Nayuta Yakushiji-Kaminatsui
@nayutayk.bsky.social
Research Scientist at Haruhiko Koseki lab. at RIKEN IMS🇯🇵 My research has focused on limb development, Polycomb group proteins, Hox and chromatin organization🐓🐀🧬 Opinions are my own
Reposted by Nayuta Yakushiji-Kaminatsui
Pervasive binding of the stem cell transcription factor SALL4 shapes the chromatin landscape https://www.biorxiv.org/content/10.1101/2025.11.14.688441v1
November 16, 2025 at 3:33 AM
Pervasive binding of the stem cell transcription factor SALL4 shapes the chromatin landscape https://www.biorxiv.org/content/10.1101/2025.11.14.688441v1
Reposted by Nayuta Yakushiji-Kaminatsui
Fabulous talk by Haruhiko Koseki today @oxfordbiochemistry.bsky.social followed by a fun dinner with Neil Brockdorff and @aleksszczurek.bsky.social ! Thanks for visiting Haruhiko!
November 7, 2025 at 10:14 PM
Fabulous talk by Haruhiko Koseki today @oxfordbiochemistry.bsky.social followed by a fun dinner with Neil Brockdorff and @aleksszczurek.bsky.social ! Thanks for visiting Haruhiko!
Reposted by Nayuta Yakushiji-Kaminatsui
Ultra-long-range Polycomb-coupled interactions underlie subtype identity of human cortical neurons https://www.biorxiv.org/content/10.1101/2025.11.05.686502v1
November 6, 2025 at 1:33 PM
Ultra-long-range Polycomb-coupled interactions underlie subtype identity of human cortical neurons https://www.biorxiv.org/content/10.1101/2025.11.05.686502v1
Reposted by Nayuta Yakushiji-Kaminatsui
The TArgeted Cohesin Loader (TACL) paper was just published. Happy that we were able to contribute to this really exciting project!
If you want to learn how targeting cohesin to defined loci in the genome affects the local chromatin environment and transcription, look no further!
rdcu.be/eLiT5
If you want to learn how targeting cohesin to defined loci in the genome affects the local chromatin environment and transcription, look no further!
rdcu.be/eLiT5
Characterization of induced cohesin loop extrusion trajectories in living cells
Nature Genetics - This study introduces a system called TArgeted Cohesin Loader (TACL) that recruits cohesin complexes at defined genomic regions and induces loop extrusion events in living cells,...
rdcu.be
October 16, 2025 at 8:17 PM
The TArgeted Cohesin Loader (TACL) paper was just published. Happy that we were able to contribute to this really exciting project!
If you want to learn how targeting cohesin to defined loci in the genome affects the local chromatin environment and transcription, look no further!
rdcu.be/eLiT5
If you want to learn how targeting cohesin to defined loci in the genome affects the local chromatin environment and transcription, look no further!
rdcu.be/eLiT5
Reposted by Nayuta Yakushiji-Kaminatsui
What is a promoter? And how does it work?
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
Enhancer-promoter compatibility is mediated by the promoter-proximal region
Gene promoters induce transcription in response to distal enhancers. How enhancers specifically activate their target promoter while bypassing other promoters remains unclear. Here, we find that the p...
www.biorxiv.org
October 16, 2025 at 3:06 PM
What is a promoter? And how does it work?
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
Reposted by Nayuta Yakushiji-Kaminatsui
Nascent CUT&Tag captures transcription factor binding after chromatin duplication https://www.biorxiv.org/content/10.1101/2025.10.13.682212v1
October 15, 2025 at 1:33 PM
Nascent CUT&Tag captures transcription factor binding after chromatin duplication https://www.biorxiv.org/content/10.1101/2025.10.13.682212v1
Reposted by Nayuta Yakushiji-Kaminatsui
Enhancer-promoter compatibility is mediated by the promoter-proximal region https://www.biorxiv.org/content/10.1101/2025.10.14.682013v1
October 15, 2025 at 5:33 PM
Enhancer-promoter compatibility is mediated by the promoter-proximal region https://www.biorxiv.org/content/10.1101/2025.10.14.682013v1
Reposted by Nayuta Yakushiji-Kaminatsui
Derivation of embryonic stem cells across avian species - @stemcell.keck.usc.edu go.nature.com/4gLAGcZ
Derivation of embryonic stem cells across avian species - Nature Biotechnology
Embryonic stem cells for chicken and seven other avian species are derived.
go.nature.com
September 30, 2025 at 3:50 PM
Derivation of embryonic stem cells across avian species - @stemcell.keck.usc.edu go.nature.com/4gLAGcZ
Reposted by Nayuta Yakushiji-Kaminatsui
Really excited to share our latest work led by @mattiaubertini.bsky.social and @nesslfy.bsky.social: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication.
www.biorxiv.org/content/10.1...
A🧵👇
www.biorxiv.org/content/10.1...
A🧵👇
September 24, 2025 at 9:45 PM
Really excited to share our latest work led by @mattiaubertini.bsky.social and @nesslfy.bsky.social: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication.
www.biorxiv.org/content/10.1...
A🧵👇
www.biorxiv.org/content/10.1...
A🧵👇
Reposted by Nayuta Yakushiji-Kaminatsui
We published a detailed protocol for our Plate-CUT&Tag method on @protocolsio.bsky.social to accompany our recent preprint (www.biorxiv.org/content/10.1...) give it a try! Feedback welcome! dx.doi.org/10.17504/protocols.io.n2bvjed5wgk5/v1
Plate CUT&Tag (Meers Lab version)
This protocol describes a method for carrying out CUT&Tag-Direct in 96 well microplates for high-throughput processing of samples by a single operator with only standard lab...
dx.doi.org
September 22, 2025 at 5:45 PM
We published a detailed protocol for our Plate-CUT&Tag method on @protocolsio.bsky.social to accompany our recent preprint (www.biorxiv.org/content/10.1...) give it a try! Feedback welcome! dx.doi.org/10.17504/protocols.io.n2bvjed5wgk5/v1
Reposted by Nayuta Yakushiji-Kaminatsui
Our work exploring a new explanation for the regulation of Hoxd genes and the #fin-to-limb transition. 🧪
It was an absolute joy working on this w/ @aurhin.bsky.social and @homeobox.bsky.social @denisduboule.bsky.social @neilshubin.bsky.social
#evo-devo #InHoxWeTrust
It was an absolute joy working on this w/ @aurhin.bsky.social and @homeobox.bsky.social @denisduboule.bsky.social @neilshubin.bsky.social
#evo-devo #InHoxWeTrust
How Did Hands Evolve? The Answer Is Behind You.
www.nytimes.com
September 17, 2025 at 5:31 PM
Our work exploring a new explanation for the regulation of Hoxd genes and the #fin-to-limb transition. 🧪
It was an absolute joy working on this w/ @aurhin.bsky.social and @homeobox.bsky.social @denisduboule.bsky.social @neilshubin.bsky.social
#evo-devo #InHoxWeTrust
It was an absolute joy working on this w/ @aurhin.bsky.social and @homeobox.bsky.social @denisduboule.bsky.social @neilshubin.bsky.social
#evo-devo #InHoxWeTrust
Reposted by Nayuta Yakushiji-Kaminatsui
Are digits modified fins, or evolutionary innovations? Read how we tackled this old question from a new angle🧪
A story with @chasebolt.bsky.social, @homeobox.bsky.social and myself, coordinated by @denisduboule.bsky.social from @college-de-france.fr and published in @nature.com today!
#InHoxWeTrust
A story with @chasebolt.bsky.social, @homeobox.bsky.social and myself, coordinated by @denisduboule.bsky.social from @college-de-france.fr and published in @nature.com today!
#InHoxWeTrust
September 17, 2025 at 5:26 PM
Are digits modified fins, or evolutionary innovations? Read how we tackled this old question from a new angle🧪
A story with @chasebolt.bsky.social, @homeobox.bsky.social and myself, coordinated by @denisduboule.bsky.social from @college-de-france.fr and published in @nature.com today!
#InHoxWeTrust
A story with @chasebolt.bsky.social, @homeobox.bsky.social and myself, coordinated by @denisduboule.bsky.social from @college-de-france.fr and published in @nature.com today!
#InHoxWeTrust
Reposted by Nayuta Yakushiji-Kaminatsui
Out today. 🙏 again to everyone for this wonderful piece of work, in particular to Aurelie @aurhin.bsky.social Chase @chasebolt.bsky.social and Brent @homeobox.bsky.social. 🙏 also to the Harris lab @fish4walking.bsky.social and @neilshubin.bsky.social @biology-unige.bsky.social @college-de-france.fr
September 17, 2025 at 5:30 PM
Out today. 🙏 again to everyone for this wonderful piece of work, in particular to Aurelie @aurhin.bsky.social Chase @chasebolt.bsky.social and Brent @homeobox.bsky.social. 🙏 also to the Harris lab @fish4walking.bsky.social and @neilshubin.bsky.social @biology-unige.bsky.social @college-de-france.fr
Reposted by Nayuta Yakushiji-Kaminatsui
CUT&TIME captures the history of open chromatin indeveloping neurons https://www.biorxiv.org/content/10.1101/2025.08.29.673195v1
September 1, 2025 at 6:31 AM
CUT&TIME captures the history of open chromatin indeveloping neurons https://www.biorxiv.org/content/10.1101/2025.08.29.673195v1
Reposted by Nayuta Yakushiji-Kaminatsui
#Preprint alert! 📣
We are thrilled to share the work led by Lara Zorro-Shahidian and Lucio di Filippo, in which we show that #MLL2 controls gene expression in both #ESC and upon #differentiation by facilitating the #enhancer like activity of #LINE1 elements
www.biorxiv.org/cgi/content/...
We are thrilled to share the work led by Lara Zorro-Shahidian and Lucio di Filippo, in which we show that #MLL2 controls gene expression in both #ESC and upon #differentiation by facilitating the #enhancer like activity of #LINE1 elements
www.biorxiv.org/cgi/content/...
MLL2 facilitates long-range gene regulation through LINE1 elements
Transcriptional regulation is tightly linked to chromatin organization, with H3K4me3 commonly marking both active and bivalent promoters. In embryonic stem cells (ESC), MLL2 is essential for H3K4me3 d...
www.biorxiv.org
August 13, 2025 at 5:54 AM
#Preprint alert! 📣
We are thrilled to share the work led by Lara Zorro-Shahidian and Lucio di Filippo, in which we show that #MLL2 controls gene expression in both #ESC and upon #differentiation by facilitating the #enhancer like activity of #LINE1 elements
www.biorxiv.org/cgi/content/...
We are thrilled to share the work led by Lara Zorro-Shahidian and Lucio di Filippo, in which we show that #MLL2 controls gene expression in both #ESC and upon #differentiation by facilitating the #enhancer like activity of #LINE1 elements
www.biorxiv.org/cgi/content/...
Reposted by Nayuta Yakushiji-Kaminatsui
MLL2 facilitates long-range gene regulation through LINE1 elements https://www.biorxiv.org/content/10.1101/2025.08.10.669526v1
August 12, 2025 at 9:32 PM
MLL2 facilitates long-range gene regulation through LINE1 elements https://www.biorxiv.org/content/10.1101/2025.08.10.669526v1
Reposted by Nayuta Yakushiji-Kaminatsui
Online Now: Single-stranded DNA-binding proteins are essential components of the architectural LDB1 protein complex Online now:
Single-stranded DNA-binding proteins are essential components of the architectural LDB1 protein complex
Wang et al. show that the architectural protein LDB1 forms a complex with single-stranded DNA-binding proteins (SSBPs) in vitro and in vivo. SSBP3 stabilizes LDB1 self-interactions to support chromatin loop formation.
dlvr.it
August 12, 2025 at 7:14 PM
Online Now: Single-stranded DNA-binding proteins are essential components of the architectural LDB1 protein complex Online now:
Reposted by Nayuta Yakushiji-Kaminatsui
Chromatin-dependent motif syntax defines differentiation trajectories
Chromatin-dependent motif syntax defines differentiation trajectories
Durdu et al. crack the code of transcription-factor specificity by integrating chromatin context and motif syntax, validated by targeted assays. Focusing on NGN2 and MyoD1, they develop predictive models, distinguish functional binding from millions of potentials, and uncover generalizable rules explaining how transcription factors drive distinct cell fates.
dlvr.it
August 11, 2025 at 3:20 PM
Chromatin-dependent motif syntax defines differentiation trajectories
Reposted by Nayuta Yakushiji-Kaminatsui
Excited to share the latest work from the lab led by @eharo84.bsky.social, in which we have used synthetic biology to explore the mechanisms by which different types of long-range enhancers ensure robust and precise developmental gene expression
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Synthetic engineering demonstrates that synergy among enhancers involves an increase in transcriptionally productive enhancer-gene contacts
Enhancers are non-coding cis-regulatory elements that control the expression of distally located genes in a tissue- and time-specific manner. Recent studies indicate that enhancers can differ in their...
www.biorxiv.org
August 11, 2025 at 2:56 PM
Excited to share the latest work from the lab led by @eharo84.bsky.social, in which we have used synthetic biology to explore the mechanisms by which different types of long-range enhancers ensure robust and precise developmental gene expression
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Nayuta Yakushiji-Kaminatsui
🧪Move over CUT&Tag, there’s a new #TranscriptionFactor mapping method in town.
Our newly developed DynaTag is faster, cleaner, more sensitive than #ChIPseq, #CUT&RUN and #CUT&Tag.
🔗 Our @natcomms.nature.com paper: www.nature.com/articles/s41...
🧵Let’s break down what makes DynaTag so powerful (1/7)
Our newly developed DynaTag is faster, cleaner, more sensitive than #ChIPseq, #CUT&RUN and #CUT&Tag.
🔗 Our @natcomms.nature.com paper: www.nature.com/articles/s41...
🧵Let’s break down what makes DynaTag so powerful (1/7)
July 28, 2025 at 9:10 AM
🧪Move over CUT&Tag, there’s a new #TranscriptionFactor mapping method in town.
Our newly developed DynaTag is faster, cleaner, more sensitive than #ChIPseq, #CUT&RUN and #CUT&Tag.
🔗 Our @natcomms.nature.com paper: www.nature.com/articles/s41...
🧵Let’s break down what makes DynaTag so powerful (1/7)
Our newly developed DynaTag is faster, cleaner, more sensitive than #ChIPseq, #CUT&RUN and #CUT&Tag.
🔗 Our @natcomms.nature.com paper: www.nature.com/articles/s41...
🧵Let’s break down what makes DynaTag so powerful (1/7)
Reposted by Nayuta Yakushiji-Kaminatsui
Extremely proud to share the PhD work of @mariamafau.bsky.social in which we have investigated the role of ZIC2 during neural induction.
It turns out that ZIC2 has a dual life, first as a promiscuous pioneer and then as a lineage-specific activator.
Find out more here 👇
bsky.app/profile/mari...
It turns out that ZIC2 has a dual life, first as a promiscuous pioneer and then as a lineage-specific activator.
Find out more here 👇
bsky.app/profile/mari...
Thrilled to share the story stemming from my PhD!
We used mESC neural differentiation, genome editing and bulk & single-cell approaches to uncover how ZIC2 controls early neural fate by playing a dual and sequential regulatory role as a promiscous pioneer and a selective lineage-specific activator.
We used mESC neural differentiation, genome editing and bulk & single-cell approaches to uncover how ZIC2 controls early neural fate by playing a dual and sequential regulatory role as a promiscous pioneer and a selective lineage-specific activator.
July 24, 2025 at 8:51 PM
Extremely proud to share the PhD work of @mariamafau.bsky.social in which we have investigated the role of ZIC2 during neural induction.
It turns out that ZIC2 has a dual life, first as a promiscuous pioneer and then as a lineage-specific activator.
Find out more here 👇
bsky.app/profile/mari...
It turns out that ZIC2 has a dual life, first as a promiscuous pioneer and then as a lineage-specific activator.
Find out more here 👇
bsky.app/profile/mari...
Reposted by Nayuta Yakushiji-Kaminatsui
Dual role of ZIC2 during neural induction: from pioneer transcription factor to enhancer activator https://www.biorxiv.org/content/10.1101/2025.07.23.666365v1
July 24, 2025 at 8:33 AM
Dual role of ZIC2 during neural induction: from pioneer transcription factor to enhancer activator https://www.biorxiv.org/content/10.1101/2025.07.23.666365v1
Reposted by Nayuta Yakushiji-Kaminatsui
Our first bat story is out! What turns a limb into a wing? Evolution's most impressive adaptation. The massive difference is achieved by small changes and the re-purposing of existing pathways - the principle of parsimony! Meis2 gene, normally expressed in proximal limb gets expressed distally.
July 24, 2025 at 9:13 AM
Our first bat story is out! What turns a limb into a wing? Evolution's most impressive adaptation. The massive difference is achieved by small changes and the re-purposing of existing pathways - the principle of parsimony! Meis2 gene, normally expressed in proximal limb gets expressed distally.
The official website is now open. I’m looking forward to meeting lots of limb researchers in Tokyo 🌸🐓🐀🐟🦎
cscenter.co.jp/limbdev26/
cscenter.co.jp/limbdev26/
Limb Development and Regeneration
cscenter.co.jp
July 24, 2025 at 9:09 AM
The official website is now open. I’m looking forward to meeting lots of limb researchers in Tokyo 🌸🐓🐀🐟🦎
cscenter.co.jp/limbdev26/
cscenter.co.jp/limbdev26/
Reposted by Nayuta Yakushiji-Kaminatsui
Excited to share our hot-off-the-press @biorxivpreprint.bsky.social
that explores how PRC1-mediated H2AK119ub deposition safeguards lineage fidelity during forebrain development. Fantastic work by @lucyadoyle.bsky.social and our colleagues & collaborators. 🥳🧬🧠🔬
www.biorxiv.org/content/10.1...
that explores how PRC1-mediated H2AK119ub deposition safeguards lineage fidelity during forebrain development. Fantastic work by @lucyadoyle.bsky.social and our colleagues & collaborators. 🥳🧬🧠🔬
www.biorxiv.org/content/10.1...
H2AK119ub Safeguards Against Ectopic Transcription Factor Mediated Gene Activation in the Developing Forebrain
The PRC1 complex regulates developmental gene expression in mammals by ubiquitinating histones (H2AK119ub) and nucleating repressive chromatin interactions. Human genetic data and functional experimen...
www.biorxiv.org
July 12, 2025 at 12:50 AM
Excited to share our hot-off-the-press @biorxivpreprint.bsky.social
that explores how PRC1-mediated H2AK119ub deposition safeguards lineage fidelity during forebrain development. Fantastic work by @lucyadoyle.bsky.social and our colleagues & collaborators. 🥳🧬🧠🔬
www.biorxiv.org/content/10.1...
that explores how PRC1-mediated H2AK119ub deposition safeguards lineage fidelity during forebrain development. Fantastic work by @lucyadoyle.bsky.social and our colleagues & collaborators. 🥳🧬🧠🔬
www.biorxiv.org/content/10.1...