1/New preprint just dropped! 🔥🔥 We investigate how the genome is destroyed in apoptotic cells in a way that prevents DNA fragments from spreading beyond the dying cell 🧬⚰
Done here at @imbavienna.bsky.social & in the super @rcollepardo.bsky.social & Rosen labs:
www.biorxiv.org/content/10.6...
A Goldilocks zone of DNA flexibility defines stable yet plastic nucleosomes, tuned by histone chemistry https://www.biorxiv.org/content/10.64898/2026.02.16.706184v1
How do DNA sequence and histone chemistry tune nucleosome stability and plasticity?
Check out our latest work to find out. Now available on bioRxiv!
www.biorxiv.org/content/10.6...
@juliamaristany.bsky.social
@janhuemar.bsky.social
@rcollepardo.bsky.social
Share with your colleagues!!
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Please visit the preprint! We are very proud of this work - but also, this paper means a lot to me:
Jan and I met and started dating while working on it. Later, we worked on many more projects together, but this was the first. Some projects shape your science - this one shaped my life, too ❤️
We computed the force profiles for 40+ different combinations of DNA sequence and histone chemistry! To explore the full data set, visit janhuemar.github.io/PullingNucle...
This widget allows you to see and compare the measurements from force-induced pulling simulations for every system we tested!
We also describe a mechanical transition: topologically protected, partially unwrapped intermediate states stabilise the nucleosome:
A) A first ~90° flip during outer-turn release
B) A second ~180° flip before inner-turn unwrapping
These define the mechanical bottlenecks of nucleosome unwrapping
Our central finding is that nucleosome stability emerges from an interplay between:
🧬 DNA elasticity
⚛️ Histone chemistry
📐 Nucleosome geometry
And that genomic sequences operate in a narrow “Goldilocks zone” of DNA flexibility that balances thermodynamic stability with mechanical plasticity
In this work, we explore a deceivingly simple question:
How does DNA sequence and histone chemistry tune the mechanical plasticity of nucleosomes?
What we find is that DNA sequence encodes a mechanical “dial” that shifts nucleosomes between stable and plastic regimes 🧬
New paper alert from the group!! 🚨: DNA flexibility tips the balance between stability and plasticity in nucleosomes
One of the works from my PhD, co-led alongside @nachper.bsky.social, is finally out! Work from @rcollepardo.bsky.social & @janhuemar.bsky.social
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www.biorxiv.org/content/10.6...
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Want to learn about how we use computational approaches at different scales to study biomolecular condensates?
Check out our latest review, out in Advances in Physics X
@juliamaristany.bsky.social @alinaemelianova.bsky.social
@rcollepardo.bsky.social
www.tandfonline.com/doi/epdf/10....
This work was a highlight of my PhD, and a true joy of a collaboration 🥳🥳
Feeling very lucky to be able to explore these deep scientific questions alongside such talented (and kind!) people!!!
Breakthrough resolution Cryo-ET by the talented @huabin-zhou.bsky.social from the Rosen lab at UTSouthwestern, with molecular dynamic simulations by the @rcollepardo.bsky.social Lab at Cambridge (alongside my awesome collegues @janhuemar.bsky.social and @kieranrussell.bsky.social)
Our latest work is out in @science.org !!!!!!! We look into #chromatin condensates at near atomistic resolution to decipher its phase behaviour and material properties 👩🔬🥼🧬
Our Science paper is out!
Huge congratulations to @huabin-zhou.bsky.social, Mike Rosen, and the brilliant @janhuemar.bsky.social @juliamaristany.bsky.social and @kieran-russell.bsky.social from our group
News: bit.ly/4avnkAr and bit.ly/3XBGVHS
Great perspective by @vram142.bsky.social +K Zhang
Super excited to share that our paper is now out in @science.org. Lots of work, but also lots of fun getting this out.
Be sure to check it out!
www.science.org/doi/10.1126/...
Also, follow:
@huabin-zhou.bsky.social @juliamaristany.bsky.social @kieran-russell.bsky.social @rcollepardo.bsky.social
This binding influences chromatin conformation, and we hypothesise that high concentrations of Oct4 promote nucleation and further coarsening of clusters on chromatin, aiding in the search for specific binding sites while overall increasing chromatin plasticity through non-specific binding
New paper from the @rcollepardo.bsky.social lab!!!!!
This time, we turn our attention to Oct4, a key pioneer transcription factor 👇👇👇👇
With simulations by @janhuemar.bsky.social, we propose a mechanism through which the clustering of Oct4 upon chromatin binding enhances chromatin plasticity 🧬⚛️👩
A rendering of multiple Oct4 molecules bound to a chromatin fibre
🚨 🚨 🚨 New preprint alert!!! 🚨 🚨 🚨
In the past, we have learnt that Oct4 can induce nucleosome breathing on the mono-nucleosome level.
But what happens when you have a fibre of multiple nucleosomes?
www.biorxiv.org/content/10.1...
@rcollepardo.bsky.social @juliamaristany.bsky.social
On a personal note, my favourite part of this project was the research team of amazing scientists behind it, lovely human beings who were a joy to work with!
Very happy and proud of this Rosen/Redding/Collepardo collaborative effort 🔥
also on bky:
@rcollepardo.bsky.social @janhuemar.bsky.social
By merging together experiments (led by Lifeng Chen), with our own coarse-grained simulations, we showcased how experimental and computational approaches can be used in tandem to unveil the molecular mechanisms that drive phase separation.
We also show the ISWI remodeler can slide nucleosomes to “on”✔️ or “off” ❌ spacings, toggling phase separation in vitro and in silico
Arrays with nucleosome spacing closer to a multiple of 10 (the DNA helical periodicity 🧬), are more compact, with increased intra-fiber contacts and lower inter-fiber valency, and form more loose, less stable networks in the condensate
These structural differences dictate condensate behaviour of chromatin arrays.
The key metric? Inter-fiber valency (how many neighbours each fiber contacts).
Higher valency in arrays (namely, arrays close to 10N+5 linkers) make for stronger inter-fiber interactions, and more stable condensates.
We designed nucleosome arrays with different linker DNA lengths, at single base pair resolution, in-vitro and in-silico.
We found that even subtle changes in spacing lead to large-scale structural differences (!)
Nucleosomes—the fundamental units of chromatin—can self-assemble into condensates. But what controls how they assemble?
Spacing between them matters: Just changing the DNA length between nucleosomes, even by a single base pair, dramatically alters how they interact and phase separate.
🚨 New paper out in Nature Comms!
From the Rosen, Redding and Collepardo Labs, we uncover how #nucleosome spacing fine-tunes the architecture of #chromatin condensates.
👇 A short thread on how physical #genome organization emerges from molecular interactions:
www.nature.com/articles/s41...
🌱Join us for the first #FragileNucleosome seminar of this spring! We are excited to host @juliamaristany.bsky.social & @chribue.bsky.social this week!
If you have registered before you can join from the same link, if not, don't forget to register!
us06web.zoom.us/webinar/regi...
We are happy to share our work on local #nucleosome dynamics integrating #temperature inputs into an #epigenetic switching mechanism.
⚠️ Preprint alert!!
www.biorxiv.org/content/10.1...
What is the multiscale structure of chromatin condensates? How does it shape thermodynamic and material properties?
We address this at near-atomistic resolution🔥🔥🔥 using cryoET (Rosen & Villa labs, led by H Zhou), a new multiscale model (K Russell) and cryoET-guided sims (J Huertas & J Maristany)
