Masa A. Shimazoe
@masaashimazoe.bsky.social
Ph. D. Student in Maeshima lab in NIG @kazu-maeshima.bsky.social
Biophysics, Chromatin / Kyoto Uni. → NIG
Biophysics, Chromatin / Kyoto Uni. → NIG
Reposted by Masa A. Shimazoe
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
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...
www.pnas.org
October 27, 2025 at 9:43 PM
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/...
Reposted by Masa A. Shimazoe
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 🔥🔥🔥
🚨 🚨 🚨 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
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
October 22, 2025 at 5:10 AM
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 🔥🔥🔥
Reposted by Masa A. Shimazoe
🚨 🚨 🚨 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
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
October 21, 2025 at 9:59 AM
🚨 🚨 🚨 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
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
Reposted by Masa A. Shimazoe
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. https://scim.ag/4mTE1Z6
October 8, 2025 at 2:00 PM
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. https://scim.ag/4mTE1Z6
Reposted by Masa A. Shimazoe
This year’s #NobelPrize in Physiology or Medicine has been awarded to three scientists for discovering how the immune system distinguishes friend from foe. https://scim.ag/3Wt5rdi
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
scim.ag
October 6, 2025 at 1:45 PM
This year’s #NobelPrize in Physiology or Medicine has been awarded to three scientists for discovering how the immune system distinguishes friend from foe. https://scim.ag/3Wt5rdi
Reposted by Masa A. Shimazoe
@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
September 9, 2025 at 5:47 PM
@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
Reposted by Masa A. Shimazoe
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/...
www.biorxiv.org/cgi/content/...
August 28, 2025 at 4:18 AM
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/...
www.biorxiv.org/cgi/content/...
Reposted by Masa A. Shimazoe
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)
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
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)
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)
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)
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/...
www.biorxiv.org/cgi/content/...
August 28, 2025 at 8:43 AM
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)
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)
Reposted by Masa A. Shimazoe
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!
@cnrs.fr @cnrsbiologie.bsky.social
Congrats to all!
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...
www.cell.com
August 9, 2025 at 10:47 AM
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!
@cnrs.fr @cnrsbiologie.bsky.social
Congrats to all!
And again, Fantastic meeting! 🔬
Single-molecule studies are advancing biology into new territory—thrilled to be involved. 💡
#EMBLSingleMolecule
Single-molecule studies are advancing biology into new territory—thrilled to be involved. 💡
#EMBLSingleMolecule
July 18, 2025 at 2:21 PM
And again, Fantastic meeting! 🔬
Single-molecule studies are advancing biology into new territory—thrilled to be involved. 💡
#EMBLSingleMolecule
Single-molecule studies are advancing biology into new territory—thrilled to be involved. 💡
#EMBLSingleMolecule
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.
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.
July 18, 2025 at 2:20 PM
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.
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.
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
Thank you to all who visited and engaged in exciting discussions.
Grateful to the organizers for an excellent event! #EMBLSingleMolecule
July 18, 2025 at 1:56 PM
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
Thank you to all who visited and engaged in exciting discussions.
Grateful to the organizers for an excellent event! #EMBLSingleMolecule
Reposted by Masa A. Shimazoe
🔬 #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!
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!
July 17, 2025 at 9:11 AM
🔬 #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!
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!
Reposted by Masa A. Shimazoe
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
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
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
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
Reposted by Masa A. Shimazoe
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
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
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
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
Reposted by Masa A. Shimazoe
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)
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)
March 10, 2025 at 9:12 AM
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)
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)
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)
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)
March 10, 2025 at 9:12 AM
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)
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)
Reposted by Masa A. Shimazoe
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!
Go check the paper on the biorXiv!
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/
@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 11:53 AM
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!
Go check the paper on the biorXiv!
Reposted by Masa A. Shimazoe
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
Congrats @masaashimazoe.bsky.social & all contributors! 🎉 2/
🔗 bit.ly/4h7S3Dn
March 7, 2025 at 12:37 AM
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
Congrats @masaashimazoe.bsky.social & all contributors! 🎉 2/
🔗 bit.ly/4h7S3Dn
Reposted by Masa A. Shimazoe
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/
@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
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/
@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/
Reposted by Masa A. Shimazoe
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
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/
@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 11:09 AM
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
Reposted by Masa A. Shimazoe
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...
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
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...
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...
This is my new account on Bluesky !!!
December 3, 2024 at 1:54 PM
This is my new account on Bluesky !!!