So grateful to my buddy the great @davidemazza.bsky.social and all the contributors from our teams to this joint effort to unravel NF-κB–p53 crosstalk. Davide’s thread nicely explains the main findings — here’s a short side note from me 🧵👇 (1/n)
Read our new preprint where we uncover a hierarchy in human PIC assembly and establish a quantitative framework that connects factor exchange kinetics to the regulation of Pol II activity in living human cells. doi: doi.org/10.64898/202...
By A. Oravecz and our collaborators @molinalab.bsky.social
Congratulations, Arnaud!
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
🧬RNA processing
🧬Translation
🧬Transcription & chromatin regulation
🧬Method development
🧬Theory
Very cool, Lars! Congrats!
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
Thanks!
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 🧬🖥️
Thanks!
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 🤩?
Muchas gracias!!!
Finally, if you've made it this far, you might be interested in testing the code. Feedback is very welcome! github.com/MolinaLab-IG...
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HiddenFoot also works with Fiber-seq data! It reveals chromatin structure and nucleosome occupancy heterogeneity at single-molecule resolution driven by TF binding.
5/6
HiddenFoot resolves Pol II and nucleosome occupancy at the HIV-1 promoter, molecule by molecule. Under transcriptional inhibition (TLD), Pol II footprints vanish, while nucleosome occupancy at the +1 and −1 positions increases.
4/6
HiddenFoot infers pairwise interaction energies from single-molecule data and compares them to simulated equilibrium profiles to distinguish true TF–TF cooperativity from nucleosome-mediated co-binding.
3/6
HiddenFoot is a thermodynamics-based model that integrates known TF PWMs and nucleosome occupancy to efficiently evaluate all possible non-overlapping binding configurations. It fits model parameters using both stochastic gradient descent and MCMC.
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