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Davide Mazza @davidemazza.bsky.social · 20d

Slightly diminish a band:
They might be quite tall.

Davide Mazza @davidemazza.bsky.social · May 15

Minflux goes to chromatin! Very interesting preprint from @andersshansen.bsky.social lab, featuring co-first author @matteomazzocca.bsky.social, that keeps on making me very proud.

matteomazzocca.bsky.social @matteomazzocca.bsky.social · May 14

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Super excited to share my first preprint from @andersshansen.bsky.social Lab! We used MINFLUX to track chromatin (H2B-Halo and Fbn2 locus) at an unprecedented 200 μs, then combined it with SPT to span μs-minutes (H2B) or SPT & Super-Res Live-Cell Imaging (SRLCI) to span μs-hours (Fbn2)

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Davide Mazza @davidemazza.bsky.social · Mar 7

That's so great, Davide! Congratulations!

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Davide Mazza @davidemazza.bsky.social · Feb 12

This looks sooo great! Congratulations @mirlab.bsky.social !!

Mir Lab @mirlab.bsky.social · Feb 12

1/n Excited to share our new preprint! Using live imaging in Drosophila embryos, we show that RNA Pol II clusters switch from sites of initiation to elongation during zygotic genome activation and that they are stably associated with an active gene: www.biorxiv.org/content/10.1...

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Davide Mazza @davidemazza.bsky.social · Feb 7

Great to see you here, Tim!

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Reposted by Davide Mazza

Christof Gebhardt @gebhardtlab.bsky.social · Feb 2

Happy to share Duyen's and Philipp's work on effective binding energy landscape and affinity of RBPJ obtained in vivo by on- and off-rate measurements is now published. Great collaboration with labs of Franz Oswald and Tilman Borggrefe doi.org/10.1038/s414...

Effective in vivo binding energy landscape illustrates kinetic stability of RBPJ-DNA binding - Nature Communications

Transcription factor binding to DNA is vital for gene regulation. Here, the authors determine the kinetics of DNA binding for RBPJ in living cells. They find that the binding is kinetically rather tha...

doi.org

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Davide Mazza @davidemazza.bsky.social · Feb 7

Fantastic Work Christof!

Davide Mazza @davidemazza.bsky.social · Jan 31

Preprint from Marklund and Greenleaf labs on TF binding: www.biorxiv.org/content/10.1...

In vitro single molecule imaging + In nuclei single molecule footprinting of KLF on engineeered sequences.

On-rates matter more than off-rates, similarly to what previously shown in baceria.

Thermodynamic principles link in vitro transcription factor affinities to single-molecule chromatin states in cells

The molecular details governing transcription factor (TF) binding and the formation of accessible chromatin are not yet quantitatively understood - including how sequence context modulates affinity, h...

www.biorxiv.org

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Reposted by Davide Mazza

Rosana Collepardo @rcollepardo.bsky.social · Jan 23

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)

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Davide Mazza @davidemazza.bsky.social · Jan 13

Thank you Laura, you are right! We should have cited that paper!

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Davide Mazza @davidemazza.bsky.social · Jan 13

This looks very interesting! www.science.org/doi/full/10....

On my reading list!

Chromatin conformation, gene transcription, and nucleosome remodeling as an emergent system

Gene transcription is an emergent phenomenon of packing domain geometry in situ.

www.science.org

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Reposted by Davide Mazza

bioRxiv Biochemistry @biorxiv-biochem.bsky.social · Jan 7

Real-time visualization of reconstituted transcription reveals RNA polymerase II activation mechanisms at single promoters https://www.biorxiv.org/content/10.1101/2025.01.06.631569v1

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Reposted by Davide Mazza

Ben Engel @cellarchlab.com · Jan 6

Towards community-driven visual proteomics! Excited to finally share this large-scale curated & annotated dataset of 1829 high-quality #cryoET tomograms of the little green alga that just keeps giving— Chlamydomonas! 🧪🧶🧬🌾🌊🌍

Preprint📜: www.biorxiv.org/content/10.1...

A short thread🧵👇

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Davide Mazza @davidemazza.bsky.social · Jan 4

Tasty, tasty phase separation. A much needed rigorous study!

Giacomo Bartolucci (he) @gbart.bsky.social · Jan 4

1/n Some time ago my colleague, excellent cook, and friend Ivan told me: "Cacio e pepe is the recipe that I screw up more often. Let's make a project studying systematically the physics of that sauce".

Prepare to get cheesy, I'm glad to share the Cacio e paper preprint:

arxiv.org/abs/2501.00536

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Davide Mazza @davidemazza.bsky.social · Dec 23

Thank you Kazuhiro.Your work was a great inspiration for this! We hope to have reported it accurately.

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Davide Mazza @davidemazza.bsky.social · Dec 23

Thanks Mark, all merit goes to Tom on this! He went through many iterations before having something that was somehow 'accurate' and yet readable.

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Reposted by Davide Mazza

Anders Sejr Hansen @andersshansen.bsky.social · Dec 20

Excited to share @domenicnarducci.bsky.social 's paper now out in Mol Cell published back-to-back with the paper from @dewitlab.bsky.social‬ - despite lots of prior work, we find that ZNF143 has no looping function
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...

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Davide Mazza @davidemazza.bsky.social · Dec 20

Thank you Lennart!

Davide Mazza @davidemazza.bsky.social · Dec 20

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.

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Davide Mazza @davidemazza.bsky.social · Dec 20

Thank you very much Carmelo! Happy to have joined this lively community!

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