Naomichi Takemata
Studying archaeal 3D genomes at Ritsumeikan University, Japan
scholar.google.co.jp/citations?user=Q34_…
- Reposted by Naomichi TakemataPreprint alert: Jiangyuan Liu developed a new workflow for chromatin loop calling across Hi-C datasets, e.g., during differentiation. Most loops are shared between datasets/cell states. Important work for all interested in chromatin loops and how to identify them! www.biorxiv.org/content/10.6...
- Reposted by Naomichi Takemata
I am very pleased to share that our database of prokaryotic and viral histones, ProHistoneDB, is now available online at prohistonedb.org. Please also see the accompanying article in J Mol Biol: doi.org/10.1016/j.jm... - Reposted by Naomichi Takemata@archaellum.bsky.social lab reveals how #cdiAMP and 4 RCK proteins shape osmotic stress responses in H. volcanii 🧬🦠. In highly halophilic #archaea, c-di-AMP coordinates ion balance and cell volume—mirroring bacterial strategies for environmental stress adaptation. 👉 buff.ly/ApWkCtg
- Reposted by Naomichi TakemataOrdering of cell cycle events by regulated proteolysis is not just for eukaryotes: @buzzbaum.bsky.social et al define mechanisms underlying switch-like degradation of archaeal ESCRT-III CvdB in Sulfolobus Thanks to @reviewcommons.org for another #RefereedPreprint link.springer.com/article/10.1...
- Reposted by Naomichi TakemataI’m honored to give a seminar at the TUM School of Life Sciences in January. I’ll be presenting our work on multi-omics analysis. I look forward to the discussion! www.ls.tum.de/en/ls/public...
- Reposted by Naomichi TakemataHappy to share a protocol for analysis of TF-nucleosome interactions and cryo-EM structure determination in STAR Protocols. I had a great opportunity to describe this protocol with @aliciakmichael.bsky.social. Thank you very much, all! www.sciencedirect.com/science/arti...
- Reposted by Naomichi TakemataMy 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....
- Reposted by Naomichi TakemataExciting new paper out! @allanaschooley.bsky.social and Sergey Venev led this project that let to the discovery of two chromosome folding programs: one inherited via mitotic chromosomes and one mitotic inherited through the cytoplasm! www.nature.com/articles/s41...
- Proud of contributing to this work on archaeal chromosome segregation! Congrats, Rachel and Steve! www.nature.com/articles/s41...
- Please also see the following papers working on archaeal chromosome segregation from slightly different angles: www.pnas.org/doi/10.1073/... www.biorxiv.org/content/10.1... www.nature.com/articles/s41...
- Reposted by Naomichi TakemataA major output of the 4D Nucleome project appeared today. This is the joint effort of many scientists working together and (publicly) sharing data and results for several years. We hope this is of interest to many genome biologists! www.nature.com/articles/s41...
- Honored to be invited as a guest speaker to EMBO MBoA 2026! Many thanks to the organizers — looking forward to inspiring talks and discussions in Cambridge! meetings.embo.org/event/26-arc...
- Reposted by Naomichi TakemataAre you a long-time fan of Archaea, an extremophile-phile, or are you simply curious? Either way, we have good news. We’re delighted to announce the 2026 EMBO Workshop on Archaea, 6–10 July. Sign up: meetings.embo.org/event/26-arc... We look forward to seeing you in Cambridge, UK. Please repost!
- Reposted by Naomichi TakemataDelighted to share our new preprint: www.biorxiv.org/content/10.6... We address a longstanding question about the role of the topoisomerase reverse gyrase in hyperthermophiles. Great collaboration with Baranello and @tobiaswarnecke.bsky.social groups. #Archaeasky #Microsky
- Delighted to share our latest preprint on reverse gyrase, a unique topoisomerase found exclusively in thermophiles! www.biorxiv.org/content/10.6...
- Please also check out the excellent complementary work from Tamara Basta @tamarabasta.bsky.social and Laura Baranello’s group. www.biorxiv.org/content/10.6...
- Reposted by Naomichi TakemataStable inheritance of the Streptomyces linear plasmid SCP1 by dual ParABS partition systems biorxiv.org/content/10.64898/20…
- Reposted by Naomichi TakemataOpen FSEP position in our team 📣 Nous recrutons un/e Ingénieur/e d’étude en biologie. Profil : être titulaire d’un poste permanent au CNRS (IE) et avoir envie d’étudier la chromatine bactérienne 😉 Date limite : jeudi 15 janvier. Détails et candidature ici : mobiliteinterne.cnrs.fr/ords/afip/ow...
- Glad to be part of this fantastic work!
- Ending my PhD with a bang: Face-to-face histones are important organizers of archaeal chromatin alongside classical histones. www.biorxiv.org/content/10.6...
- Reposted by Naomichi Takemata📢 Interested in #chromosomes 🧬 & #archaea thriving at the edge of life? PhD project in York,UK on how archaea pass on their genome to daughter cells.Friendly supervisors: me, @steve-quinn-lab.bsky.social & @georgerheath.bsky.social www.findaphd.com/phds/project... 📅 January 7, 2026 Please RP🙏thx!
- Reposted by Naomichi TakemataLab’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...
- Reposted by Naomichi TakemataThis 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 biorxiv.org/content/10.1101/202…
- Reposted by Naomichi TakemataCheck 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 👇
- Our work on viruses and virus satellites of haloarchaea and their DPANN symbionts is out today in Nature Microbiology! @mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social www.nature.com/articles/s41...
- Reposted by Naomichi TakemataOur 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...
- Reposted by Naomichi TakemataHappy 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.
- Reposted by Naomichi Takematanew 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.
- Reposted by Naomichi TakemataHow 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...
- 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...
- 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.
- Reposted by Naomichi TakemataOur 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...
- Happy to share the beautiful structure of a Wadjet SMC complex by @roisnehamelinf.bsky.social, with support from the DCI and @drhonsworth.bsky.social ! This is a type II Wadjet with unique characteristics including a tandem KITE subunit, distinct coiled coil architecture and a deviant hinge.
- Reposted by Naomichi TakemataOur 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/...
- Reposted by Naomichi TakemataCheck 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...
- Reposted by Naomichi TakemataArchaea 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/...
- Reposted by Naomichi TakemataMy attempt to become a professor was unsuccessful again but the diplonema tagging paper is now published in Open Biology. royalsocietypublishing.org/doi/10.1098/...
- I am happy to share a preprint on the marine plankton project I started one year ago (thanks to Julius and Drahomira's help) www.biorxiv.org/content/10.1...
- 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...
- 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...
- Reposted by Naomichi TakemataAnd 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
- 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...
- Reposted by Naomichi TakemataOur 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
- Reposted by Naomichi TakemataWe 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... 1/
- Reposted by Naomichi TakemataI 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
- Reposted by Naomichi TakemataFantastic opportunity to start your independent career at the JIC here. Great startup package. Repost = nice. Thank you!!!
- New Independent Fellowship position in Microbiology to launch your lab in our department @johninnescentre.bsky.social (UK). We are conducting a broad search in the area of plant-associated microbial interactions. Message me if you have any questions. Apply here: www.jic.ac.uk/vacancies/in...
- Reposted by Naomichi TakemataDelighted 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...
- Reposted by Naomichi TakemataNew 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...
- Reposted by Naomichi TakemataOur 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/...
- Reposted by Naomichi TakemataThis reveals parallels with DNA end protection in eukaryotes and highlights the challenges of having linear chromosomes as well as functional repair of DNA double strand break. www.biorxiv.org/cgi/content/...
- Reposted by Naomichi TakemataPublished now. doi.org/10.1242/jcs....
- Reposted by Naomichi TakemataWould you like to work with us? At JAMSTEC, we are recruiting postdoctoral researchers through the Young Research Fellow program. This program allows fellows to independently pursue their own research projects. www.jamstec.go.jp/recruit/e/jy...
- Reposted by Naomichi TakemataExciting new study from Iwasaki lab, led by Kotaro @ktomuro.bsky.social & Yuichi @u1-7no.bsky.social, that I was lucky to be part of! A new method reveals many mRNAs are locally translated. Too much for one tweet—check it out: www.biorxiv.org/content/10.1...
- Congrats to the team!
- An archaeal nucleoid-associated protein binds an essential motif in DNA replication origins | Nature Communications nature.com/articles/s41467-025…
- Reposted by Naomichi TakemataWe are excited to share our preprint describing how Sulfolobus cells coordinate DNA segregation with cell division! In eukaryotes this type of regulation involves checkpoints and CDK-cyclins. But how does this work in archaea? This is the question we ask in our paper: www.biorxiv.org/content/10.1...
- Reposted by Naomichi TakemataThis method chapter describes the CUT&Tag approach for profiling transcription factors during murine ZGA. I hope it will be helpful for others studying TF binding profiles in similar contexts. link.springer.com/protocol/10....
- Reposted by Naomichi TakemataWe’ve uncovered Asgard chromatin structures formed by a Hodarchaeal histone : closed hypernucleosome conserved in archaea and an open form resembling the H3-H4 eukaryotic octasome. Fantastic work by @harshranawat.bsky.social! www.biorxiv.org/content/10.1... #Chromatin #Asgard #Archaea #cryoEM
- Reposted by Naomichi TakemataTuning the interaction of a ParA-type ATPase with its partner separates bacterial organelle positioning from partitioning biorxiv.org/content/10.1101/202…
- Reposted by Naomichi TakemataI’m excited that the work by Diego Ramirez and Lei Yin is out, where they gained several key insights into what provides the force underlying bacterial cell division doi.org/10.1101/2025.... To divide, cells must first bend the membrane inward, a process that’s energetically expensive
- Reposted by Naomichi TakemataOur new paper comes out! Single-cell genomics linked many freshwater virus-host pairs and identified wanted CL500-11 viruses. The varying infection rates among host lineages highlighted their diverse defense strategies depending on their ecological characteristics: academic.oup.com/ismecommun/a...
- Reposted by Naomichi TakemataThe peer-reviewed VOR for the MagIC-cryo-EM paper by @yarimura.bsky.social and @1001hak.bsky.social is finally published! Congrats Yasu!
- Reposted by Naomichi TakemataDelighted to share a new preprint from the lab! We identified zinc-finger associated domain (ZAD)-containing C2H2 zinc-finger proteins (ZAD-ZnFs) as insulator-binding proteins in Drosophila. www.biorxiv.org/content/10.1...
