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

Tokyo-to, Japan
Joined September 2019
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…
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New Online! Scaling up measurements of the interactions that build condensates dlvr.​it/TVv4S9
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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 👇
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Intraspecific sequence variation and complete genomes refine the identification of rapidly evolved regions in humans dlvr.​it/TVw7SB
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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…
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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
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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…
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Now online! Mechanisms of transcription control by distal enhancers from single-gene nanoscopy dlvr.​it/TVvy9B
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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!
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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
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We've now deployed the Minerva language model and its interaction heads on the Proto MCP! Here is an example using @ChatGPT to revisit an existing annotation of a non-coding RNA: chatgpt.com/share/6abe9cea-c…
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New online! Single-molecule chromatin tracing reveals a diversity of megabase heterochromatin domains dlvr.​it/TVl7pq
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In the latest issue! Condensates of the chromatin regulator ANKRD11 restrict hypertranscribed genes to safeguard development dlvr.​it/TVkrgn
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Online Now: Transcription factor clusters enhance gene expression in vivo without modulating bursting dynamics dlvr.it/TVhtS2
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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…
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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.
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