Davide Mazza
@davidemazza.bsky.social
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How do dynamics of signalling molecules skew cell fate decisions? With this review we try to move our first steps in the signalling dynamics field, together with the expert lead of
@samuzambrano.bsky.social
! Kudos to Fulvio, Sara and Erika for their excellent work!
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3 months ago
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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.
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8 months ago
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This looks sooo great! Congratulations
@mirlab.bsky.social
!!
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11 months ago
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reposted by
Davide Mazza
Christof Gebhardt
11 months ago
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...
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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...
https://doi.org/10.1038/s41467-025-56515-4
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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.
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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...
https://www.biorxiv.org/content/10.1101/2025.01.27.635162v2
11 months ago
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reposted by
Davide Mazza
Rosana Collepardo
12 months ago
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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This looks very interesting!
www.science.org/doi/full/10....
On my reading list!
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Chromatin conformation, gene transcription, and nucleosome remodeling as an emergent system
Gene transcription is an emergent phenomenon of packing domain geometry in situ.
https://www.science.org/doi/full/10.1126/sciadv.adq6652
12 months ago
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Davide Mazza
bioRxiv Biochemistry
about 1 year ago
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
about 1 year ago
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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Tasty, tasty phase separation. A much needed rigorous study!
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about 1 year ago
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reposted by
Davide Mazza
Anders Sejr Hansen
about 1 year ago
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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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.
about 1 year ago
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