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Takashi Fukaya

@fukayalab.bsky.social
1K followers 308 following 43 posts

Institute for Quantitative Biosciences, UTokyo. Mechanism of transcriptional regulation in the early embryo. sites.google.com/view/fukaya-lab-iq…

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Reposted by Takashi Fukaya
Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 13/09/2026
Fold Spacer lets you fly through protein structures (Weekend project #2). It’s my first game: I originally set out to build a racer with structures as the tracks, but was a little too crazy. So it became this instead. You can upload your own structures. 🌐 martin-steinegger.github.io/Fold-Spacer/
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Takashi Fukaya @fukayalab.bsky.social · 04/09/2026
Happy to have contributed to the in vivo local translation part of this study using APEX-Ribo-Seq in Drosophila! www.biorxiv.org/content/10.1...
biorxiv.org
Sequence features and dynamics of subcellular translation revealed by APEX-Ribo-Seq
Local translation at specific subcellular regions is proposed to define appropriate protein destinations and functions. However, our understanding of local translation still remains far from complete ...
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Takashi Fukaya @fukayalab.bsky.social · 22/08/2026
youtu.be/56EG957YinM?...
youtu.be
PAPERS
YouTube video by yoshinaoよしながき
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Takashi Fukaya @fukayalab.bsky.social · 22/08/2026
youtu.be/pRgHYWOtqqc?...
youtu.be
Angine de Poitrine - Fabienk (Live on KEXP)
YouTube video by KEXP
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Reposted by Takashi Fukaya
Jack Bateman @jbateman01.bsky.social · 19/08/2026
Single-cell 3D genome imaging shows super-enhancer hubs are rare, nonspecific, and neither necessary nor sufficient for transcriptional bursting www.cell.com/cell-genomic...?
cell.com
Single-cell 3D genome imaging shows super-enhancer hubs are rare, nonspecific, and neither necessary nor sufficient for transcriptional bursting
Super-enhancers have been proposed to cluster in the nucleus when compared to other genomic elements. Le et al. found that super-enhancer clustering was rare and driven by non-specific interactions. P...
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Reposted by Takashi Fukaya
Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 15/07/2026
Our preprint is now out in @natgenet.nature.com ! doi.org/10.1038/s415... We measured Sox2 promoter bursting dynamics with the SCR enhancer positioned at different distances within a genomic locus devoid of confounding effects in mESC: Main findings in the 🧵 below:
doi.org
Enhancer control of promoter activity and variability via frequency modulation of clustered transcriptional bursts - Nature Genetics
Tünnermann et al. use live-cell imaging to study promoter activity under the control of an enhancer inserted at different genomic distances. RNA production from the promoter occurs in clusters of tran...
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Reposted by Takashi Fukaya
Elias Friman @eliasfriman.bsky.social · 11/05/2026
Is distal gene activation by enhancers inherently different from promoter-proximal activation? We propose not. But both cohesin and cooperativity are important aspects of how transcription is affected. Happy to share our recent preprint (thread below) 1/ www.biorxiv.org/content/10.6...
biorxiv.org
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Takashi Fukaya @fukayalab.bsky.social · 06/07/2026
We have an open professor position at my institute, the Institute for Quantitative Biosciences, The University of Tokyo! www.iqb.u-tokyo.ac.jp/recruiting/2...
iqb.u-tokyo.ac.jp
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Reposted by Takashi Fukaya
Joachim Goedhart @joachimgoedhart.bsky.social · 01/07/2026
A High-Affinity Nanobody Recognizing mNeonGreen Enables Versatile Biochemical, Cellular, and in vivo Applications. by Steffen Frey and team: www.biorxiv.org/content/10.6...
mNeonGreen Selector: a pulldown resin for mNeonGreen-fusion proteins. (A) Sketch of mNG
Selector binding mNG fusion proteins. (B, C) Immunoprecipitation from E.coli lysate in the presence (B) or
absence (C) of target protein (mNG-Halo fusion, arrowhead). Proteins were eluted in boiling SDS sample
buffer. mNG Selector enables highly specific one-step capture of mNG-tagged proteins. (D) Binding assay to
evaluate the cross-reactivity of the mNG Selector to other recombinant fluorescent proteins. Shown is a figure
of the equilibrium bound fraction of each indicated fluorescent protein prior to buffer washing. (E)
Compatibility of mNG Selector to various reagents applied during binding (top panel) or during washing steps
(lower panel). mNG fluorescence is lost in the presence of 2 M Gua-HCl. The symbols below each row indicate
binding efficiency: ++: strong binding, + binding, -: no binding
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Takashi Fukaya @fukayalab.bsky.social · 27/06/2026
Look forward to visiting IMP in Vienna on June 30 (Tue)!! www.imp.ac.at/calendar/eve...
imp.ac.at
Dynamics of ultra-long-range enhancer-promoter communication in early embryos
Dynamics of ultra-long-range enhancer-promoter communication in early embryos
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Takashi Fukaya @fukayalab.bsky.social · 26/06/2026
Thanks Claudio @claudiocantu81.bsky.social and Silvia @remeseiro-lab.bsky.social for having me as a lecturer at the PALS Summer School. It was such a wonderful meeting!!
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Reposted by Takashi Fukaya
Claudio Cantù @claudiocantu81.bsky.social · 24/06/2026
What a Start of the PALS Summer School in Transcriptomics with Prof. Silvia Nicolis @btbsunimib.bsky.social on Transcription factors in the brain and Prof. @fukayalab.bsky.social @utokyoofficial.bsky.social on enhancers imaging @remeseiro-lab.bsky.social @scilifelab.se @kawresearch.bsky.social
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Takashi Fukaya @fukayalab.bsky.social · 23/06/2026
Excited to join the PALS Summer School as a lecturer! Looking forward to meeting and interacting with young students and researchers!! event.trippus.net/Home/Index/A...
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Takashi Fukaya @fukayalab.bsky.social · 23/06/2026
We named three newly identified genes as boundary-associated factors! www.science.org/doi/10.1126/...
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Anders Sejr Hansen @andersshansen.bsky.social · 22/06/2026
(1/n) Very excited to share tri-lab collab (Mirny & Zechner) led by Harvey, Henrik & Jack: Q: How do enhancers & promoters interact in space (contact vs. action-at-a-distance) and time (stable vs. transient)? A: Transient E-P contact (~25-42 nm lasting ~10-20 sec): www.biorxiv.org/content/10.6...
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Takashi Fukaya @fukayalab.bsky.social · 20/06/2026
Looking forward to discussing our new studies at Karolinska Institute next Monday, June 22! news.ki.se/calendar/gue...
news.ki.se
Guest seminar - Takashi Fukaya
Title: “Dynamics of ultra-long-range enhancer-promoter communication in early embryos”. Monday, June 22 at 10:30 in room D1012, Biomedicum.
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Takashi Fukaya @fukayalab.bsky.social · 15/06/2026
Huge thanks to Mounia @laghalab.bsky.social for a fantastic seminar! So many exciting unpublished stories!!
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Takashi Fukaya @fukayalab.bsky.social · 04/06/2026
Excited to host Mounia Lagha (IGMM, Montpellier) @laghalab.bsky.social IQB on June 15 (Mon)! Everyone is welcome, including non-IQB members. Hope to see you there!!
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Reposted by Takashi Fukaya
Karolin Luger @nucleosomepolice.bsky.social · 08/05/2026
Sad news - he certainly was a towering figure with many influential discoveries - see below. Why he was never awarded the 'big' prize is truly baffling, but his many contributions to science will be remembered much longer than any prize. Thank you @alexis-verger.cpesr.fr for putting this together.
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Takashi Fukaya @fukayalab.bsky.social · 07/05/2026
www.youtube.com/watch?v=Nxtv...
youtube.com
Ohio Players. Sweet Sticky Thing
YouTube video by CJ'z GROOVE-A-THON
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Takashi Fukaya @fukayalab.bsky.social · 03/05/2026
New preprint alert! Together with Tetsuya Yamamoto at Hokkaido University, we propose a “polymer micelle” model of transcriptional bursting. www.biorxiv.org/content/10.6...
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Takashi Fukaya @fukayalab.bsky.social · 06/04/2026
www.youtube.com/watch?v=VRj8...
youtube.com
Numb (Live In - Studio Performance) / Shintaro Sakamoto (zelone official)
YouTube video by zelonerecords
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Takashi Fukaya @fukayalab.bsky.social · 02/04/2026
Happy to have been part of the study! “Transient residence of the repulsive client Shutdown in Yb bodies plays a critical role in Piwi-piRISC biogenesis and maintaining fertility” www.cell.com/molecular-ce...
cell.com
Transient residence of the repulsive client Shutdown in Yb bodies plays a critical role in Piwi-piRISC biogenesis and maintaining fertility
Hirakata et al. reveal that Shutdown rapidly returns from Yb bodies to the cytosol through its repulsive N-terminal property. This dynamic release enables piRNA maturation and safeguards fertility, pr...
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Takashi Fukaya @fukayalab.bsky.social · 02/04/2026
IQB seminar today! Open to everyone. Feel free to drop by!!
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Takashi Fukaya @fukayalab.bsky.social · 25/03/2026
Very much looking forward to it!!
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Takashi Fukaya @fukayalab.bsky.social · 25/03/2026
Another seminar announcement! We are excited to host Hernan Garcia (UC Berkeley) at IQB on April 2nd (Thu). Everyone is welcome to join!!
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Takashi Fukaya @fukayalab.bsky.social · 23/03/2026
Excited to host Evgeny Kvon (UC Irvine) @evgenykvon.bsky.social at IQB on March 30 (Mon)! Everyone is welcome, including non-IQB members. Hope to see you there!! 来週3/30月曜に、UC IrvineのEvgeny Kvonさんのセミナーを開催します!定量研外からの参加もウェルカムですので、是非ご参加ください!!
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Reposted by Takashi Fukaya
Tineke Lenstra @tinekelenstra.bsky.social · 12/03/2026
Ever wondered how a eukaryotic transcription factor finds its specific DNA motif in the vast genome? In this preprint, we directly measured the dynamics of this search process in living cells, revealing a cooperative mechanism mediated by disordered regions. 1/10 doi.org/10.64898/202...
doi.org
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Takashi Fukaya @fukayalab.bsky.social · 06/03/2026
The Karolinska-UTokyo Joint PhD Course has wrapped up! It was a real pleasure serving as a course director and interacting with such talented students. Excited to see how your research grows from here!!
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Takashi Fukaya @fukayalab.bsky.social · 04/03/2026
Thanks Ibrahim for stimulating talk and discussion!!
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Takashi Fukaya @fukayalab.bsky.social · 27/02/2026
Diving into evolutionary biology! What is the origin of the most abundant class of insect transcription factors, ZAD-ZnFs? We suggest that they evolved from ancestral insulator-binding proteins that control 3D genome topology. www.science.org/doi/10.1126/...
science.org
Decoding the molecular logic of rapidly evolving ZAD zinc finger proteins in Drosophila
Identification of ZAD-ZnF genes as key regulators of genome organization during Drosophila embryogenesis.
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Takashi Fukaya @fukayalab.bsky.social · 24/02/2026
We are excited to host Ibrahim Cissé (Director, Max Planck Institute of Immunobiology & Epigenetics) at IQB, on March 3 (Tue)!!
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Reposted by Takashi Fukaya
Ben Sabari @bsabari.bsky.social · 06/02/2026
I am excited to share a new review @cp-molcell.bsky.social written in collaboration with @tanjamittag.bsky.social , Mikayla Eppert, and Ambuja Navalkar where we review the current evidence for and against the role of density transitions in regulating transcription www.cell.com/molecular-ce...
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Takashi Fukaya @fukayalab.bsky.social · 05/02/2026
New preprint from the lab! We identify the ZnF protein Mulberry as a condensation-dependent structural regulator of genome topology that organizes “multi-way regulatory hubs” in early Drosophila embryos. www.biorxiv.org/content/10.6...
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Reposted by Takashi Fukaya
Job Dekker @jobdekker.bsky.social · 03/02/2026
Terrific paper on a new chromosomal compartment where extensive loop extrusion isolates domains from other such domains
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Hannah Long @hannahlong.bsky.social · 10/11/2025
📣 Paper alert! I am delighted that our paper exploring the impact of Neanderthal-derived variants on the activity of a disease-associated craniofacial enhancer has been published in Development today! journals.biologists.com/dev/article/...
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Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 08/09/2025
Become our colleague at @fmiscience.bsky.social! The FMI is a very special place to start your lab: a vibrant international institute with world-class research groups and facilities, core funding, fantastic trainees, great colleagues😅, and a collegial culture. Get in touch if you're interested!
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Takashi Fukaya @fukayalab.bsky.social · 31/08/2025
Fun visit to Rockefeller after the CSHL transcription meeting. It was great to catch up with Bob Roeder since his visit to Japan for the Kyoto Prize!
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Nature @nature.com · 07/07/2025
Japan is the only country in the world that legally requires married couples to share the same family name go.nature.com/4lfbXPL
go.nature.com
Japan requires name change after marriage — with big effects on female scientists
Nature - Survey finds law requiring married couples to share the same family name causes havoc for researchers.
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Takashi Fukaya @fukayalab.bsky.social · 06/07/2025
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...
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Grace Bower @gracebower.bsky.social · 02/07/2025
A dream come true: my first first-author publication! 🧬 🎉 Working to unravel the mysteries of long-range gene regulation has been an incredible journey. Endless gratitude to Evgeny, the lab, and all of the amazing collaborators who helped make this happen 🙌
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Takashi Fukaya @fukayalab.bsky.social · 28/06/2025
Looks like I’m going to miss my flight from Frankfurt to Tokyo because of a delay at Basel airport🥺
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Takashi Fukaya @fukayalab.bsky.social · 27/06/2025
Thanks Luca @lucagiorgetti.bsky.social for hosting me at FMI. It was absolutely a fun visit and I got many nice feedback!
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Takashi Fukaya @fukayalab.bsky.social · 26/06/2025
Giving a seminar at FMI Basel tomorrow! Looking forward to it!!
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Mannervik Lab @mannerviklab.bsky.social · 18/06/2025
Curious about epigenetics, gene regulation, and developmental biology? Apply for the PhD position in Mannervik lab at Stockholm University! We use single-cell genomics and genetic approaches to uncover how cells acquire their identities during development. Explore the chromatin landscape with us!
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Takashi Fukaya @fukayalab.bsky.social · 20/06/2025
Look forward to visiting University of Lausanne next week!
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Takashi Fukaya @fukayalab.bsky.social · 25/05/2025
Pachypodium gracilius has finally bloomed with yellow flowers after seven years of growing it from seed. パキポディウム グラキリス、種から育てて7年、黄色い花が咲きました。
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Takashi Fukaya @fukayalab.bsky.social · 22/05/2025
Delighted 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...
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Anton Goloborodko @golobor.bsky.social · 11/04/2025
Earnshaw, Goloborodko, Dekker & Mirny labs are excited to present our latest work, "Rules of engagement for condensins and cohesins guide mitotic chromosome formation" - now accepted!! www.science.org/doi/10.1126/... A short clip describing the key results: www.youtube.com/watch?v=pmvO...
youtube.com
Rules of Engagement
YouTube video by Johan Gibcus
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Takashi Fukaya @fukayalab.bsky.social · 13/04/2025
Nice to catch up with Luca @lucagiorgetti.bsky.social in Tokyo!
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