12/n This is just the beginning! We're excited to apply this and capture genome architecture dynamics across new systems. Watch this space! 👀🧬
10.03.2026 17:42
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12/n This is just the beginning! We're excited to apply this and capture genome architecture dynamics across new systems. Watch this space! 👀🧬
11/n We also used the protocol partnering with Ulrike Kutay's lab to ask: what happens when you perturb nuclear heterochromatin tethering?
The result? Stunning linked changes between architecture and landscape in HCT116 cells at compartment switches.
www.nature.com/articles/s41...
10/n We also used @protocolsio.bsky.social, which was super helpful. Protocols below — I’ll keep adding more for other cell types and tweaks. Feel free to ask questions there 🙂
Fixation: doi.org/10.17504/pro...
Pico-C: doi.org/10.17504/pro...
9/n I am also very thankful for the support through the years from my lab & mentor @vaquerizaslab.bsky.social @vaquerizasjm.bsky.social
8/n This was overall a mammoth effort from everyone, and I am very thankful for everyone that helped along the way, this includes @shelbyflies.bsky.social who also took the time to try to do some funky mutants for me.
7/n To test this further we collaborated with @harrisonflylab.bsky.social to simultaneously deplete pioneer factors Zelda and GAF in embryos. This led to beautiful context-specific perturbations in architecture, further highlighting a modular regulatory logic behind genome establishment.
6/n We asked if this was encoded in the sequence. Collaborating with @Jian Zhou and @ycz23.bsky.social, they built a deep learning model on our high-resolution data. The models predicted that different motifs make distinct, independent contributions to genome architecture.
5/n We first blocked transcriptional elongation, now with a better granular view, we found that the effects were site-specific: some early loops stuck around, while insulation at active promoters mildly weakened, suggesting different regulatory dependencies.
4/n Using cluster analysis (and ChromHMM), we found that the genome is shaped by a diverse landscape with strong context-dependent enrichments. So we set out to test this.
3/n To our surprise, while much of the architecture emerges at NC14 with ZGA, we also found many stage-specific looping events that occur despite the very short time between interphases (~1.5 hours between NC9-NC14).
2/n Pico-C let us take advantage of a beautiful system where we can stage distinct nuclear cycles (NCs) at interphase despite dramatic embryo-wide mitotic waves. This gave us unprecedented temporal and architectural resolution from NC 9–14.
Excited to share my PhD work!
The question: How is genome organization established? Here, we developed a low-input Micro-C method, Pico-C, and used it to map chromatin architecture across early stages of fly development.
Here’s a quick Blue-torial 🙂 (1/n)
www.nature.com/articles/s41...
Thanks Noelia ❤️
Congratulations to @nmaziak.bsky.social, @vaquerizasjm.bsky.social et al: Pico-C (low-input Micro-C) shows 3D genome architecture reorganises before major zygotic genome activation in Drosophila, with early loop formation and stronger insulation.
@natgenet.nature.com: www.nature.com/articles/s41...
Thanks a ton Ilya 😊
Thanks Damir!!! 😊
Thanks a ton Tobias, and always for the support!
It’s finally out! 😊
How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...
Bipartisanship at the face of fascism. Still. My god, you guys are just fantastic at everything but working.
Wellcome Connecting Science laboratory and computational course. Low Input Epigenomics Course dates: 9-16 May 2025 Location: Wellcome Genome Campus, UK Application and bursary deadline: 11 February 2025
Do you want to explore the #chromatin of an organism?
Join our expert instructors at #LowInput25, and learn how to use low input techniques to support your #epigenomics research at the gene & genome-wide level
⏰Application deadline: 11 February
📎bit.ly/40fdETV
#ChromatinSky @nmaziak.bsky.social
I never expected my first post here to be anything but science, yet today we celebrate the fall of a regime that’s brought decades of pain. The joy of this moment is worth sharing a thousand times over.
