Naomichi Takemata
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naomichitakemata.bsky.social
Naomichi Takemata
@naomichitakemata.bsky.social
Studying archaeal 3D genomes at Kyoto Univ, Japan
https://scholar.google.co.jp/citations?user=Q34_N9wAAAAJ&hl=ja#
Reposted by Naomichi Takemata
Lab’s first paper is out!! We show the first structures of #Asgard #chromatin by #cryo-EM 🧬❄️
Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...
October 28, 2025 at 3:07 PM
Reposted by Naomichi Takemata
This was a fun collaboration between Ophélie & the @seegerlab.bsky.social using sybody libraries to target the SMC complex in living bacteria. With a suprising finding: the 14 isolated sybodies bind to the middle of the SMC coiled coil rather than the more conserved ATPase heads.
Single Domain Antibody Inhibitors Target the Coiled Coil Arms of the Bacillus subtilis SMC complex https://www.biorxiv.org/content/10.1101/2025.10.16.682983v1
October 20, 2025 at 8:15 AM
Reposted by Naomichi Takemata
Check out our paper on intricate nested interactions between viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts. Excellent collaboration with @deemteam.bsky.social, @anagtz.bsky.social and Michail Yakimov
Free access link: rdcu.be/eLtCH
🧵 by @yifanzhou.bsky.social 👇
October 17, 2025 at 10:28 AM
Reposted by Naomichi Takemata
Our paper on chromosome segregation in the archaeon Sulfolobus Acidocaldarius has been published in PNAS! This has been a great collaboration with @joeparham19.bsky.social and the rest of @buzzbaum.bsky.social's team. Stay tuned for more to come!😉 @istaresearch.bsky.social

doi.org/10.1073/pnas...
Temporal and spatial coordination of DNA segregation and cell division in an archaeon | PNAS
Cells must coordinate DNA segregation with cytokinesis to ensure that each daughter cell inherits a complete genome. Here, we explore how DNA segre...
doi.org
October 16, 2025 at 8:53 AM
Reposted by Naomichi Takemata
Happy that the final version of our Lamassu work @yli18smc.bsky.social is now out:

www.nature.com/articles/s41...

Thanks again to our awesome collaborators @mblokesch.bsky.social and David and co and Mark Szczelkun and @steven-shaw.bsky.social and the DCI Lausanne @fbm-unil.bsky.social
Glad to share the work of @yli18smc.bsky.social and co on Lamassu, a bacterial defense system related to Rad50/Mre11 (RM). While RM carefully trims DNA ends for repair, Lamassu chops up the host chromosome. Our study reveals how it is regulated to minimize damage, activating only during infection.
October 14, 2025 at 9:28 AM
Reposted by Naomichi Takemata
new preprint from our group & Antoine Hocher: www.biorxiv.org/content/10.1...
A fantastic collaboration with Antoine, with Jovana Kaljevic' initiated the collaboration and drives the project.
Versatile NTP recognition and domain fusions expand the functional repertoire of the ParB-CTPase fold beyond chromosome segregation
Nucleotide triphosphate (NTP)-dependent molecular switches regulate essential cellular processes by cycling between active and inactive states through nucleotide binding and hydrolysis. These mechanis...
www.biorxiv.org
October 11, 2025 at 11:36 AM
Reposted by Naomichi Takemata
How do SMC complexes load onto DNA to get ready for loop extrusion?

@roisnehamelinf.bsky.social & co discovered that Wadjet, an SMC complex involved in bacterial DNA immunity, performs some impressive molecular gymnastics 🤸‍♂️🤸‍♂️🤸‍♂️.

Check out the new paper: www.cell.com/molecular-ce...
October 9, 2025 at 2:43 PM
Reposted by Naomichi Takemata
📝New preprint! #MicroSky

🕰️We chart the full, synchronized lifecycle of a predatory bacterium using Hi-C, RNA-seq, ChIP-seq & microscopy.

🧬We uncover dramatic shifts in nucleoid architecture & transcription, tightly coordinated with predation.

www.biorxiv.org/content/10.1...
Dynamics and interplay of gene expression and chromosome organization across a predatory lifecycle
The obligate predatory bacterium Bdellovibrio bacteriovorus alternates between a motile attack phase and a growth phase inside another bacterium, during which it undergoes multiple rounds of DNA repli...
www.biorxiv.org
September 25, 2025 at 7:12 AM
Thank you to @tamarabasta.bsky.social for hosting my visit to I2BC @i2bcparissaclay.bsky.social in Paris! I truly enjoyed the inspiring scientific interactions and the beauty of the city.
September 12, 2025 at 6:03 PM
Reposted by Naomichi Takemata
Our Wadjet-II paper by @roisnehamelinf.bsky.social is out in polished form: www.cell.com/structure/fu...

With a great preview by @kevincorbett.bsky.social & @amardeeep.bsky.social highlighting the potential of Wadjets:

Wadjet—Keeping a watchful eye on circular DNA.

www.cell.com/structure/fu...
September 5, 2025 at 6:29 AM
Reposted by Naomichi Takemata
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 Naomichi Takemata
Check out our paper in PLoS Genetics with @umbertorosani.bsky.social and Marco Gerdol on the highly dynamic pangenome of basal chordates. It is enriched in defence and immunity genes (like in prokaryotes) and follows Mendelian inheritanceis rules. @plos.org journals.plos.org/plosgenetics...
August 18, 2025 at 10:30 PM
Reposted by Naomichi Takemata
Archaea are often surrounded by bacteria. But is there ever active conflict between the two? Can archaea kill bacteria? If so, how do they do it?

Work by @romainstrock.bsky.social shows that some archaea can kill bacteria by secreting peptidoglycan hydrolases. journals.plos.org/plosbiology/...
Archaea produce peptidoglycan hydrolases that kill bacteria
Archaea regularly interact with bacteria but reports of archaea killing bacteria are very rare. This study shows that many archaea encode peptidoglycan hydrolases, which specifically target bacterial ...
journals.plos.org
August 14, 2025 at 6:50 PM
Reposted by Naomichi Takemata
My attempt to become a professor was unsuccessful again but the diplonema tagging paper is now published in Open Biology. royalsocietypublishing.org/doi/10.1098/...
August 6, 2025 at 4:05 PM
Reposted by Naomichi Takemata
📣Huge congrats to our postdoc, Takaya Totsuka, on his new paper @currentbiology.bsky.social 🎉 He found that Ca2+ oscillations regulate oocyte spindle rotation! 🐭The project started during his PhD with Prof. Miho Ohsugi.

Free link: authors.elsevier.com/c/1lUqk3QW8S...
authors.elsevier.com
July 27, 2025 at 6:27 AM
Reposted by Naomichi Takemata
#MicroSky Summer read!

Predatory bacteria kill and eat other bacteria. Their deadly actions come in many flavors, often via direct physical contact between predator &
prey 🧛

How do they do it?
Our review 📖 @coralietesseur.bsky.social @ysantin.bsky.social

www.sciencedirect.com/science/arti...
Strategies and mechanisms of contact-dependent predation in bacteria
Predatory bacteria kill other bacteria to acquire nutrients. Among diverse strategies to kill and feed on prey, contact-dependent predation stands out…
www.sciencedirect.com
July 25, 2025 at 4:59 PM
Reposted by Naomichi Takemata
And the story is published now!🍾
www.nature.com/articles/s41...

Open access link: rdcu.be/exnOc

Many years in the making, great collaboration with @archaellum.bsky.social & @tunglejic.bsky.social

Thanks @ukri.org BBSRC & @leverhulme.ac.uk for funding, reviewers & editor!! 🙏
#microsky #archaeasky
July 22, 2025 at 9:06 PM
Reposted by Naomichi Takemata
🚨Our latest work on selfish centromeres is published @currentbiology.bsky.social 🐭🧬We found that the spindle checkpoint contributes to non-Mendelian segregation! Huge congrats to our lab manager, Zaak Walton, who led the project🎉

Free link:
authors.elsevier.com/a/1lQzN3QW8S...
authors.elsevier.com
July 15, 2025 at 12:39 AM
Reposted by Naomichi Takemata
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 Naomichi Takemata
We found a new asymmetry in the large-scale chromosome structure: sister chromatids are systematically shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! The work was led by Flavia Corsi, in close collaboration with the Daniel Gerlich lab.
www.biorxiv.org/content/10.1...
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July 15, 2025 at 8:11 AM
Reposted by Naomichi Takemata
I am pleased to share our new review on the role of bacterial nucleoid-aasociated proteins in mediating responses to changes in environment. Important: some NAPs can directly ‘sense’ physico-chemical changes. www.sciencedirect.com/science/arti... @pingzhuangge.bsky.social
The role of nucleoid-associated proteins in mediating responses to environmental changes
Bacteria face diverse environmental challenges, such as changes in temperature, pH, and osmolarity, and exposure to antibiotics, which necessitate ada…
www.sciencedirect.com
July 10, 2025 at 6:21 AM
Reposted by Naomichi Takemata
Fantastic opportunity to start your independent career at the JIC here. Great startup package. Repost = nice. Thank you!!!
July 10, 2025 at 6:52 AM
Reposted by Naomichi Takemata
Delighted to share a new review paper from the lab. We summarized/discussed recent key findings in enhancer biology. Thanks Dan Larson and @tinekelenstra.bsky.social for this opportunity!!

www.sciencedirect.com/journal/jour...
July 6, 2025 at 12:59 AM
Reposted by Naomichi Takemata
New preprint from Kelsey Fryer in the lab using ChAR-seq to identify RNAs that are bound to human centromeres. Lots of surprises! #centromere #RNA www.biorxiv.org/content/10.1...
www.biorxiv.org
June 20, 2025 at 12:40 AM
Reposted by Naomichi Takemata
Our new review paper is out@JMB!🧬
@katsuminami.bsky.social@semeigazin.bsky.social‬ ‪@kakonakazato.bsky.social‬ discuss DNA accessibility in euchromatin and heterochromatin of live cells.
Free access: authors.elsevier.com/a/1lHgb54HFZ...
Also check our previous work: www.science.org/doi/10.1126/...
June 18, 2025 at 6:20 AM