🚀 Our new paper is out @natmethods.nature.com! Kuffer & Marzilli engineered conditionally stable MS2 & PP7 coat proteins (dMCP & dPCP) that degrade unless bound to RNA, enabling ultra–low-background, single-mRNA imaging in live cells. 🔗 www.nature.com/articles/s41... 🧬 www.addgene.org/John_Ngo/

We’ve developed the first-ever method to control nucleic acid activity and gene-expressing synthetic cells with a deeply tissue penetrating alternating magnetic field 🧬 🧪 🧲!!! Published in *Nature Chemistry* Led by Ellen Parkes @syncelleu.bsky.social #chemsky www.nature.com/articles/s41...

How many photons are in a GFP? — more than last year, and more than you thought. Here's a simple, cheap, and practical method to break a fundamental limit in fluorescence microscopy. But it only works in light sheet!

Excited to share the latest work from the lab led by @eharo84.bsky.social, in which we have used synthetic biology to explore the mechanisms by which different types of long-range enhancers ensure robust and precise developmental gene expression www.biorxiv.org/content/10.1...

Pleased to see this study out, combining experimental work from our lab at the @cbitoulouse.bsky.social, in particular by @nathaliebastie.bsky.social and @beckof.bsky.social, and from Laura Chaptal and @alengronne.bsky.social at IGH Montpellier @cnrs.fr @cnrsbiologie.bsky.social Congrats to all!

How do enhancer-gene contacts relate to transcription activation? In mouse embryonic stem cells, a combo of STED, oligoFISH & RNA FISH shows that 3% of Dppa3 alleles transcribe. For these, enhancers and promoters come closer (panel E). Stumberger ... Leonhardt & Harz www.biorxiv.org/content/10.1...

Our paper is now out in Molecular Cell! Check the thread in this former post: www.cell.com/molecular-ce...

This seems like a really important paper comparing chromosome tracing methods, demonstrating that classical denaturing DNA-FISH and chromosome tracing leads to substantial distortion of 3D genome structure, likely due to the high-temperatures involved (70-90C): www.nature.com/articles/s41...

Designed protein pockets recognize intrinsically disordered protein regions @science.org www.science.org/doi/10.1126/... www.science.org/doi/10.1126/... www.statnews.com/2025/07/17/n...

What's the best software for making and styling a protein sequence alignment? Please tell me there's something better than MS Word?

Our new preprint 🧬🔗 www.biorxiv.org/content/10.1... BRD4-NUT forms liquid-like condensates that locally constrain nucleosomes via BRD4-mediated crosslinking— physical control of #chromatin by #LLPS transcription condensates. @semeigazin.bsky.social @katsuminami.bsky.social @masaashimazoe.bsky.social

Optogenetic storage and release of protein and mRNA in live cells and animals | Nature Communications share.google/gz8nYXZ3hUVh... #spatialbiology #imagingtools #fluorescencemicroscopy

www.nature.com/articles/s41... #spatialbiology #imagingtools #fluorescencemicroscopy

Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/

(1/n) Excited to present the latest work from the de Wit lab, where we identify and characterise loop extrusion-mediated fountains in mammalian genomes using acute depletion of 3D genome regulators: doi.org/10.1093/nar/.... A Bluetorial🧵:

Project 'Pierre Menard'

How do transcription compartments form — and does phase separation drive gene expression? I enjoyed discussing these questions with @akispapantonis.bsky.social a lot, and we put our thoughts together for @naturerevgenet.bsky.social, now out at rdcu.be/erP1u

In the nucleus, many intrinsically disordered proteins (IDPs) form condensates. What IDP sequence features drive this behavior? We developed CondenSeq, a high-throughput approach to measure nuclear condensate formation, and applied it to ~14,000 IDPs to find out! rdcu.be/eq975

If heterochromatin is really a liquid-like condensate, why is it not spherical? We investigated whether mechanical interactions between a condensate and a fiber network can explain the variety of morphologies seen in phase-separated nuclear compartments www.biorxiv.org/content/10.1...

Springer-Nature launched a series of "Discover" journals that closely mimic MDPI titles -- sharing *identical* journal names, and likely similar business model. What is going on, and why researcher will - as always - fall for it? A 🧵 the-strain-on-scientific-publishing.github.io/website/post...

We’ve pioneered a disease-agnostic screening platform for aberrant biomolecular condensates—cellular structures linked to incurable neurological diseases. We screened genes and FDA-approved drugs that modulate disease-relevant nuclear condensates: www.biorxiv.org/cgi/content/...

Thrilled to share that my first #micropublication is out! 🧬🔬 I created a user-friendly ImageJ/FIJI plugin for nuclear segmentation and multi-channel fluorescence analysis that doesn't require programming skills. www.micropublication.org/journals/bio...

www.nature.com/articles/s41... From Denis Hnisz lab

Dear colleagues, Science in Argentina is under siege. Government funding has stopped and the system is about to collapse. Please help us spread the word to stop the exodus of our best human resources. youtu.be/76tYd-QRIfI?... www.nature.com/articles/d41...

Great to see this published @genesdev.bsky.social. Evidence that enhancers can activate a bystander gene in an adjacent TAD, and that cohesin facilitates this. @uoe-igc.bsky.social. pubmed.ncbi.nlm.nih.gov/40436628/

@science.org Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation | Science www.science.org/doi/10.1126/... @jbuenrostro.bsky.social @eboyden3.bsky.social + al @broadinstitute.org @harvard.edu #ExIGS #Chromatin #Lamin #Progeria #Aging #ExpansionMicroscopy

#spatialbiology #RNAbiology www.nature.com/articles/s41...

Excited our paper is out in Cell @cp-cell.bsky.social! 🧬⚡ DNA photo-crosslinking proteomics in living cells 🎯 Pinpoints protein-DNA interactions to single amino acids 🌎 Globally quantifies DNA binding for >1800 proteins at a timescale of minutes 🔗 www.cell.com/cell/fulltex... 🧵

Our new paper is out in iScience. Congratulations for Belen! We have found new evidence that supports the involvement of glucocorticoid receptor condensates in transcription control.

Extensive differences observed in 3D genome structure between homologous heterozygous chromosomes revealed by Genome Architecture Mapping #GAM in the @apombo1.bsky.social lab ➡️ www.embopress.org/doi/full/10....

🚨The formation of 3D chromatin hubs is a poorly understood phenomenon. I wrote a N&V about the excellent work Karpinska, Zhu and colleagues, from @mariekeoudelaar.bsky.social lab, who shed new light on the formation and function of these structures. rdcu.be/elPt3

I am excited to share the latest paper from my lab where we leverage the selection bias of condensate-promoting oncofusions to uncover molecular rules governing condensate specificity and function. www.cell.com/cell/fulltex....

High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH www.cell.com/cell/abstrac... #spatialbiology

From enhancer hijacking to ecDNA and onco-condensates – we review how changes in nuclear architecture drive oncogenic gene expression by disrupting enhancer–promoter communication. doi.org/10.1002/ijc..... Kudos to Isabelle Seufert, @claire-vrgs.bsky.social and Sina Wille 👏

1/n: Excited to share our new preprint. We find that Dorsal transcription factor hubs exhibit gene-specific biophysical properties that tune transcriptional output. Read here: www.biorxiv.org/content/10.1.... Project was led by amazing graduate student Samantha Fallacaro (not on bsky)

Bio foundation models are great design and engg tools. But can they help decode the fundamental principles of life? We harnessed a single-cell FM for decoding the long-debated relationship between genome arch. and gene coregulation. 1/ Preprint here: www.biorxiv.org/content/10.1...

Celebrating 10 years of our lab with a new preprint: www.biorxiv.org/content/10.1... How does enhancer location within a TAD control transcriptional bursts from a cognate promoter? Experiments by Jana Tünnermann and modelling by Gregory Roth

Check out Masahiro Nagano's preview www.sciencedirect.com/science/arti... for a very interesting paper from Tjalsma...Wouter de Laat www.cell.com/cell-genomic...

Glad to see that our review on the functional role of transcriptional condensates was one of the Top20 most downloaded articles from Communications Biology in 2024!

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)

Our study on how TAD boundaries actively influence the neighboring domains published today in @pnas.org: www.pnas.org/doi/10.1073/... Exciting outcomes from this interdisciplinary genomics/biophysical modeling strategy. See the thread for the BioRxiv preprint for a summary of highlights.

Our new preprint is out＠bioRxiv: www.biorxiv.org/content/10.1... @masaashimazoe.bsky.social et al. reveal that linker histone H1 acts as a liquid-like glue to organize chromatin in living cells. 🎉 Fantastic collab with @rcollepardo.bsky.social @janhuemar.bsky.social and others—huge thanks! 🙌 1/

Looking for folks from Argentina &/or Hungary who'd be willing to come on the podcast. Hoping to do an episode about the impact of what's currently happening in the US by focussing on places where similar attacks have already happened.

Y mientras tanto tenemos a un dogmático, arcaico y nefasto jugando al liberalismo.

Plasmids for our destabilized MCP (dMCP) & PCP (dPCP) coat proteins are now on @addgene.bsky.social here: www.addgene.org/browse/article/28252367/ These proteins are degraded by cells except when bound to their RNA hairpin targets (MS2 & PP7): www.biorxiv.org/content/10.1101/2024.11.21.624393v1

Neighborhood phenomenon

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Welcome to the Bluesky account for Stand Up for Science 2025! Keep an eye on this space for updates, event information, and ways to get involved. We can't wait to see everyone #standupforscience2025 on March 7th, both in DC and locations nationwide! #scienceforall #sciencenotsilence

Our new review on how the #chromatin domain is formed in the cell is now available @Curr Opin Struct Biol.📄✨ We critically discuss the domain formation mechanism from a physical perspective, including #phase-separation and #condensation. 📥 Free-download link: authors.elsevier.com/a/1keGn,LqAr...

La guerra contra las universidades es ideológica, no económica. Capítulo mil quinientos cuatro.