Institute for Quantitative Biosciences, UTokyo. We study the mechanism of transcriptional regulation in the Drosophila embryo.
Tokyo-to, Japan
Joined September 2019
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Takashi Fukaya retweeted
The Nozaki Lab at UMass Amherst is recruiting graduate students! We study chromosome dynamics and meiosis using live-cell imaging. Apply through MCB or Plant Biology. Both programs welcome! Any questions? Feel free to DM me. nozakilab.org/
#Chromosome #Meiosis #Imaging
Takashi Fukaya retweeted
1/12 CTCF has updated its LinkedIn again! Our preprint tracks CTCF's “career” across Bilateria.
From DNA-binding to transcription regulation & genome architecture. Read it: biorxiv.org/content/10.64898…
And back-to-back work from Darío Lupiáñez's group: biorxiv.org/content/10.64898…
vvv
Takashi Fukaya retweeted
Integration by parts: the multi-layered mechanisms of cis-regulatory control. Check out this review by @jake_cs_ @briscoejames & @joadelas in @molecularcell #ASHG26 hubs.ly/Q04BHsSC0
Takashi Fukaya retweeted
Excited to share a preprint on the structural mechanism of transcriptional activation by human Mediator, studied using integrative structural modeling.
Many thanks to Lacra Bintu @BintuLacra for helpful discussions!
biorxiv.org/content/10.64898…
@generegulation @MED_COMPLEX
Takashi Fukaya retweeted
An excellent story on condensate ageing and amyloid fibril.
For FUS, ageing condensates become glassy and arrested, while amyloid fibres grow mostly in the dilute phase outside them.
Two distinct solid states coexist without directly interconverting.
Fibres are thought to emerge from a dense protein condensate ageing into a glassy state. It is now shown that protein fibres and glassy condensates may result from two competing ageing pathways.
nature.com/articles/s41567-0…
Takashi Fukaya retweeted
Design of synthetic activators for programmable
gene expression
doi.org/10.64898/2026.10.19.…
Takashi Fukaya retweeted
Thrilled to share my freshly "baked" Baker lab paper. We took a bottom-up approach to designing transcriptional regulators. Instead of relying on natural activation domains, we designed compact proteins that recruit specific cofactors. Activators for now, repressors to come!
Takashi Fukaya retweeted
Ever wanted to watch chromosomes fold?
lefsim simulates loop extrusion live in your browser. Add, remove and drag CTCF sites around, watch contact maps emerge, and more.
lefsim.abdenlab.org
Takashi Fukaya retweeted
Transcription factor specificity isn’t encoded by DNA motifs alone. Live-cell single-molecule imaging shows that unstructured transcription factor interactions enable emergent specificity.
science.org/doi/10.1126/scie…
Takashi Fukaya retweeted
New Online! Scaling up measurements of the interactions that build condensates dlvr.it/TVv4S9
Takashi Fukaya retweeted
Nifty new paper on supercoiling influence in C. elegans!
"Genome architecture shapes transcriptional responses to topoisomerase depletion in C. elegans." work from Morao et al. link below 👇
Takashi Fukaya retweeted
Intraspecific sequence variation and complete genomes refine the identification of rapidly evolved regions in humans dlvr.it/TVw7SB
Takashi Fukaya retweeted
A bright protein cluster inside a nucleus is not, by itself, evidence for a liquid droplet.
In living fruit-fly embryos, researchers watched Dorsal, a protein that helps regulate the developing body plan. They changed the number of places it could bind on regulatory DNA. More binding sites produced stronger, more persistent local protein accumulations.
A model based on binding, diffusion and cooperation between nearby binding events reproduced key features without requiring proteins to form a separate liquid-like phase.
The result does not rule out droplets elsewhere. It gives a concrete alternative to test: perhaps the DNA binding sites help explain the crowd.
New Science Advances paper:
doi.org/10.1126/sciadv.aeh10…
Takashi Fukaya retweeted
Our Department of Developmental & Cell Biology
@UCIBioSci @UCIrvine is looking for a Professor & Chair! Join our diverse and collegial team in the premier UC public system. Dept: devcell.bio.uci.edu/
Details: recruit.ap.uci.edu/JPF10452
Takashi Fukaya retweeted
Check out our new preprint led by @mileshuseyin unexpectedly discovering Polycomb 3D interactions independent of cPRC1.
Miles led this ambitious study. He's also on the faculty job market, and I can't recommend him highly enough for important and comprehensive science!
1/9) Excited to share my preprint on Polycomb 3D chromatin interactions from my postdoc with @Anders_S_Hansen!
We were surprised to find that canonical PRC1 doesn't seem to be the only contributor to these interactions:
biorxiv.org/content/10.64898…
Takashi Fukaya retweeted
Are weak TF motifs important? @ZeitlingerLab use deep learning to systematically map low-affinity pioneer binding sites in mESCs and show that they cooperate with strong motifs to open chromatin. Preview w/ @gracecbower: cell.com/cell-genomics/fullt… Paper: cell.com/cell-genomics/fullt…
Takashi Fukaya retweeted
Very interesting historical perspective on cohesin and its role in transcriptional regulation:
link.springer.com/article/10…
