In their Tools and Resources article, Martin Stortz @mdstor.bsky.social, Tom Misteli and colleagues present OptoLoop, an optogenetic tool to probe the functional role of genome organisation. journals.biologists.com/jcs/article/... #CellBio #nucleus
Martin Stortz
@mdstor.bsky.social
PhD, Molecular and Cell Biologist 🔬Transcription factors, genome organization, nuclear architecture, biomolecular condensates, optogenetics, fluorescence microscopy 🗣️Views are my own
🧬💡 OptoLoop: An optogenetic tool to probe the functional role of genome organization - thanks for sharing, @mdstor.bsky.social! www.addgene.org/browse/artic...
Addgene: OptoLoop: An optogenetic tool to probe the functional role of genome organization.
addgene.org
MMartin Stortz@mdstor.bsky.social · 5mo ago
Want to try our new OptoLoop constructs for optogenetic control of chromatin looping? Check out our plasmids now available at @addgene.bsky.social www.addgene.org/browse/artic... And don't forget to read our new article published in @jcellsci.bsky.social journals.biologists.com/jcs/article/...
Want to try our new OptoLoop constructs for optogenetic control of chromatin looping? Check out our plasmids now available at @addgene.bsky.social www.addgene.org/browse/artic... And don't forget to read our new article published in @jcellsci.bsky.social journals.biologists.com/jcs/article/...
OptoLoop – an optogenetic tool to probe the functional role of genome organization
Summary: The development of OptoLoop – an optogenetic tool to induce chromatin looping in a controlled fashion using light and how this tool can be applied to study genome structure–function relations...
journals.biologists.com
📣📣We are glad to have our new preprint out! 1) This work has been made as part of my postdoc at the Tom Misteli's lab at NCI/NIH. Here we introduce OptoLoop, an optogenetic tool to interrogate the not fully understood relationship between 3D genome organization and gene regulation.
bioRxivpreprint@biorxivpreprint.bsky.social · 9mo agoOptoLoop: An optogenetic tool to probe the functional role of genome organization https://www.biorxiv.org/content/10.1101/2025.11.06.686574v1
OptoLoop: An optogenetic tool to probe the functional role of genome organization https://www.biorxiv.org/content/10.1101/2025.11.06.686574v1
OptoLoop: An optogenetic tool to probe the functional role of genome organization https://www.biorxiv.org/content/10.1101/2025.11.06.686574v1
1. The $20 billion taxpayer-funded rescue package for Argentina, announced last week by the Treasury Secretary Scott Bessent, delivers an enormous windfall to hedge fund billionaire Rob Citrone. Citrone has a longstanding personal and professional relationship with Bessent.
Trump’s Argentina bailout enriches one well-connected billionaire
A $20 billion taxpayer-funded rescue package for Argentina is a gift for a hedge fund manager with personal and professional ties to the Treasury Secretary
popular.info
🚀 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...
Magnetic activation of spherical nucleic acids enables the remote control of synthetic cells - Nature Chemistry
The programmability of synthetic cells, comprising lipid vesicles that are capable of imitating the structure and function of living cells, facilitates their application as drug delivery devices. Now,...
nature.com
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...
Synthetic engineering demonstrates that synergy among enhancers involves an increase in transcriptionally productive enhancer-gene contacts
Enhancers are non-coding cis-regulatory elements that control the expression of distally located genes in a tissue- and time-specific manner. Recent studies indicate that enhancers can differ in their...
biorxiv.org
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!
RNA Pol II-based regulations of chromosome folding
How transcription and cohesin complexes interact to regulate 3D genome organization remains unclear. Chapard et al. dissect their respective contributions and their interplay in shaping the genome arc...
cell.com
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...
Chromatin architecture mapping by multiplex proximity tagging
Delamarre et al. develop a technology named PCP that can simultaneously map complex spatial relationships between millions of molecules. Using PCP, they investigate chromatin structure and describe si...
cell.com
Axel Delamarre@axeldelamarre.bsky.social · last yr.Hi everyone! The latest method from the Whitehouse lab: PCP PCP uses a novel proximity barcoding strategy to simultaneously map 3D genome organization at various resolutions at the single molecule level: Out soon, check the updated BioRxiv – little thread: 1/11 www.biorxiv.org/content/10.1...
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...
Disorder meets its match
Designed protein pockets recognize intrinsically disordered protein regions
science.org
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
Optogenetic storage and release of protein and mRNA in live cells and animals - Nature Communications
Spatiotemporal control of biomolecules is a key challenge in cell biology. Here, authors introduce RELISR, an optogenetic condensate system enabling reversible, light-dependent sequestration and relea...
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www.nature.com/articles/s41... #spatialbiology #imagingtools #fluorescencemicroscopy
Genetically encoded affinity reagents are a toolkit for visualizing and manipulating endogenous protein function in vivo - Nature Communications
Probing endogenous protein localization and function in vivo remains challenging due to laborious gene targeting and monofunctional alleles. Here, using a toolkit consisting of genetically-encoded epi...
nature.com
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/
Range extender mediates long-distance enhancer activity - Nature
The REX element is associated with long-range enhancer–promoter interactions.
nature.com
(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🧵:
Extrusion fountains are restricted by WAPL-dependent cohesin release and CTCF barriers
Abstract. Interphase chromosomes are mainly shaped by loop extrusion and compartmentalisation mechanisms. However, their temporal component and cause-effec
doi.org
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
Characterizing protein sequence determinants of nuclear condensates by high-throughput pooled imaging with CondenSeq
Nature Methods - CondenSeq is an imaging-based, high-throughput platform for characterizing condensate formation within the nuclear environment, uncovering the protein sequence features that...
rdcu.be
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...
Springer Nature Discovers MDPI – The Strain on Scientific Publishing
Home page for the paper ‘The Strain on Scientific Publishing’ by Mark A Hanson, Dan Brockington, Paolo Crosetto and Pablo Gomez Barreiro
the-strain-on-scientific-publishing.github.io
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...
Multi-Channel Nuclear Analysis: An ImageJ/FIJI Plugin for Automated Nuclear Segmentation and Multi-Channel Fluorescence Analysis | microPublication
micropublication.org
www.nature.com/articles/s41... From Denis Hnisz lab
Probing condensate microenvironments with a micropeptide killswitch - Nature
Targeting a non-natural micropeptide ‘killswitch’ to several biomolecular condensates altered condensate compositions and revealed condensate functions in human cells
nature.com