Takashi Fukaya

Institute for Quantitative Biosciences, UTokyo. We study the mechanism of transcriptional regulation in the Drosophila embryo.

[Takashi Fukaya @FukayaLab]

How do distal enhancers control transcription dynamics in living cells? Check out our latest work published in @MolecularCell!! We show that the dynamic assembly and disassembly of TF clusters at enhancers are a major source of transcriptional bursting. https://t.co/vpOSWJAfBq

[Molecular Cell @MolecularCell]

Online Now: A sequence-encoded promoter-proximal super pause stabilizes an offline RNA polymerase II state dlvr.​it/TWHrfz

[Žiga Avsec @Avsecz]

AlphaGenome 2 is live! A step change in performance and new capabilities over AG1! @adamgayoso's thread covers the key results.

Manuscript: https://t.co/exVx6kxCxY
Blog: https://t.co/YkuyxDHs0D
API: https://t.co/I7zaZobbLx

A few notes under the hood & what's next:

[九州大学動物繁殖生理学研究室 @Kyushu_miyamoto]

We are thrilled to announce that our paper has been published in @Nature.
Nuclei become soft for starting life!

https://t.co/GBgxkzy7O0

[Gene Regulation @generegulation]

Guo et al, 2026. P-TEFb regulates nucleosome positioning at promoters https://t.co/IhsO8EvrMr
➡️Inhibition of P-TEFb, the kinase component of the super elongation complex (SEC), disrupts nucleosome positioning and leads to cryptic transcription within the early elongation zone

[Molecular Cell @MolecularCell]

Inherent electrochemical activity of extrachromosomal DNA hub shapes spatial redox environment in nucleus dlvr.​it/TWDSDl

[Archit Ghosh, PhD @ArchitGhosh1]

SWI/SNF complexes shape 3D chromatin architecture through CTCF and cohesin. @Nature https://t.co/n9iNc5HRlz

[Cell Reports @CellReports]

Sex-biased enhancers shape transcriptional sex differences across human tissues dlvr.​it/TWCd06

[Wesley Wong Lab @WesleyWongLab]

Out today in Science! With FIND each drug candidate gets its own experiment on a DNA nanoswitch—billions per tube—to find molecules that change how proteins interact, not just bind a target. Congrats to Clinton Hansen, Mark Lipstein & the rest of our team! https://t.co/iqBdqQKm2g

[Selena Setsu @sesameandrea]

Our preprint is out on bioRxiv! We measured monomeric protein yield in E. coli at scale and built predictors to help guide protein design. Huge thanks to all my co-authors and collaborators! 1/6
https://t.co/H0yNuvgrJ6

[Kotaro Tsuboyama @KotaroTsuboyama]

We can now design all kinds of fancy de novo proteins. But can we produce them at scale, at a reasonable cost, and without extensive optimization? That’s what got this project started. Our preprint is now out! Much of the work was led by Selena @sesameandrea  and Kaori. 1/8

[Julia Zeitlinger (@[email protected]) @JuliaZeitlinger]

Apply to our Ph.D. program! Deadline is December 1 (no application fee).

[Michael Perry @michaelwperry]

1/ We built a fruit fly with butterfly eyes!

Then we found out its brain already knew what to do with them.

New paper out in Science Advances.

[Sergey Ovchinnikov @sokrypton]

https://t.co/7OlBz2wKP1 updated to include:
- bioemu2 @FrankNoeBerlin
- mol1 @MolenceBio
- fastplm (confidence modules for esmfold fast models) @Logan_Hallee
- af3x crosslinks @jankosinski
- faster diffusion (exponential update and geometric noise schedule) @vinay_matt

[Kazuhiro Maeshima @kazu_maeshima]

Our new paper @CellReports, led by @katsu_s_minami et al.! 🎉🧬🔬
https://t.co/CrVCefnASc
Machine learning-assisted Repli-Histo labeling and single-nucleosome imaging reveal distinct transcription-dependent chromatin constraints across euchromatin and heterochromatin. Congrats!

[Takashi Fukaya @FukayaLab]

https://t.co/uyq5jlZ3c4

[Frank Noe @FrankNoeBerlin]

Public preview of BioEmu2! @MSFTResearch AI for Science’s new foundation model for biomolecular structure, dynamics and function. Open weights, MIT license.
https://t.co/wsqcLPh8Sk

Movie: BioEmu2-simulated binding of intrinsically disordered peptide PUMA to MCL-1 receptor. 🧵⬇️

[ISHIGURO Lab @IshiguroL]

Our study on OMC1 is now published in Nature Aging!
We discovered an oocyte-specific protein that helps maintain chromosome cohesion throughout reproductive life.
https://t.co/yESOKU4Srn

[Tadasu Nozaki @tadasu443]

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. https://t.co/Y03YbCPJ39
#Chromosome #Meiosis #Imaging

[minja @minjaf]

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: https://t.co/IqT3FitijD

And back-to-back work from Darío Lupiáñez's group: https://t.co/rzNiwHafae

vvv

[Takashi Fukaya @FukayaLab]

https://t.co/f2yxsEyFfd

[Takashi Fukaya @FukayaLab]

羊土社より出版された理系総合のための生命科学第6版、４章「遺伝子の発現1」を担当しました。セントラルグマの記載について、1957年のCrickによるオリジナルの定義に従い、「配列情報の一方向性」を示すものとして改訂を行いました。
https://t.co/iBVEI8PVHM

[Takashi Fukaya @FukayaLab]

いわゆる「DNA>RNA>Protein」は後年、Watsonが1965年出版のMolecular Biology of the Geneにおいて単純化して記載したものであり、オリジナルの定義とは異なる(こちらが一般に普及し、高校教科にもそのように記載されるに至った)