Daniel Jost - Physical Biology of Chromatin group

Our work on the interplay between loop extrusion and chromatin mechanics is finally out in @physrevresearch.bsky.social . Congrats @hosseinsalari.bsky.social for the hard work ! 👏
journals.aps.org/prresearch/a...

Happy to share our Current Opinion review on the key challenges in accurately predicting 3D distances between chromatin segments and computing their dynamics. Thanks to @djost-physbiol.bsky.social @lucagiorgetti.bsky.social for the invitation to write this review! @shuvadipdutta.bsky.social

Thanks also to @lucagiorgetti.bsky.social and @djost-physbiol.bsky.social for the invitation and for putting together a very interesting themed issue - the other reviews in the issue can be found here
www.sciencedirect.com/special-issu...

🚨SUMOylation regulates the formation and function of Polycomb foci. New preprint from Cavalli lab where we performed modeling: SUMOylation regulates the PRC1 self-attractions mediating PcG condensate. Look at the preprint 👇https://www.biorxiv.org/content/10.64898/2026.02.05.704038v1

Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding - Nature Genetics Acute perturbation of histone acetylation induces changes in chromatin organization that are only partially reversed once the perturbation is removed and are associated with transcriptional memory eff...

TSA treatment may induce cellular and structural memory !! Happy to have been part of this beautiful story, lead by @fpaldi.bsky.social in Giacomo Cavalli's lab. Now published in @natgenet.nature.com 👏.
www.nature.com/articles/s41...

Thanks Job ! Our modeling and conclusions nicely fits with your original findings. All comments are welcome as the paper is still far from being published :-)

🤔 Open question: If sister chromatids are partially and asymmetrically aligned, how does the cell ensure accurate repair and segregation?

Our results are very similar to recent findings in mammals from @golobor.bsky.social and Gerlich labs, suggesting possible conserved properties.

We show that cohesin is sparsely distributed, leading to loosely aligned, mildly compacted sister chromatids. Moreover, cohesion is asymmetric—sister chromatids are tethered more strongly in cohesin-rich regions, even if they’re non-homologous.

Our study combines:
✔️ Polymer modeling
✔️ Data analysis of Genome-wide contact maps (WT vs. mutants) of SisterC, Hi-C and Micro-C datasets.

How does cohesin keep sister chromatids together and organize them after DNA replication?
Cohesin isn’t just a “glue” for sister chromatids (cohesion function)—it also shapes their 3D organization via loop extrusion. But how do these two functions interact?

🚨 New preprint from the lab. Combining modeling and data analysis of SisterC data in yeast, we investigate cohesion of replicated chromosomes and show that sister chromatids are loosely and asymmetrically aligned in G2/M. Check the tweetorial below ⬇️ www.biorxiv.org/content/10.6...

SMC and recombination enthusiasts: we updated our work describing the loop extrusion properties of budding yeast condensin and its function in biasing donor usage for mating-type switching. Lots of cool new data, check it out!
www.biorxiv.org/content/10.1...

Our Mini Review went online last night in Current Opinion in Genetics & Development
"Block copolymer concepts of how transcription organizes the stem cell genome"
doi.org/10.1016/j.gd...

Fig. 1: Stem cell–typical organization of the genome and transcription, and the block copolymer sorting concept.

🚨Our work on the impact of DNA replication on 3D genome is out in Genome Biology: replication-dependent loop extrusion by sister-forks, wave of replication, no evidence for large-scale replication factory. Great collab with @aurelepiazza.bsky.social. More here: link.springer.com/article/10.1...

www.insb.cnrs.fr/fr/cnrsinfo/...

BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)

Chromatin gets stiffer when pulled gently but softer when yanked hard—thanks to loop extrusion. SMCs may play the role fo shock absorbers, protecting the genome from weak mechanical perturbations but allowing adaptation for persistent strong stresses.

Loop extrusion provides mechanical robustness to chromatin Chromosomes are complex biopolymers folded into dynamic loops via a loop extrusion process and may experience various mechanical forces in vivo . We develop a force-dependent model of chromatin loop e...

New preprint from the lab !! Loop extrusion may provide mechanical robustness to chromatin. Great work by Hossein Salari. @cnrs.fr @lbmcinlyon.bsky.social
www.biorxiv.org/content/10.1...

YouTube video by CNRS À la découverte des chromosomes | Conférence immersive | Les Échappées inattendues

"A la découverte des chromosomes", la conférence immersive imaginée par @djost-physbiol.bsky.social est en ligne sur la chaine Youtube du CNRS.

www.youtube.com/watch?v=CHh_...

@cnrsbiologie.bsky.social
@cnrs-rhoneauvergne.bsky.social
@ensdelyon.bsky.social

Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes Although significant progress has been made on our understanding of DNA replication and spatial chromosome organization in eukaryotes, how they both interplay remains elusive. In particular, from the ...

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If you're interested in genome biology, chromatin structure, or computational modeling, this one's for you. Great collaboration with Piazza lab @aurelepiazza.bsky.social
🧬👾🔁
📄 Full preprint/paper: www.biorxiv.org/content/10.1...
🧵Thanks for reading! RTs appreciated.

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💡 Big picture:
Replication doesn’t just use the genome’s 3D structure—it actively reshapes it.
Our model bridges replication dynamics with genome architecture, offering a new view of chromatin duplication in 3D.

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Our model also reveals a dynamic effect:
As forks move, they temporarily slow down chromatin motion.
Why? Due to the mechanical constraints of fork passage and intertwining of sister chromatids. 🧷

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Zooming out: replication forks are not evenly spread in early S-phase.
They concentrate at one nuclear pole, then redistribute more evenly later on.
This spatial bias could explain how forks cluster into Replication Foci, seen in microscopy! 🧪

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Then we asked: does this pattern exist in real cells?
✅ We confirmed it in vivo using new Hi-C data collected during early S-phase thanks to a collaboration with @aurelepiazza.bsky.social
And it holds across different conditions.
Importantly, it’s:
🔄 Replication-dependent
🚫 Cohesin-independent

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What did we find?
A striking “fountain” pattern forms around early origins of replication, caused by the colocalization of sister forks moving outward.
This pattern emerges spontaneously from our model! 🚰

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We built a computational model of the yeast genome that integrates:
📍Realistic 3D chromatin architecture
🕒 Accurate replication timing
With this, we simulated how replication unfolds spatially inside the nucleus.

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DNA replication doesn’t happen in isolation—it’s tightly linked to how chromatin is organized in space.
But from the behavior of sister replication forks to the formation of replication domains, many mechanisms are still debated. So, we turned to modeling. 💻

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How does DNA replication shape the 3D structure of the genome? 🧬
Despite major advances, we still don’t fully understand how replication and chromosome architecture interact. In our new study, we dive into this interplay using Saccharomyces cerevisiae as a model. 🔬

Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes Although significant progress has been made on our understanding of DNA replication and spatial chromosome organization in eukaryotes, how they both interplay remains elusive. In particular, from the ...

🚨 new preprint from the lab. Combining modeling, new Hi-C data in yeast and data analysis, our study offers new insights into the spatial and dynamic organization of chromatin during replication in eukaryotes. Check the tweetorial below ⬇️ www.biorxiv.org/content/10.1...