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Sendoel Lab @sendoellab.bsky.social · Sep 2

Our first PhD generation is flying out of the nest. Thank you Merve and Clara for shaping our lab from day one on.

Wishing you all the best in your next chapters, we’re excited to see what comes next for you!

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NCCR RNA & Disease @nccr-rna-disease.bsky.social · Sep 1

🔬✨ Join us this Saturday (September 6) | 16:00-23:00 at Nacht der Forschung 2025 at the University of Bern ✨ Come and check out our booth "RNA – Master of Versatility" 👩‍🔬

Meet our researchers & enjoy pipetted cocktails at the reproduzierBAR!
www.nachtderforschung.unibe.ch
#ndfunibern @unibe.ch

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David Taborsky @dadita.bsky.social · Aug 6

If you are interested in #DevBio, #organoids, #gastruloids or #CRISPR, check out the tweetorial to our new preprint on uncovering novel regulators of body plan formation in gastruloids using single cell CRISPR screens!

A big thank you to all co-authors that made this paper possible!

Sendoel Lab @sendoellab.bsky.social · Aug 6

The establishment of the body plan during gastrulation is a hallmark of animal life, yet much of its regulation remains unclear. Here, we combine gastruloids and single-cell CRISPR screenings to uncover new regulators of the body plan.

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

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Nikolai Slavov @slavov-n.bsky.social · Aug 7

The authors report that all seven tested deep learning models failed to outperform simple baselines in predicting transcriptome changes after single or double perturbations.

I will duck for cover.

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bioRxivpreprint @biorxivpreprint.bsky.social · Aug 7

Genome-wide chromatin recording resolves dynamic cell state changes https://www.biorxiv.org/content/10.1101/2025.08.05.668773v1

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Sendoel Lab @sendoellab.bsky.social · Aug 6

Many thanks to all members of our lab and to our collaborators in the Lutolf and Zavolan labs!

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Sendoel Lab @sendoellab.bsky.social · Aug 6

In sum, our findings highlight polyadenylation-mediated control of transcript stability as a critical mechanism in shaping the mammalian body plan and position gastruloid-based single-cell CRISPR screening as a powerful platform for systematic discovery of developmental regulators.

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Sendoel Lab @sendoellab.bsky.social · Aug 6

Cells adopting notochord identity in Cnot8 KO gastruloids closely matched embryonic notochord cell profiles. This was accompanied by increased Nodal signaling and a profound loss of Hox gene expression, with a shift toward dorso-ventral and anterior primitive streak fates.

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Sendoel Lab @sendoellab.bsky.social · Aug 6

Single-cell RNA sequencing of Cnot8-deficient gastruloids demonstrated severely altered mesodermal patterning, with paraxial mesoderm largely absent and a bias toward axial mesoderm and notochord differentiation.

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Sendoel Lab @sendoellab.bsky.social · Aug 6

Intriguingly, Cnot8 KO organoids exhibited indeed transcript stabilization of Nodal along with multiple components and modulators of the TGF-β and Wnt signaling pathways, consistent with profoundly altered patterning cues.

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Sendoel Lab @sendoellab.bsky.social · Aug 6

Given the established role of the CCR4-NOT complex in mRNA deadenylation and turnover, we profiled the poly(A) landscape in Cnot8 knockout organoids and observed marked poly(A) tail elongation of key signaling transcripts, including Nodal.

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Sendoel Lab @sendoellab.bsky.social · Aug 6

Interestingly, transcriptomic analysis of these Brachyury-positive cells in Cnot8 KO organoids revealed signatures of notochord cells, a cell type usually absent in mammalian gastruloids.

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Sendoel Lab @sendoellab.bsky.social · Aug 6

Our screen revealed several novel regulators of germ layer differentiation, including a strong paraxial mesoderm-specific role of the CCR4-NOT component Cnot8. Loss of Cnot8 resulted in gastruloid patterning defects such as the formation of multiple Brachyury poles and aberrant growth.

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Sendoel Lab @sendoellab.bsky.social · Aug 6

Validation of our screen revealed strong global depletion of general depletion controls, while germ layer controls were selectively depleted in their respective germ layers, accompanied by the loss of characteristic transcriptomic markers.

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Sendoel Lab @sendoellab.bsky.social · Aug 6

Led by the brilliant @dadita.bsky.social‬, we first established a single-cell CRISPR screening platform in gastruloids and designed a library targeting 200 RNA-binding proteins as well as known regulators of germ layer differentiation.

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Sendoel Lab @sendoellab.bsky.social · Aug 6

The establishment of the body plan during gastrulation is a hallmark of animal life, yet much of its regulation remains unclear. Here, we combine gastruloids and single-cell CRISPR screenings to uncover new regulators of the body plan.

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

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Sendoel Lab @sendoellab.bsky.social · Aug 4

Third defense this summer officially in the books. Huge congrats to Fabiola for a brilliant presentation and defense! #Summerofdefenses

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Alfonso Martinez Arias @amartinezarias.bsky.social · Jul 23

….and more #gastruloid preprint with proof of how to use their robustness and scalabiliy in high throughput screens to learn about #posttranscriptional regulation of gene expression @ Sendoel and Lutolf labs www.biorxiv.org/content/10.1...

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NCCR RNA & Disease @nccr-rna-disease.bsky.social · Jul 25

Preprint by the @sendoellab.bsky.social in collab w/ the Lutolf & Zavolan labs w/1st author David Taborsky "Regulation of mRNA polyadenylation governs mammalian body plan formation in gastruloids" @biorxivpreprint.bsky.social
buff.ly/mL3a71T
@dadita.bsky.socia
@mihaelazavolan.bsky.social

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David Taborsky @dadita.bsky.social · Jul 25

How can we identify novel regulators of germ layer differentiation and body patterning? I am happy to announce that my preprint using single-cell CRISPR screens in gastruloids to answer this question is now online! Thank you to the rest of the @sendoellab.bsky.social and all coauthors!

bioRxiv Developmental Biology @biorxiv-devbio.bsky.social · Jul 22

Regulation of mRNA polyadenylation governs mammalian body plan formation in gastruloids https://www.biorxiv.org/content/10.1101/2025.07.22.666114v1

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Merve Yigit @merveyigit.bsky.social · Jun 29

PhDone 🥳🎓

The last few years was full of successes, failures, ups and downs, but also full of amazing people, countless talks, great conferences, incredible science and endless support from my supervisor and my thesis committee. Thanks to all people who helped me in this amazing journey! #eIF2A

Sendoel Lab @sendoellab.bsky.social · Jun 27

The summer of defenses continues, huge congratulations Dr. Yigit for a superbly delivered talk and an excellent defense!

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Sendoel Lab @sendoellab.bsky.social · Jun 27

The summer of defenses continues, huge congratulations Dr. Yigit for a superbly delivered talk and an excellent defense!

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Barbara Marte @barbmarte.bsky.social · May 28

new out in Nature today www.nature.com/articles/s41...

Cross-tissue multicellular coordination and its rewiring in cancer - Nature

Comprehensive single-cell transcriptomic analysis of 35 human tissues reveals 12 cross-tissue coordinated cellular modules that exhibit intramodule communication and dynamic changes with ageing, and w...

www.nature.com

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Sendoel Lab @sendoellab.bsky.social · May 28

The very first PhD graduate of our lab! Great science, fantastic presentation and expertly defended. Huge congratulations on this well-earned milestone Dr. Duré!

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NCCR RNA & Disease @nccr-rna-disease.bsky.social · May 27

Preprint by the Sendoel Lab ( @sendoellab.bsky.social ) with first author Merve Yigit ( @merveyigit.bsky.social‬ "The alternative initiation factor eIF2A regulates 40S subunit turnover in ribosome-associated quality control"
@biorxivpreprint.bsky.social‬
buff.ly/hP9Iani
‪@anupamd.bsky.social‬

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