Naomichi Takemata
@naomichitakemata.bsky.social
Studying archaeal 3D genomes at Ritsumeikan University, Japan
https://scholar.google.co.jp/citations?user=Q34_N9wAAAAJ&hl=ja#
https://scholar.google.co.jp/citations?user=Q34_N9wAAAAJ&hl=ja#
Reposted by Naomichi Takemata
Preprint 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...
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 21, 2026 at 11:20 AM
Preprint 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...
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...
ProHistoneDB
prohistonedb.org
January 16, 2026 at 8:47 AM
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
👉 buff.ly/ApWkCtg
January 13, 2026 at 8:01 AM
@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
👉 buff.ly/ApWkCtg
Reposted by Naomichi Takemata
Ordering 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...
@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...
January 12, 2026 at 2:19 PM
Ordering 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...
@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 Takemata
I’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...
www.ls.tum.de/en/ls/public...
TUM Life Science Talks: Prof. Ryuichiro Nakato (University of Tokyo)
TUM Life Science Talks start with Prof. Ryuichiro Nakato: “Can multi-omics analysis elucidate genome regulatory mechanisms?”
www.ls.tum.de
January 5, 2026 at 11:26 AM
I’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...
www.ls.tum.de/en/ls/public...
Reposted by Naomichi Takemata
Happy 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...
www.sciencedirect.com/science/arti...
Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination
Pioneer transcription factors (TFs) possess the ability to read out DNA motifs embedded within nucleosomes, driving changes in gene expression during …
www.sciencedirect.com
December 29, 2025 at 9:11 PM
Happy 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...
www.sciencedirect.com/science/arti...
Reposted by Naomichi Takemata
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....
doi.org/10.1247/csf....
December 23, 2025 at 2:34 AM
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....
doi.org/10.1247/csf....
Reposted by Naomichi Takemata
Exciting 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...
www.nature.com/articles/s41...
Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm - Nature Cell Biology
Schooley et al. find that mitotically bookmarked loci drive a transient chromosome folding state during G1 entry that is subsequently modulated by factors inherited through the cytoplasm.
www.nature.com
December 22, 2025 at 11:45 AM
Exciting 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...
www.nature.com/articles/s41...
Proud of contributing to this work on archaeal chromosome segregation! Congrats, Rachel and Steve!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Coordination of chromosome segregation and cell division in the archaeon Sulfolobus acidocaldarius - Nature Communications
Very little is known about the molecular basis of chromosome segregation in archaea. Here, the authors describe conformational changes in the chromosome during the cell cycle of the archaeon Sulfolobu...
www.nature.com
December 22, 2025 at 1:54 AM
Proud of contributing to this work on archaeal chromosome segregation! Congrats, Rachel and Steve!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Naomichi Takemata
A 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...
www.nature.com/articles/s41...
An integrated view of the structure and function of the human 4D nucleome - Nature
The 4D Nucleome Project demonstrates the use of genomic assays and computational methods to measure genome folding and then predict genomic structure from DNA sequence, facilitatin...
www.nature.com
December 17, 2025 at 8:59 PM
A 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...
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...
Many thanks to the organizers — looking forward to inspiring talks and discussions in Cambridge!
meetings.embo.org/event/26-arc...
Molecular Biology of Archaea: Life Through the Prism of Archaea
In 1977, Woese and colleagues revealed Archaea as a distinct domain of life. Building on this insight, the discovery of Asgard archaea has strengthened the view that many hallmarks of eukaryotic cell…
meetings.embo.org
December 16, 2025 at 10:26 PM
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...
Many thanks to the organizers — looking forward to inspiring talks and discussions in Cambridge!
meetings.embo.org/event/26-arc...
Reposted by Naomichi Takemata
Are 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!
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!
Molecular Biology of Archaea: Life Through the Prism of Archaea
In 1977, Woese and colleagues revealed Archaea as a distinct domain of life. Building on this insight, the discovery of Asgard archaea has strengthened the view that many hallmarks of eukaryotic cell…
meetings.embo.org
December 16, 2025 at 12:00 PM
Are 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!
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 Takemata
Delighted 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
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
Localised activity of reverse gyrase at gene regulatory elements
DNA topoisomerases are essential enzymes found in all cells, where they regulate DNA supercoiling. Reverse gyrase (RG) is a unique type of topoisomerase that introduces positive supercoils into DNA an...
www.biorxiv.org
December 11, 2025 at 1:15 PM
Delighted 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
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
Reposted by Naomichi Takemata
Stable inheritance of the Streptomyces linear plasmid SCP1 by dual ParABS partition systems https://www.biorxiv.org/content/10.64898/2025.12.10.693275v1
December 11, 2025 at 5:16 AM
Stable inheritance of the Streptomyces linear plasmid SCP1 by dual ParABS partition systems https://www.biorxiv.org/content/10.64898/2025.12.10.693275v1
Delighted to share our latest preprint on reverse gyrase, a unique topoisomerase found exclusively in thermophiles!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reverse gyrase and 3D genome architecture suppress hyperthermophile genome instability arising from horizontal gene transfer
Reverse gyrase (Rgy), a distinctive topoisomerase conserved in all hyperthermophiles, has the unique ability to introduce positive DNA supercoils. It has long been hypothesized that Rgy overwinds geno...
www.biorxiv.org
December 11, 2025 at 6:40 AM
Delighted to share our latest preprint on reverse gyrase, a unique topoisomerase found exclusively in thermophiles!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Naomichi Takemata
Open 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...
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...
Détails de la fonction choisie
mobiliteinterne.cnrs.fr
December 8, 2025 at 12:52 PM
Open 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...
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...
Face-to-face histones are important organizers of archaeal chromatin alongside classical histones.
www.biorxiv.org/content/10.6...
December 8, 2025 at 1:34 PM
Glad to be part of this fantastic work!
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!
www.findaphd.com/phds/project...
📅 January 7, 2026
Please RP🙏thx!
November 9, 2025 at 5:20 PM
📢 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!
www.findaphd.com/phds/project...
📅 January 7, 2026
Please RP🙏thx!
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...
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
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...
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 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
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.
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 👇
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...
@mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social
www.nature.com/articles/s41...
Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions - Nature Microbiology
An exploration of the viromes of haloarchaea and their ultra-small DPANN symbionts reveals plasmid-derived satellites of viruses from both archaeal groups, highlighting the complexity of nested symbio...
www.nature.com
October 17, 2025 at 10:28 AM
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 👇
Free access link: rdcu.be/eLtCH
🧵 by @yifanzhou.bsky.social 👇
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...
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
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...
doi.org/10.1073/pnas...
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
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
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
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
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.
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
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.
A fantastic collaboration with Antoine, with Jovana Kaljevic' initiated the collaboration and drives the project.
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...
@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
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...
@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...