(1/n) Excited to present the latest work from the de Wit lab, where we identify and characterise loop extrusion-mediated fountains in mammalian genomes using acute depletion of 3D genome regulators: doi.org/10.1093/nar/.... A Bluetorial🧵:

Extrusion fountains are restricted by WAPL-dependent cohesin release and CTCF barriers

Abstract. Interphase chromosomes are mainly shaped by loop extrusion and compartmentalisation mechanisms. However, their temporal component and cause-effec

doi.org

The review on live-cell SMT that I contribute to the jmolbiol.bsky.social special issue ‚Imaging of the central dogma‘ is now online as pre-proof: www.sciencedirect.com/science/arti...

This is a piece that I and @karsten-rippe.bsky.social discussing a lot, and a topic that is very close to my heart. The editors @naturerevgenet.bsky.social gave us the stage to do so, and the final version of our review is now available under this link: rdcu.be/erP1u A short thread follows 1/n

@science.org Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation | Science www.science.org/doi/10.1126/... @jbuenrostro.bsky.social @eboyden3.bsky.social + al @broadinstitute.org @harvard.edu #ExIGS #Chromatin #Lamin #Progeria #Aging #ExpansionMicroscopy

Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation

Microscopy and genomics are used to characterize cell function, but approaches to connect the two types of information are lacking, particularly at subnuclear resolution. Here, we describe expansion i...

science.org

Great to see this published @genesdev.bsky.social. Evidence that enhancers can activate a bystander gene in an adjacent TAD, and that cohesin facilitates this. @uoe-igc.bsky.social. pubmed.ncbi.nlm.nih.gov/40436628/

1/ 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)

📣 New preprint from the lab – Massive work entirely driven by super-talented @simsakong.bsky.social , jointly betw. @beatfierz.bsky.social lab and mine – combining in vitro and in vivo TF single molecule imaging www.biorxiv.org/content/10.1...

Intriguing mechanism to balance production and degradation rates of proteins

David Suter@davidsuter.bsky.social · last yr.

3/ Through these twin controls, cells protect their proteins well, even through shifts. Thus, life adapts fast— a story of balance told through turnover rates. 🥳 Fantastic work spearheaded by Michael Sun and Benjamin Martin www.biorxiv.org/content/10.1...

Program is out for our first EMBL #singlemolecule gene regulation meeting! Check out the dedicated panel sessions on single molecule genomics, single molecule imaging and theory where we would like to brainstorm the future of the field: Registration is open! 👇 www.embl.org/about/info/c...

Gene regulation: one molecule at a time

embl.org

Single molecules, in living zebrafish embryos, during hour-long period of development: Jonas' work on binding kinetics of cohesin and CTCF around ZGA now online. Great collab with labs of @lucagiorgetti.bsky.social @akispapantonis.bsky.social doi.org/10.1038/s414...

Increasingly efficient chromatin binding of cohesin and CTCF supports chromatin architecture formation during zebrafish embryogenesis - Nature Communications

Using single-molecule tracking of cohesin and CTCF during zebrafish embryogenesis, the molecular kinetics underlying chromatin architecture formation was revealed and gradual emergence of chromatin st...

doi.org

#Cellpose 3 paper now out. Not all images are perfect. Restore your images with Cellpose3 to get better segmentations, w/ @marius10p.bsky.social www.nature.com/articles/s41...

Our new review on how the #chromatin domain is formed in the cell is now available @Curr Opin Struct Biol.📄✨ We critically discuss the domain formation mechanism from a physical perspective, including #phase-separation and #condensation. 📥 Free-download link: authors.elsevier.com/a/1keGn,LqAr...

After a long journey, Segment Anything for Microscopy is now published in Nature Methods! We significantly improve SAM for interactive and automatic segmentation in light and electron microscopy and build a user-friendly tool. www.nature.com/articles/s41...

Big thanks to all people involved @armelletollenaere.bsky.social , Enes Ugur, Susanna Dalla-Longa, Cédric Deluz, Devin Assenheimer, @gebhardtlab.bsky.social , and Heinrich Leonhardt And thanks ChatGPT for haikuing the abstract

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...

Great work and very useful developments!

@tim_stasevich@tim-stasevich.bsky.social · last yr.

Making intrabodies from antibodies just got easier! Learn how we made 𝟭𝟵 intrabodies to bind and light up peptides and histone modifications in live cells. And thanks to Academia, all sequences are freely available. (video credit: Yuko Sato @YukoSatoT2) (1/15) www.biorxiv.org/content/10.1...

Measuring morphogen transport over multiple spatial scales in live zebrafish embryos https://www.biorxiv.org/content/10.1101/2025.02.06.636788v1

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

Thermodynamic principles link in vitro transcription factor affinities to single-molecule chromatin states in cells www.biorxiv.org/content/10.1... ▶️40-fold flanking sequence effect on TF binding ▶️Motif recognition beats kinetics ▶️Minutes-long residence times ▶️Models of TF-nucleosome competiton