Yasu Arimura

Fred Hutchinson Cancer Center Fred Hutch is dedicated to the elimination of cancer and related diseases as causes of human suffering and death.

Looking for your next step in fly genetics? The Rajan Lab at Fred Hutch is hiring a staff scientist + postdoc for projects on fat–brain signals, immunity, and brain aging. Stable, long-term role in a collaborative lab. Apply: careers-fhcrc.icims.com/jobs/30062/j...

Fred Hutchinson Cancer Center Fred Hutch is dedicated to the elimination of cancer and related diseases as causes of human suffering and death.

My awesome Drosophila colleague Akhila Rajan at Fred Hutch (Seattle) is recruiting both a staff scientist and a postdoc to study fat–brain communication, innate immunity, mitochondrial signaling, and brain senescence. Great team, great environment. Apply here: careers-fhcrc.icims.com/jobs/30062/j...

Computational design of sequence-specific DNA-binding proteins Nature Structural & Molecular Biology, Published online: 12 September 2025; doi:10.1038/s41594-025-01669-4The authors develop a computational method to design small DNA-binding proteins (DBPs) that target specific sequences. Designed DBPs show structural accuracy and function in both bacterial and mammalian cells for transcriptional regulation.

New online: Computational design of sequence-specific DNA-binding proteins

One more movie!
Using the RL algorithm (from pnas.org/doi/10.1073/...),
@masaashimazoe.bsky.social analyzed our nucleosome tracking data and classified them by their mobility.
Hotter color = faster motion (Slow🔵→ 🟢 → 🟡 → 🟠 Fast)

Spike mutations that affect the function and antigenicity of recent KP.3.1.1-like SARS-CoV-2 variants SARS-CoV-2 is under strong evolutionary selection to acquire mutations in its spike protein that reduce neutralization by human polyclonal antibodies. Here we use pseudovirus-based deep mutational sca...

In new study led by @bdadonaite.bsky.social, we measure how spike mutations affect function & antigenicity of spike of KP.3.1.1 strain of SARS-CoV-2.

Sheds light on how key neutralizing epitopes are changing & importance of RBD up/down motion.

www.biorxiv.org/content/10.1...

WORK!

I currently have 5 (!) open positions for postdocs/PhD students in our CDlab for projects:

- Nanopore protein sequencing
- Archaeal CDV cell division
- Microfluidics for synthetic cells
- Nuclear Pore Complex
- Origami mimics of peroxisomes

Please apply! ceesdekkerlab.nl/come-join-us/

RT=👍

The peer-reviewed VOR for the MagIC-cryo-EM paper by @yarimura.bsky.social‬ and @1001hak.bsky.social‬ is finally published!
Congrats Yasu!


🧬🎉Thrilled to share our new chromatin remodeling study! We reveal three states of human CHD1 and identify a novel "anchor element" that interacts with the acidic patch—conserved among remodelers. Our structures clarify mechanisms of remodeler recruitment! Link: authors.elsevier.com/a/1l2ik3vVUP...

Excited to share our preprint on the molecular architecture of heterochromatin in human cells 🧬🔬w/ @jpkreysing.bsky.social, @johannesbetz.bsky.social,
@marinalusic.bsky.social, Turoňová lab, @hummerlab.bsky.social @becklab.bsky.social @mpibp.bsky.social

🔗 Preprint here tinyurl.com/3a74uanv

Histone H3 cysteine 110 enhances iron metabolism and modulates replicative life span in Saccharomyces cerevisiae Histone H3 cysteine 110 enhances iron metabolism and modulates replicative life span in yeast.

Ever wondered what the lonely histone H3C110 does? We found that it’s lost in many fungi. Adding it back boosts histone H3 copper reductase activity, rescues iron defects and modulates lifespan, suggesting an evolutionary tradeoff between these effects.
www.science.org/doi/10.1126/...

New preprint on 3D heterochromatin architecture in human cells! Great collab with @sergiocruzleon.bsky.social & @johannesbetz.bsky.social from @hummerlab.bsky.social, @marinalusic.bsky.social & the Turoňová lab. Many thanks to my supervisor @becklab.bsky.social. bioRxiv: tinyurl.com/3a74uanv 🧵👇

🔬 New from the Farnung Lab: We established a fully in vitro reconstituted chromatin replication system and report the first cryo-EM snapshots of the human replisome engaging nucleosomes. Brilliant work by @felixsteinruecke.bsky.social with support from @jonmarkert.bsky.social! tinyurl.com/replisome

Our new paper is out@ScienceAdvances👇
www.science.org/doi/10.1126/...
🧬Our Repli-Histo labeling marks nucleosomes in euchromatin and heterochromatin in live human cells.
🔍 @katsuminami.bsky.social et al. have developed a chromatin behavior atlas within the nucleus. 1/2

We quantitatively measured nucleosome motion across the 4 chromatin classes, from euchromatin to heterochromatin.
🧪 More euchromatic regions (i.e., earlier-replicated regions) show greater nucleosome motion.
🎉 Congrats @katsuminami.bsky.social @kakonakazato.bsky.social and all collaborators!
2/2

Indels allow antiviral proteins to evolve functional novelty inaccessible by missense mutations Tenthorey et al. compare the effects of missense and indel mutations on the acquisition of functional novelty by the rapidly evolving antiviral protein TRIM5α. They find that single indel mutations al...

Proud of this work, led by the amazing Jeannette Tenthorey (now Assistant Professor at UCSF), demonstrating the adaptive power of single indel mutations in host-virus arms races, but a little sad that this is the coda to her amazing postdoc in the Malik & Emerman labs.

www.cell.com/cell-genomic...

Local nuclear to cytoplasmic ratio regulates H3.3 incorporation via cell cycle state during zygotic genome activation Early embryos often have unique chromatin states prior to zygotic genome activation (ZGA). In Drosophila, ZGA occurs after 13 reductive nuclear divisions during which the nuclear to cytoplasmic (N/C) ...

First post on bsky. We've updated our preprint about the change in the histone H3 variant on chromatin during Zygotic Genome Activation. Thanks to new experiments by Anusha, it seems like our initial, simplistic idea that the embryo "ran out" of H3 was not right.

www.biorxiv.org/content/10.1...

In a new Science study, cryo–electron tomography captures the in-cell architecture of the mitochondrial respiratory chain, illuminating how the coordinated action of molecular machines drives life’s fundamental energy conversion.

Learn more in this week's issue: scim.ag/3FA3Ygq

Cryo-ET visualization of chromatin at the nucleosome level in RPE-1 cells arrested in G1 phase and metaphase.

Cryotomograms of a metaphase RPE-1 cell.

3-D class averages of mononucleosomes and ordered stacked dinucleosomes in G1 and metaphase.

Happy that Jon Chen @jonchenjk.bsky.social's cryo-ET and confocal study of RPE-1 chromatin in situ is online www.embopress.org/doi/full/10.1038/s44318-025-00407-2
Congrats also to coauthors Tingsheng Liu, @shujuncai.bsky.social, Cai Tong Ng, Jian Shi and collaborators Weimei Ruan Uttam Surana.

Wonderful visit to @hutchbasicsci.bsky.social today and thanks to @yarimura.bsky.social for hosting and dinner with the always entertaining @suebiggins.bsky.social and @harmitmalik.bsky.social. A day discussing science with amazing people is unbeatable.

Thank you for visiting us and giving the exciting seminar!

My first, first author paper is now on bioRxiv! 🤩

Linker histone H1 is a liquid-like "glue" condensing chromatin, which revises textbooks! 📖✨
biorxiv.org/content/10.1...

Huge thanks to my PI, @kazu-maeshima.bsky.social, for supervision.
Amazing collab with @rcollepardo.bsky.social’s group!" (1/n)

I am super excited to share that my work at @yifan_ucsf has just been published in Nature🎉 From developing pYC KI system, it was a long journey to understand endogenous protein dynamics. I appreciate the support from FASN team! 🕺Let's dive into the endogenous & dynamic protein world🏊🏄🚣

Researchers at Fred Hutch have discovered an overlooked mechanism driving aggressive breast and brain tumors involving genes so ancient — more than 2 billion years old — that they fly under the radar of standard genetic sequencing methods. 1/9 www.science.org/doi/10.1126/...

Huge congratulations @jbloomlab.bsky.social!

We did a thing... We purified native transcriptional complexes from Drosophila embryos, obtaining +/- stalk Pol II elongation complexes, native nucleosomes, as well as a nucleosome elongation complex. For more details please check out: doi.org/10.1101/2025...

On changes to #NIH indirect rates, there is a law in place that prohibits NIH from making such changes without the approval of Congress. See Division D, Title II Section 224 of The Further Consolidated Appropriations Act, 2024 (Public Law No: 118-47) grants.nih.gov/grants/guide...

Structural Characterization of Native RNA Polymerase II Transcription Complexes and Nucleosomes in Drosophila melanogaster https://www.biorxiv.org/content/10.1101/2025.02.03.636274v1

Cryogenic Electron Microscopy: MagIC beads for scarce macromolecules Specialized magnetic beads that bind target proteins to a cryogenic electron microscopy grid make it possible to study the structure of protein complexes from dilute samples.

Check out a fantastic @elife.bsky.social article highlighting @yarimura.bsky.social’s MagIC #cryoEM technique - a method using specialized magnetic beads that makes it possible to study the structure of proteins from dilute samples. elifesciences.org/articles/105...

Exciting new preprint alert! 🚨 The Collepardo lab, teaming up with Huabin Zhou and the Rosen lab we took a deep, high-resolution look into chromatin condensates! [1/6] #Chromatin #MD @rcollepardo.bsky.social @juliamaristany.bsky.social
www.biorxiv.org/content/10.1...

Multiscale footprints reveal the organization of cis-regulatory elements - Nature We developed PRINT, a computational method that identifies footprints of DNA–protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein size.

Super excited to share our new study from the @jbuenrostro.bsky.social Lab in @nature.com! We developed a computational method for tracking transcription factor and nucleosome binding using single-cell ATAC-seq and deep learning.
Paper: www.nature.com/articles/s41...