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Yasu Arimura

@yarimura.bsky.social
853 followers 854 following 17 posts

Elucidating the structural basis of biological events on chromosomes | chromatin, Xenopus egg extract, cryo-EM | Assistant Professor at Fred Hutch research.fredhutch.org/arimura/en.h…

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Yasu Arimura @yarimura.bsky.social · 04/03/2026
We’re recruiting a postdoc to start at the end of this year or early next year! We use cryo-EM to uncover the structural basis of key chromatin events using native complexes isolated from human cells or assembled in Xenopus (frog) egg extracts!
careers-fhcrc.icims.com
Fred Hutchinson Cancer Center
Fred Hutch is dedicated to the elimination of cancer and related diseases as causes of human suffering and death.
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Harmit Singh Malik @harmitmalik.bsky.social · 03/03/2026
My awesome colleague, @yarimura.bsky.social, is recruiting a postdoc to start at the end of 2026 or early 2027! His lab uses cryo-EM to uncover structural basis of key chromatin events using native complexes isolated from human cells or Xenopus egg extracts! careers-fhcrc.icims.com/jobs/30706/p...
careers-fhcrc.icims.com
Fred Hutchinson Cancer Center
Fred Hutch is dedicated to the elimination of cancer and related diseases as causes of human suffering and death.
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Fred Hutch @fredhutch.org · 14/02/2026
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Yasu Arimura @yarimura.bsky.social · 29/10/2025
@jhigginswriter.bsky.social wrote an article about my lab and our frog 🐸 at the Hutch! Thank you!
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Fred Hutch @fredhutch.org · 27/10/2025
Dr. @yarimura.bsky.social brings frogs back to Fred Hutch after a long absence to study the structure of DNA-linked molecular complexes that change during the cell cycle and malfunction in cancer and other diseases. bit.ly/3J8S5Ae
bit.ly
Frogs help Fred Hutch find the shape of small things
Frogs have made significant contributions to Fred Hutch science over the years as a model organism that shares much of our biology, but they've been absent from the menagerie for about two decades. Dr...
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Sue Biggins @suebiggins.bsky.social · 17/09/2025
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...
careers-fhcrc.icims.com
Fred Hutchinson Cancer Center
Fred Hutch is dedicated to the elimination of cancer and related diseases as causes of human suffering and death.
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Harmit Singh Malik @harmitmalik.bsky.social · 17/09/2025
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...
careers-fhcrc.icims.com
Fred Hutchinson Cancer Center
Fred Hutch is dedicated to the elimination of cancer and related diseases as causes of human suffering and death.
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Nature Structural & Molecular Biology @natsmb.nature.com · 12/09/2025
New online: Computational design of sequence-specific DNA-binding proteins
go.nature.com
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.
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Shiori Iida @shiori-iida.bsky.social · 29/08/2025
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)
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Bloom lab @jbloomlab.bsky.social · 20/08/2025
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...
biorxiv.org
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...
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Cees Dekker @ceesdekker.bsky.social · 13/08/2025
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=👍
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Hironori Funabiki @hirofunabiki.bsky.social · 20/05/2025
The peer-reviewed VOR for the MagIC-cryo-EM paper by @yarimura.bsky.social‬ and @1001hak.bsky.social‬ is finally published! Congrats Yasu!
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Lucas Farnung @lucas.farnunglab.com · 06/05/2025
 🧬🎉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...
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Sergio Cruz-León @sergiocruzleon.bsky.social · 11/04/2025
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
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Siavash @siavashk.bsky.social · 11/04/2025
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/...
science.org
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.
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Jan Philipp Kreysing @jpkreysing.bsky.social · 11/04/2025
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 🧵👇
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Lucas Farnung @lucas.farnunglab.com · 06/04/2025
🔬 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
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Kazuhiro Maeshima @kazu-maeshima.bsky.social · 29/03/2025
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
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Kazuhiro Maeshima @kazu-maeshima.bsky.social · 29/03/2025
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
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Harmit Singh Malik @harmitmalik.bsky.social · 27/03/2025
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...
cell.com
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...
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Amanda Amodeo @aaamodeo.bsky.social · 13/12/2024
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...
biorxiv.org
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) ...
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Science Magazine @science.org · 20/03/2025
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
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Mitosis Lab @mitosislab.bsky.social · 17/03/2025
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.
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.
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Aaron Straight @astraight.bsky.social · 12/03/2025
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.
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Masa A. Shimazoe @masaashimazoe.bsky.social · 10/03/2025
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)
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Wooyoung Choi @wooyoungchoi.bsky.social · 02/03/2025
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🏊🏄🚣
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Fred Hutch @fredhutch.org · 13/02/2025
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/...
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Fred Hutch Basic Sciences Division @basicsci.fredhutch.org · 15/02/2025
Huge congratulations @jbloomlab.bsky.social!
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Jean-Paul Armache @valendraica.bsky.social · 05/02/2025
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...
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Tim Clancy @viewfromarchstreet.com · 08/02/2025
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...
grants.nih.gov
NOT-OD-24-110: Notice of Legislative Mandates in Effect for FY 2024
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Notice of Legislative Mandates in Effect for FY 2024 NOT-OD-24-110. NIH
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bioRxivpreprint @biorxivpreprint.bsky.social · 04/02/2025
Structural Characterization of Native RNA Polymerase II Transcription Complexes and Nucleosomes in Drosophila melanogaster www.biorxiv.org/content/10.1101/202…
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Fred Hutch Basic Sciences Division @basicsci.fredhutch.org · 24/01/2025
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...
elifesciences.org
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.
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Jan Huertas @janhuemar.bsky.social · 22/01/2025
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...
biorxiv.org
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Yan Hu @yanhu97.bsky.social · 23/01/2025
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...
nature.com
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.
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Hironori Funabiki @hirofunabiki.bsky.social · 22/01/2025
Pleased to share my thoughts on the new eLife publication model. elifesciences.org/inside-elife...
elifesciences.org
Publishing with eLife: “make positive impacts by contributing to such nourishing culture”
Why do authors choose the eLife Model? We spoke to Hironori Funabiki at the Rockefeller University to learn his reasons.
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Sagar Khavnekar @cryosagar.subspatial.org · 29/12/2024
Hey #teamtomo checkout our #teamscience approach to #cellbio #cryoET I can’t thank @cellarchlab.com enough for this one 😍😍 Awesome team science from @mpibiochem.bsky.social @biozentrum.bsky.social Thermo Fisher Scientific and more #firstpost on Bluesky www.biorxiv.org/content/10.1...
biorxiv.org
Towards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii
In situ cryo-electron tomography (cryo-ET) has emerged as the method of choice to investigate structures of biomolecules in their native context. However, challenges remain in the efficient production...
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Yasu Arimura @yarimura.bsky.social · 30/12/2024
Nice resolution nucleosome cryo-ET🤩
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Fred Hutch Basic Sciences Division @basicsci.fredhutch.org · 18/12/2024
2024 was an amazing year for Basic Sciences @fredhutch.bsky.social, including the opening of the @yarimura.bsky.social Lab, the Pathfinders Postdoc Symposium, a wonderful retreat, many scientific discoveries, and more. Get all the highlights in our annual report: www.fredhutch.org/en/research/...
fredhutch.org
2024 Annual Report
The 2024 Annual Report from the Basic Sciences Division at Fred Hutch features the divisions reflections for the year, as well as celebrations of faculty retiring and joining the division, events and...
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Structura Biotechnology @structurabio.bsky.social · 13/12/2024
1/ A new series of #CryoSPARC tutorial videos from this year’s S2C2 #cryoEM image processing workshop are now online! These videos will be interesting to all users and especially those newer to #cryoEM. www.youtube.com/playlist?lis...
youtube.com
2024 S2C2 Single-Particle Cryo-EM Image Processing Workshop - YouTube
This playlist contains six recordings covering single particle cryo-EM data processing in CryoSPARC from the 2024 Single-Particle Cryo-EM Image Processing Wo...
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Brian Beliveau @oligopain.bsky.social · 15/11/2024
The pSABER paper is now online! pSABER is a new method for amplifying in situ hybridization signals This work was driven by Sahar Attar and co-led by Ram Akliesh ([at] podocytes on the other app) with help from @shechnerlab.bsky.social @dschweppe.bsky.social doi.org/10.1038/s415... 🧵 1/12
doi.org
Efficient and highly amplified imaging of nucleic acid targets in cellular and histopathological samples with pSABER - Nature Methods
pSABER combines the power of signal amplification by exchange reaction (SABER) with the deposition of fluorescent or colorimetric substrates by horseradish peroxidase to enable enhanced signals for in...
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Vijay Ramani @vram142.bsky.social · 15/11/2024
The latest from our group, led by Megan Ostrowski and @martyyang.bsky.social, is now published in final form (www.cell.com/cell/fulltex...! Many thanks to our excellent peer reviewers for suggesting several experiments (including CAF-1 perturbation) to really improve the study =) #epigenetics
cell.com
The single-molecule accessibility landscape of newly replicated mammalian chromatin
By developing a long-read sequencing method to simultaneously map replication status and protein-DNA contacts in cells, Ostrowski, Yang, et al. show that newly replicated chromatin is enriched for unw...
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Yasu Arimura @yarimura.bsky.social · 14/11/2024
Wow🐸🐸 congratulations! 🎉
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FragileNucleosome @fnucleosome.bsky.social · 13/11/2024
Hey Skeeters, A big new batch of our @fnucleosome.bsky.social seminar videos have gone public in the past couple weeks! Here's a thread:
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Yasu Arimura @yarimura.bsky.social · 13/11/2024
This week's lesson: You never know until you try. You might just discover a hidden talent.
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Harmit Singh Malik @harmitmalik.bsky.social · 10/11/2024
Hello! I’m new here. If you follow me on the other place give me a follow here so I can find you
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Aaron Straight @astraight.bsky.social · 10/11/2024
Don’t forget Xenbase (www.xenbase.org/xenbase/)!! Power to the frog 🐸 #xenopus #frog
xenbase.org
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Yasu Arimura @yarimura.bsky.social · 22/02/2024
Please repost! Arimura Lab is hiring! We are seeking the next generation of MagICians (technicians and a postdoc) to elucidate the structural basis of events on chromosomes🧙‍♀️ No prior structural biology experience is required!! Link research.fredhutch.org/arimura/en/j...
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bioRxivpreprint @biorxivpreprint.bsky.social · 22/01/2024
Cryo-EM analysis on magnetic beads for scarce macromolecules in heterogeneous samples www.biorxiv.org/content/10.1101/202…
biorxiv.org
Cryo-EM analysis on magnetic beads for scarce macromolecules in heterogeneous samples https://www.biorxiv.org/content/10.1101/2024.01.21.576499v1
Here, we introduce Magnetic Isolation and Concentration (MagIC)-cryo-EM, a technique enabling direct
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