Preprint alert!
We combined microfluidics, proteomics, and RNA-seq to map spatiotemporal protein expression during mouse somitogenesis and found a novel regulatory strategy: dynamic antagonistic gradients fine-tune signalling strength.

doi.org/10.1101/2025...

📣 It is my pleasure to announce our recent review with Margherita on the current approaches, challenges, and perspectives in studying human maternal-fetal interface using in vitro models www.cell.com/cell-stem-ce... 🚀✨️

We've updated our biorxiv! Check it out if you're interested in a new technique co-profiling RNA and epigenetics in single cells, extended gastruloid culture, and our proposed model for an epigenetic timer determining sequential perceptiveness to different lineages! ➡️ www.biorxiv.org/content/10.1...

I am very excited to share our latest work where we describe a new method to profile genome-wide chromatin transitions over time in single cells. Great collaborative effort with the van Oudenaarden group @hubrechtinstitute.bsky.social @oncodeinstitute.bsky.social www.nature.com/articles/s41....

What an honor. Look at all these other people!! Congrats to all (and see you in October!?). I wanna thank all mentors, lab-members and collaborators for making this possible. Science is a community effort, and I love it @fbm-unil.bsky.social @mpi-cbg.de @schierlab.bsky.social

Great job opportunity at The Center for Integrative Genomics, Lausanne University, Switzerland unil.ch/cig/en/home....
For a tenure-track Assistant Professor position. More details for how to apply are here nature.com/naturecareer...

Excited our paper is out! G-quadruplex (G4) unwinding via an intricate G-loop assembly and disassembly mechanism maintains genome integrity. Pioneered by Koichi Sato with great collaborators Jing Lyu and @simonelsasser.bsky.social Check it out: www.science.org/doi/10.1126/science.adr0493 🧵(1/4)

🧬Postdoc position alert! 🚨 We're hiring a postoc in Computational Modeling of Epigenetic Inheritance at the Hubrecht Institute (Alexander van Oudenaarden, Utrecht 🇳🇱) & Danish Cancer Institute (Anja Groth, Copenhagen 🇩🇰).

Come work in our collaberative team of top scientists

shorturl.at/avBBy

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social.
I'm so excited about this!
www.biorxiv.org/content/10.1...

Delighted to share the latest preprint from the lab led by Janith Seneviratne

We reveal novel roles for #embryonic regulators DPPA2/4 in facilitating a H2AK119Ub primed #chromatin state when aberrantly up-regulated in non-small cell lung #cancers 🧬🔬 (1/6)

www.biorxiv.org/content/10.1...

Thank you! So nice to hear :)

Martino Ugolini and I wrote a review on how useful embryos are to understand the role of transcription bodies in gene expression. I am sure
@mirlab.bsky.social, @harrisonflylab.bsky.social, @lennarthilbert.bsky.social and others would agree. Enjoy the read! portlandpress.com/biochemsoctr....

Thank you Vlad! ✨️

Most importantly - thank you to Lianne, Peter, and @vivekbhr.bsky.social for kickstarting this project, and Danique, Hendrik, Joëlle and Thijs for the wonderful collaboration and adding crucial experiments to our study

We emphasise that the effects of pre-culture conditions are cell line-dependent, necessitating optimisation for each cell line (more info in our discussion!). Even so, this study helped us a lot in increasing reproducibility and recovery of complex cell types. We hope it is helpful to you too! [7/7]

Lastly, we asked what the effect of these pre-cultures is on cell fate specification. We chose the ESLIF conditions and sequenced 5 individual gastruloids for each. This showed that ESLIF-only skewed gastruloids towards a neural fate, whereas short pulses of 2i increase the mesoderm fraction. [6/7]

We profiled H3K27me3 and DNA methylation, and found differential coverage of both modifications in a subset of developmentally associated genes across pre-culture conditions. These genes were not yet transcribed, indicating that epigenetic priming plays a role. [5/7]

RNA sequencing revealed distinct transcriptome profiles between pre-cultures ending with ESLIF vs 2i incubation, with differential expression of epigenetic factors such as Polycomb subunits and DNA methyltransferases. [4/7]

Changing the pre-culture condition, as we call it, affects not only the mESC morphology but also gastruloid elongation, time point of symmetry breaking and reproducibility between experiments, and different cell lines display different optimal pre-culture conditions. But what determines this? [3/7]

This project started with observations of considerable variability in our gastruloid experiments, coupled to variable morphology in ESCs at time point of aggregation. We decided to systematically test this by applying different pulses of 2i and ESLIF medium, followed by gastruloid aggregation. [2/7]

Very happy to share that our paper on stem cell culture conditions is now out! doi.org/10.1371/jour... We found that modulating mESC culture conditions influences gastruloid elongation and lineage specification, and helps with making the protocol more reproducible in our hands! more below 🧵⬇️ [1/7]

Query from Slack tankspace: “Looking for transgenic lines [preferably in Europe] marking mesoderm/mesendoderm and ectoderm, with expression before 6hpf. Thinking of mezzo and sox3, if anyone has these? Any other suggestions would also be great.” #AskZebrafish

How do embryos ensure precise tissue patterning? It’s all about timing cell divisions! Our new preprint reveals how cell proliferation syncs with signaling oscillations to regulate precision of somite formation and growth. Check the full story: www.biorxiv.org/content/10.1...