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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. cell.com/molecular-cell/full…
Very sad to hear of Nori Satoh’s passing. oist.jp/news-center/news/202…
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
Now online! Mechanisms of transcription control by distal enhancers from single-gene nanoscopy dlvr.it/TVvy9B
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…
Celebrated the 20th anniversary of the Tomari Lab! Had a great time co-organizing the anniversary symposium with Hotaka Kobayashi!
泊ラボ20周年おめでとう!
Takashi Fukaya retweeted
Very interesting historical perspective on cohesin and its role in transcriptional regulation:
link.springer.com/article/10…
Takashi Fukaya retweeted
hooray for optogenetics! very happy for karl, peter & dr. nagel - three *very* worthy winners.
for those with interests outside of neurons & ion channels, here is a fun 2002 paper from Peter Quail that i think kicked off light-controlled gene expression: nature.com/articles/nbt734
Takashi Fukaya retweeted
New online! Single-molecule chromatin tracing reveals a diversity of megabase heterochromatin domains dlvr.it/TVl7pq
Takashi Fukaya retweeted
In the latest issue! Condensates of the chromatin regulator ANKRD11 restrict hypertranscribed genes to safeguard development dlvr.it/TVkrgn
Takashi Fukaya retweeted
Online Now: Transcription factor clusters enhance gene expression in vivo without modulating bursting dynamics dlvr.it/TVhtS2
Takashi Fukaya retweeted
Now online! Single-cell visual proteomics of a minimal bacterium reveals structural coordination of gene expression machineries dlvr.it/TVgMq5
Takashi Fukaya retweeted
Excited to share that our work from RIKEN is now published in Nature! 🎉
We uncovered how protein intake during development shapes lifespan and identified a mechanism that transmits a “nutritional memory” into adulthood.
nature.com/articles/s41586-0…
Takashi Fukaya retweeted
Excited to share Minerva, our approach using genome language models for biological discovery! Using Minerva, we find that UG27 reverse transcriptase systems encode variable arrays of diverse ncRNAs with a shared structure, each templating a short DNA hairpin. With @garykbrixi.



























