimensional structured illumination microscopy within euchromatic regions show that cohesin-mediated loops constrain condensed euchromatic...
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Reposted by Masa A. Shimazoe
Kazuhiro Maeshima @kazu-maeshima.bsky.social · 08/09/2026
Is euchromatin really “open”? 🧬 Using super-resolution imaging🔬 our new study @natgenet.nature.com reveals: Euchromatin forms condensed domains in live cells. Cohesin constrains them and prevents domain mixing for proper transcriptional insulation🚧 🔗 www.nature.com/articles/s41... (1/2)
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Masa A. Shimazoe @masaashimazoe.bsky.social · 09/09/2026
Our paper on euchromatin and cohesin is now published!!🙌 Euchromatin forms condensed domains, and cohesin constrains their local mixing. This organization maintains transcriptional insulation. This work was truly a team effort, and I’m grateful to everyone who contributed to it.
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Masa A. Shimazoe @masaashimazoe.bsky.social · 28/04/2026
Great to be back at CSHL!!! Tomorrow I’ll be giving a talk at the CSHL meeting “Genome Organization & Nuclear Function” #cshlnucleus Can’t wait to share our work and discuss!
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Rosana Collepardo @rcollepardo.bsky.social · 15/04/2026
Check out our latest work in collaboration with @kazu-maeshima.bsky.social and @masaashimazoe.bsky.social We show that H1 is a dynamic, multivalent “liquid-like” glue of chromatin in cells: it bridges multiple nucleosomes & exchanges partners frequently to enable both compaction and flexibility
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eltsovmikhail.bsky.social @eltsovmikhail.bsky.social · 13/04/2026
I am not afraid to say it: this is the most fundamental advance in our understanding of chromatin structure since the zig-zag fiber model. Congratulations!
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Science Magazine @science.org · 10/04/2026
A new model provides insight into chromatin organization and dynamics in living cells. Learn more in this week’s issue of #ScienceAdvances: scim.ag/4sYMeyS
A molecular dynamics simulation of nucleosomes and linker histone H1 with single-H1 trajectories (background).
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Reposted by Masa A. Shimazoe
Kazuhiro Maeshima @kazu-maeshima.bsky.social · 08/04/2026
Our H1 paper is out #ScienceAdvances: www.science.org/doi/10.1126/... @masaashimazoe.bsky.social et al. reveal that linker histone H1 acts as a liquid-like glue to organize chromatin in live cells. 🎉 Fantastic collab with @rcollepardo.bsky.social @janhuemar.bsky.social and others—huge thanks! 🙌 1/
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Masa A. Shimazoe @masaashimazoe.bsky.social · 09/04/2026
My first, first author paper is now on #ScienceAdvances ! Linker histone H1 is a liquid-like "glue" condensing chromatin, which revises textbooks! 📖✨ science.org/doi/10.1126/sc… Huge thanks to @kazu-maeshima.bsky.social , for supervision. Amazing collab with @rcollepardo.bsky.social ’s group! 1/
science.org
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Kazuhiro Maeshima @kazu-maeshima.bsky.social · 10/02/2026
My student Aoi Otsuka ’s PhD work is now officially published @csf-jscb.bsky.social! 🔬 Single-nucleosome imaging uncovers biphasic local chromatin dynamics in an oncogene-inducible human carcinogenesis model (1–3 d: same, 5–7 d: ↑, back by week 4). Congrats! www.jstage.jst.go.jp/article/csf/...
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Kazuhiro Maeshima @kazu-maeshima.bsky.social · 23/12/2025
My PhD students Aoi Otsuka @masaashimazoe.bsky.social et al. published @csf-jscb.bsky.social 🎉 Single-nucleosome imaging in an oncogene-inducible human carcinogenesis model shows biphasic chromatin dynamics (1–3 d same; 5–7 d ↑; back by week 4). Congrats! 👉 doi.org/10.1247/csf....
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Gerlich Lab @gerlichlab.bsky.social · 05/12/2025
Excited to share our latest fully in-house paper! 🎉 We show how cohesin integrates loop extrusion with sister tethering to guide the homology search during DNA repair. Huge congratulations to all authors, and to @fedeteloni.bsky.social for leading this work 👏 We’re excited to see his next steps!
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Federico Teloni @fedeteloni.bsky.social · 04/12/2025
I am happy to share that my postdoctoral work in the @gerlichlab.bsky.social at @imbavienna.bsky.social is finally out 🎉! Our study reveals how cohesin guides focused and accurate homology search. Read more 👉 www.science.org/doi/10.1126/... Follow along for key insights and updates! 🧵
science.org
Cohesin guides homology search during DNA repair using loops and sister chromatid linkages
Accurate repair of DNA double-strand breaks (DSBs) is essential for genome stability, and defective repair underlies diseases such as cancer. Homologous recombination uses an intact homologous sequenc...
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Rosana Collepardo @rcollepardo.bsky.social · 05/12/2025
Our Science paper is out! Huge congratulations to @huabin-zhou.bsky.social, Mike Rosen, and the brilliant @janhuemar.bsky.social @juliamaristany.bsky.social and @kieran-russell.bsky.social from our group News: bit.ly/4avnkAr and bit.ly/3XBGVHS Great perspective by @vram142.bsky.social +K Zhang
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Luke Lavis @rhodamine110.bsky.social · 27/10/2025
A new, nerdy paper. We figured out (some) of the rules underlying cell-permeability of probes and designed ligands that light up, grab, and move proteins around. Awesome @hhmijanelia.bsky.social x @uwmadison.bsky.social x @stjuderesearch.bsky.social collaboration! www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Rosana Collepardo @rcollepardo.bsky.social · 22/10/2025
Check out our new work, led by talented @janhuemar.bsky.social, where we uncover that pioneer factor Oct4 remodels chromatin for DNA access not by opening it but by exploiting nucleosome breathing and forming clusters 🔥🔥🔥
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Jan Huertas @janhuemar.bsky.social · 21/10/2025
🚨 🚨 🚨 New preprint alert!!! 🚨 🚨 🚨 In the past, we have learnt that Oct4 can induce nucleosome breathing on the mono-nucleosome level. But what happens when you have a fibre of multiple nucleosomes? www.biorxiv.org/content/10.1... @rcollepardo.bsky.social @juliamaristany.bsky.social
A rendering of multiple Oct4 molecules bound to a chromatin fibre
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Science Magazine @science.org · 08/10/2025
This year’s #NobelPrize in Chemistry has gone to the architects of molecular “cages” that could be used for everything from carbon capture to drug delivery. scim.ag/4mTE1Z6
Architects of molecular cages win Chemistry Nobel
Susumu Kitagawa, Richard Robson, and Omar Yaghi honored for developing metal-organic frameworks
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Science Magazine @science.org · 06/10/2025
This year’s #NobelPrize in Physiology or Medicine has been awarded to three scientists for discovering how the immune system distinguishes friend from foe. scim.ag/3Wt5rdi
scim.ag
Medicine Nobel goes to three researchers who identified immune system’s security guards
Mary Brunkow, Fred Ramsdell, and Shimon Sakaguchi discovered regulatory T cells that prevent autoimmune disease
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janeskok.bsky.social @janeskok.bsky.social · 09/09/2025
@kazu_maeshima from the Genome Dynamics Laboratory at the National Institute of Genetics (@NIG_idenken) will present groundbreaking research on chromatin organization and behavior in live cells revealed by super-resolution imaging. nyulangone.zoom.us/webinar/regi... #chromatin2025
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Kazuhiro Maeshima @kazu-maeshima.bsky.social · 28/08/2025
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/...
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Shiori Iida @shiori-iida.bsky.social · 29/08/2025
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)
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Masa A. Shimazoe @masaashimazoe.bsky.social · 28/08/2025
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)
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Christophe Chapard @christophechapard.bsky.social · 09/08/2025
Pleased to see this study out, combining experimental work from our lab at the @cbitoulouse.bsky.social, in particular by @nathaliebastie.bsky.social and @beckof.bsky.social, and from Laura Chaptal and @alengronne.bsky.social at IGH Montpellier @cnrs.fr @cnrsbiologie.bsky.social Congrats to all!
cell.com
RNA Pol II-based regulations of chromosome folding
How transcription and cohesin complexes interact to regulate 3D genome organization remains unclear. Chapard et al. dissect their respective contributions and their interplay in shaping the genome arc...
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Masa A. Shimazoe @masaashimazoe.bsky.social · 18/07/2025
And again, Fantastic meeting! 🔬 Single-molecule studies are advancing biology into new territory—thrilled to be involved. 💡 #EMBLSingleMolecule
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Masa A. Shimazoe @masaashimazoe.bsky.social · 18/07/2025
I had an amazing time at EMBL Heidelberg! I was absolutely impressed by the facilities—everything operates on a completely different scale here. Definitely hope to work in an environment like this someday.
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Masa A. Shimazoe @masaashimazoe.bsky.social · 18/07/2025
Honored to receive 1st Place Poster Award 🏆 at the EMBL meeting "Gene Regulation: One Molecule at a Time"! Thank you to all who visited and engaged in exciting discussions. Grateful to the organizers for an excellent event! #EMBLSingleMolecule
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EMBL Events @events.embl.org · 17/07/2025
🔬 #EMBLSingleMolecule poster session highlights 📜 Big ideas, bold questions, and lots of sticky notes! From molecular mechanics to late-breaking results – the poster session was buzzing with energy and conversation 💬 Loved seeing early-career researchers shine!
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Kazuhiro Maeshima @kazu-maeshima.bsky.social · 10/07/2025
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
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Kazuhiro Maeshima @kazu-maeshima.bsky.social · 29/03/2025
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
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Masa A. Shimazoe @masaashimazoe.bsky.social · 10/03/2025
My first, first author paper is now on bioRxiv! 🤩 Linker histone H1 is a liquid-like "glue" condensing chromatin, which revises textbooks! 📖✨ biorxiv.org/content/10.1... Huge thanks to my PI, @kazu-maeshima.bsky.social, for supervision. Amazing collab with @rcollepardo.bsky.social’s group!" (1/n)
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Masa A. Shimazoe @masaashimazoe.bsky.social · 10/03/2025
My first, first author paper is now on bioRxiv! 🤩 Linker histone H1 is a liquid-like "glue" condensing chromatin, which revises textbooks! 📖✨ biorxiv.org/content/10.1... Huge thanks to my PI, @kazu-maeshima.bsky.social, for supervision. Amazing collab with @rcollepardo.bsky.social’s group!" (1/n)
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Jan Huertas @janhuemar.bsky.social · 07/03/2025
Excited to share our newest collaboration with @kazu-maeshima.bsky.social and @masaashimazoe.bsky.social, where we show that H1 acts as a liquid-like glue in chromatin. Go check the paper on the biorXiv!
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Kazuhiro Maeshima @kazu-maeshima.bsky.social · 07/03/2025
Using single-H1 imaging and computational modeling, we show that most H1 behaves like a liquid inside chromatin domains rather than binding stably to nucleosomes as in the textbook model. Congrats @masaashimazoe.bsky.social & all contributors! 🎉 2/ 🔗 bit.ly/4h7S3Dn
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Kazuhiro Maeshima @kazu-maeshima.bsky.social · 07/03/2025
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/
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Rosana Collepardo @rcollepardo.bsky.social · 07/03/2025
In this wonderful collaboration with K Maeshima and M Shimazoe we show that H1 in living cells acts as a liquid-like glue not a driver of stiff zigzag fibers 🔥🔥🔥 Each H1 bridges multiple nucleosomes and exchanges nucleosomes frequently: boosting both compaction and dynamical behaviour of chromatin
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Kazuhiro Maeshima @kazu-maeshima.bsky.social · 20/02/2025
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...
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Masa A. Shimazoe @masaashimazoe.bsky.social · 03/12/2024
This is my new account on Bluesky !!!
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