This is not a HiC map! Ever wondered if multiple enhancers get activated simultaneously? We measured chromatin accessibility on thousands of molecules by nanopore to create genome-wide co-accessibility maps. Proud of @mathias-boulanger.bsky.social @kasitc.bsky.social Biology in the thread👇

Activity of most genes is controlled by multiple enhancers, but is there activation coordinated? We leveraged Nanopore to identify a specific set of elements that are simultaneously accessible on the same DNA molecules and are coordinated in their activation. www.biorxiv.org/content/10.1...

Excited to see this published with additional data following our preprint a while back. Cool combination (in our biased view) of controlled TF expression and machine learning to decode chromatin sensitivity. www.sciencedirect.com/science/arti....

Now available in its final form @narjournal.bsky.social ! doi.org/10.1093/nar/... Find out how we can reconstruct enhancer activity in vivo in the Drosophila embryo using scRNAseq data and Optimal Transport.

#EMBLsinglemolecule was a blast! Happy to host the birth of single molecule genomics as a field and to think about the future with the microscopy crowd. Thanks to participants and organizers!

Carrying on with Session 4 on #EMBLSingleMolecule Day 3 🤓💪🏼 ➡️ 'Decoding Gene Regulation at the Single-Molecule Level through Biophysical Modeling of DNA Footprinting Data' 🎙️ Nacho Molina – Institute of Genetics and Molecular and Cellular Biology @molinalab.bsky.social @igbmc.bsky.social @embl.org

The talk by @andrewleduc.bsky.social at #SCP2025 is on YouTube: 𝐐𝐮𝐚𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐨𝐟 𝐠𝐞𝐧𝐞 𝐞𝐱𝐩𝐫𝐞𝐬𝐬𝐢𝐨𝐧 𝐜𝐨𝐧𝐭𝐫𝐨𝐥 𝐢𝐧 𝐚 𝐦𝐚𝐦𝐦𝐚𝐥𝐢𝐚𝐧 𝐭𝐢𝐬𝐬𝐮𝐞 𝐚𝐭 𝐬𝐢𝐧𝐠𝐥𝐞 𝐜𝐞𝐥𝐥 𝐫𝐞𝐬𝐨𝐥𝐮𝐭𝐢𝐨𝐧 youtu.be/adkY6txDyqs?...

🚨 Only a few more days to REGISTER for the TriRhena Gene Regulation Club in Freiburg. Whether you are new or an established researcher in the Basel-Freiburg-Strasbourg region, this is your meeting when working in transcription, chromatin & gene regulation! ✍️ www.ie-freiburg.mpg.de/gene-regulat...

🟦 Label-free single-cell proteomics (blue bars). 🟧 Multiplexed single-cell proteomics affords higher throughput (orange bars). ⬛️ Proteome depth & quantitative accuracy are comparable. We aim to make the 🟧 bars taller. www.parallelsq.org/psmtags www.biorxiv.org/content/10.1...

For Spanish speakers, this is a fantastic podcast about science and much more!

No doubt, this is one of the most exciting meetings of the year! And we will present our new method, HiddenFoot 😉: www.biorxiv.org/content/10.1...

‼️Last chance to join us in person for #EMBLSingleMolecule! Attend talks, network, socialise, and experience the atmosphere on the campus 🤩 🎫 Register by 3 Jun 👉🏼 http://s.embl.org/grg25-01-bl#EMBLSingleMolecule 🧬RNA processing 🧬Translation 🧬Transcription & chromatin regulation 🧬Method development 🧬Theory

Out @nature.com: Clonal tracing with somatic epimutations 🧬 Single cell methylome encodes cell state & clonal identity 🔨 EPI-Clone reads out both (+mutations, +RNA) at scale 🩸 Clonal expansions of HSCs are universal from age 50, not driven by CH mutations doi.org/10.1038/s415... 🧵

Just in case you missed this and it’s something that might interest you. #SingleMoleculeBiology, #Chromatin, #Transcription, #TF, #Nucleosome, #PolII, #Biophysics, #MachineLearning, #ComputationalBiology 👇

Time for a short thread! We developed HiddenFoot, a biophysics-inspired approach to decode single-molecule footprinting data and infer TF, nucleosome, and RNA Pol II binding profiles on individual DNA molecules. One molecule at a time! www.biorxiv.org/content/10.1... 1/6

Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️

I'm neighboring the chromatin biology field at the moment and there is a lot I need to understand. Especially, the specific techniques/methodologies in use to study chromatin, however this one looks 🔥🔥🔥. Many congratulations 👏🏻 🎉 to all those involved! Hey #ChromatinSky people where are you at 🤩?

Time for a short thread! We developed HiddenFoot, a biophysics-inspired approach to decode single-molecule footprinting data and infer TF, nucleosome, and RNA Pol II binding profiles on individual DNA molecules. One molecule at a time! www.biorxiv.org/content/10.1... 1/6

🚨 New preprint out! Do you think Single Molecule Footprinting and Fiber-seq are super cool but aren't sure how to unlock their full potential? HiddenFoot can help you: www.biorxiv.org/content/10.1...

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...

New research by @kasitc.bsky.social @molinalab.bsky.social @arnaudkr.bsky.social reveals limited RNA polymerase II pausing at mouse promoters compared to flies ➡️ www.embopress.org/doi/full/10....

US colleagues: Looking to launch or move your lab to France? The ARC Foundation is recruiting outstanding US-based scientists to lead research in oncology. Generous support & relocation help included. Details here: www.fondation-arc.org/projets/recr... Interested? Contact us!

Here is-🥳🥳😇 tremendous effort by @palmrinmoy.bsky.social brilliantly supported by @tamas-schauer.bsky.social &super help by federico,iliya,tsune,adam,@mamartirenom.bsky.social Very happy to see this come to fruition- Look forward to feedback from colleagues ! More 👉 www.cell.com/cell/fulltex...

1/2. I am pleased to announce that the preprint of our latest study characterizing mouse and human EEC development is now on BioRxiv. A great collaboration with the @molinalab.bsky.social and Maxime Mahe (not on bluesky) www.biorxiv.org/cgi/content/...

Send us your abstract before easter! Extended deadline! we got lots of cool stories already! We would also welcome submissions with a focus on Translation and life of RNA!

🚨3 weeks left to apply!🚨 We’re hiring 2 new Group Leaders at IGBMC – early career researchers welcome 🌟 We offer salary support for up to 3 years while you secure a permanent position in the French system. Come join an international research environment in Strasbourg! www.nature.com/naturecareer...

🚨 Last chance to submit abstract for 'Gene regulation: one molecule at a time' 🧬✍🏼 👉🏼 s.embl.org/grg25-01-bl ℹ️ #EMBLSingleMolecule will catalyse the emergence of a new generation of mechanistic models of the regulation of genes across each steps of the central dogma. 📅 Deadline: 8 April!

The importance of moving away from bulk! Occupancy of Pol II at promoters is dramatically different between fly and mouse cells! When looking single molecule! Proud of the team! @kasitc.bsky.social @molinalab.bsky.social doi.org/10.1038/s443...

Hey! Check out our latest publication. A great collaboration with @longchrom.bsky.social and a nice example of how a negative result, the absence of a response to a transcriptional perturbation, can actually reveal an intriguing gene-specific buffering mechanism. www.science.org/doi/10.1126/...

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

Come start your lab in beautiful Strasbourg 🇫🇷 www.nature.com/naturecareer...

Hey! This was the result of a fantastic collaboration with the @longchrom.bsky.social lab, where we found evidence for a gene-specific buffering mechanism to compensate for transcriptional perturbations.

Almost 17 years after opening our yeast cell division lab, our first transcription paper in mouse embryonic stem cells! www.science.org/doi/10.1126/...

Don’t forget to register for this special conference. If you like gene regulation from single molecule approaches, please join us #EMBLSingleMolecule. Imaging and Omics and a bit of theory for lots of fun!

We're hiring! The Development & Stem Cells department at @igbmc.bsky.social, Strasbourg 🇫🇷 is recruiting a group leader working in cell & developmental biology. Our Integrated Structural Biology department also has an open call. More details below! + contact me for informal enquiries #sciencejobs

The pro-EU demonstration 'una piazza per l'Europa', March 15th in Rome, is a great initiative but... www.comune.roma.it/partecipa/pu... Why not reproducing it in ALL Italian cities? Actually... Why not reproducing it in ALL European cities, from Madrid to Tallinn? (We the 🇪🇺 people are ready!)

PUBMED is down. This is disaster !! We do not have the system and organization to replace it. (EuroPMC is great but not a replacement) It is crystal clear that we cannot depend on critical systems provided by a single provider. European reaction has to include science and science infrastructures.

(6/6) #Epigenetics #StemCells Check out the preprint: www.biorxiv.org/content/10.1...

Making intrabodies from antibodies just got easier! Learn how we made 𝟭𝟵 intrabodies to bind and light up peptides and histone modifications in live cells. And thanks to Academia, all sequences are freely available. (video credit: Yuko Sato @YukoSatoT2) (1/15) www.biorxiv.org/content/10.1...

Friday Lectures – Giacomo Cavalli Join us on Friday, 7th February at 3pm for a talk by Giacomo Cavalli, expert in Polycomb regulation and 3D genome architecture. He’ll explore how these mechanisms affect epigenetic inheritance and cancer development. Don’t miss it! #Epigenetics #Genomics #Cancer

Come join us for this very first conference on single molecule approaches (both omics et imaging) to understand gene expression regulation. Lots of slots for young selected speakers!

The next TriRhena Gene Regulation Club takes place at IGBMC #Strasbourg. Save your seat & submit a talk. Strengthen your local #epigenetics network & collaborate with peers. 📅 5 Feb. 2025 | 14:00 🎟️ Free entry, registration required ✍️ Register by: 24. Jan. www.ie-freiburg.mpg.de/gene-regulat...

We often speak about chromatin as being accessible or inaccessible, but what does it mean? We wrote a short review on this, 🔬 focused: sciencedirect.com/science/arti... A big thank you to Tom Fillot for his efforts on this and to @hansen_lab @marcelonollmann for their help as editors.

1/ One more preprint before the holidays! In which we find that chromatin compaction scales with cell size from interphase through mitosis. A collaboration from waaay back (see end of thread) with Melike Lakadamyali @melikel.bsky.social and Jerome Solon. A thread: 👇 www.biorxiv.org/content/10.1...

Gene regulation is more complex than you think, even in bacteria! Check out the preprint from the PhD work of Luca Galbusera. TLDR: Within single cells, transcription factor (TF) levels can undergo large transient changes that occur on the same time-scale as 1/n www.biorxiv.org/content/10.1...

#paperalert! In our new study, we ask the question: Can we predict RNA stability across conditions and protocols, based solely on experimental and/or computationally predicted RNA binding protein target sites? Read the paper to find out ! www.biorxiv.org/content/10.1...

Very interesting work! Although we had a different inference approach, we similarly predicted peaks of degradation rate, predominantly in G1 & G1/S phase and peaks of transcription rate and burst frequency, predominantly in S phase and the late cell cycle: www.cell.com/cell-systems...

Any RNA biologists in the room? Does this makes sense? Is your favourite RBP in the list? #RNAbiology #RNAexport #RNAstability

Huge effort resulting in improved TF binding site models. Congrats to the winners but also all participants for pushing analytical borders and finally also to Vanja Kulakovskiy @halfacrocodile.bsky.social‬ & team for organizing it all!