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Grosshans Lab @labgrosshans.bsky.social · 1d

Absolute fun project with lead authors Dimos Gaidatzis (@fmiscience.bsky.social Comp Bio), Maike Graf-Landua and @smethot.bsky.social - and many other wonderful collaborators @labgrosshans.bsky.social ky.social and @fmiscience.bsky.social. Thanks to @snsf.ch and @erc.europa.eu for funding! n/n

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Grosshans Lab @labgrosshans.bsky.social · 1d

For >1,100 peaks, we could match their phase and amplitude to rhythmically expressing genes. The model also predicted the effects of GRH-1 depletion on the mRNA levels of those genes correctly. 10/n

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Grosshans Lab @labgrosshans.bsky.social · 1d

We validated the model experimentally, by acutely depleting GRH-1. The model reliably predicted the resulting changes in chromatin opening, even in those cases where they were not caused by GRH-1 directly, but, indirectly, through GRH-1’s effect on other TFS. 9/n

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Grosshans Lab @labgrosshans.bsky.social · 1d

In an extreme case, such additive activity can lead to a phenomenon of “destructive interference”, where the rhythmic activities of different TFs cancel each other out to cause non-rhythmic chromatin opening. 8/n

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Grosshans Lab @labgrosshans.bsky.social · 1d

Using a model with only these 9 TFs, and considering their binding strengths, we could predict chromatin dynamics of any phase and amplitude. Since we used linear models without interaction terms, this reveals that new phases and amplitudes can be generated by adding up the activity of TFs. 7/n

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Grosshans Lab @labgrosshans.bsky.social · 1d

This worked surprisingly well: we achieved a predictive power of >30%. 9 TFs stood out – with our old friends GRH-1, NHR-23, BLMP-1, NHR-25 on top. These were among six hits from a previous reverse genetic screen for TFs required for rhythmic molting dx.doi.org/10.15252/embj.2022111895 6/n

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Grosshans Lab @labgrosshans.bsky.social · 1d

We wondered if we could explain this dispersion through TF binding. Conveniently, the modEncode/modERN consortia have generated ChIP-seq data for ≥1/3 of C. elegans TFs. We used the data to try and predict phase and amplitude of each element. 5/n

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Grosshans Lab @labgrosshans.bsky.social · 1d

So then what generates these broad peak phase dispersion? Knowing that oscillations are transcriptional, we went to identify regulatory elements through an ATAC-seq timecourse. Strikingly, we saw extensive rhythmic opening and closing of chromatin – again with broad peak phase dispersion. 4/n

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Grosshans Lab @labgrosshans.bsky.social · 1d

Shout-out to @heiman.bsky.social for additionally demonstrating rhythmic gene expression in glial socket cells doi.org/10.1101/2025..., which were depleted from our samples.

Systematic identification of oscillatory gene expression in single cell types

Many biological cycles are driven by oscillatory gene expression coordinated across cell types. For example, larval development in Caenorhabditis elegans involves coordinated cyclic changes in cell di...

doi.org

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Grosshans Lab @labgrosshans.bsky.social · 1d

So we did scRNA-seq at different time points during a larval stage - and found oscillations in 7 epithelial tissues. Yet, these each had a broad peak phase dispersion. Moreover, most genes were predominantly expressed in only one of the tissues. 3/n

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Grosshans Lab @labgrosshans.bsky.social · 1d

This was the starting point doi.org/10.15252/msb... 1000s of "oscillating" genes, all peaking once per larval stage, but at different times. How is this broad dispersion of peak phases achieved? Perhaps a superposition of different tissues, given that the observation was with whole animal data? 2/n

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Grosshans Lab @labgrosshans.bsky.social · 1d

Paper alert! doi.org/10.1038/s443... - "A scheduler for rhythmic gene expression". We show how 9 txn factors suffice for rhythmic gene expression of thousands of genes with any phase or amplitude in #Celegans larvae (and also look at the tissues where oscillations happen) 1/n

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Reposted by Grosshans Lab

Meera Sundaram @meera-sundaram.bsky.social · 18d

The 2025-2026 #aECM club schedule is now posted on our website, where you can also find the link to sign up for access. I’m looking forward to lots of great talks and discussions! sundaramlab.com/blog/aecm-cl...

aECM Club Seminars

A virtual seminar series to highlight work on apical ECM across different systems Organizers: Meera Sundaram, UPennMax Heiman, Boston Children’s, Harvard U.Nathalie Pujol, U. Aix MarseilleJor…

sundaramlab.com

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Reposted by Grosshans Lab

FMI science @fmiscience.bsky.social · 24d

Another FMI Annual Meeting is in the books! After a night of follies and plenty of dancing, today brought the announcement of our internal prize winners, more inspiring talks, and a vibrant poster session. Already looking forward to next year! 🙌

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Reposted by Grosshans Lab

NCCR RNA & Disease @nccr-rna-disease.bsky.social · 26d

📅 Program of the NCCR RNA & Disease Seminar Series for the Autumn Semester 25/26: For more information visit: nccr-rna-and-disease.ch/news/article... 
@unibe.ch @ethz.ch @snf-fns.ch

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Reposted by Grosshans Lab

FMI science @fmiscience.bsky.social · 29d

📣The Turco group is seeking a computational biologist to analyze large omics datasets. Work on cutting-edge 3D organoid models of the human placenta and be embedded in our Computational Biology Platform (part of @sib.swiss). Apply here: www.fmi.ch/education-ca...

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Reposted by Grosshans Lab

FMI science @fmiscience.bsky.social · Sep 8

🚨 We're hiring, please share! The FMI seeks a tenure-track Group Leader (Assistant Prof) in Structural Biology 🔬
Innovative scientists in genome regulation, RNA metabolism, or protein homeostasis—especially using cutting-edge approaches—apply now at www.fmi.ch/education-ca...

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Grosshans Lab @labgrosshans.bsky.social · Sep 8

Thanks for highlighting - thread to follow. Mini-summary: beyond assigning oscillatory genes expression by scRNA-seq to individual cell types, we also show that chromatin opens rhythmically and that we can predict this (and gene expression) with a small set of TFs in a mathematical model.

Max Heiman @heiman.bsky.social · Sep 7

It accompanies a beautiful preprint from @labgrosshans.bsky.social whose pioneering work laid the foundation for the approach we took:
"A scheduler for rhythmic gene expression"
doi.org/10.1101/2025...

A scheduler for rhythmic gene expression

Genetic oscillators drive precisely timed gene expression, crucial for development and physiology. Using the C. elegans molting clock as a model, we investigate how oscillators can schedule the orderl...

doi.org

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Grosshans Lab @labgrosshans.bsky.social · Sep 8

Here is some recommended reading 👇 (and enjoy the associated thread for clarity and the beautiful imagery 👍) Lots of different genes, oscillating in different cell types

Max Heiman @heiman.bsky.social · Sep 7

In this study with @alexiswe.bsky.social and the Hammarlund lab we develop rigorous statistical methods to identify oscillatory gene expression using single-cell RNA data.

"Systematic identification of oscillatory gene expression in single cell types"
doi.org/10.1101/2025...

Systematic identification of oscillatory gene expression in single cell types

Many biological cycles are driven by oscillatory gene expression coordinated across cell types. For example, larval development in Caenorhabditis elegans involves coordinated cyclic changes in cell di...

doi.org

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Reposted by Grosshans Lab

Max Planck Institute of Immunobiology and Epigenetics @mpi-ie.bsky.social · Sep 4

🎊 Congratulations to Juliane Glaser (@julianeg.bsky.social) and Valentin Flury (@flurylab.bsky.social) on being awarded each an @erc.europa.eu Starting Grant! – #ERCStG

www.ie-freiburg.mpg.de/6057908/2025...

Two ERC Starting Grants for Max Planck in Freiburg

Two young scientists from the Max Planck Institute in Freiburg, Juliane Glaser and Valentin Flury, have each received €1.5 million in ERC Starting Grants to conduct research into epigenetic mechanisms...

www.ie-freiburg.mpg.de

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Reposted by Grosshans Lab

David Brückner @davidbrueckner.bsky.social · Sep 4

Super excited that our group will be supported by an ERC Starting Grant!

In project "InfoFate" we will study how cells use information in dynamical, neighborhood & mechanical signals to make decisions.

We'll have PhD and Postdoc positions available, please get in touch if interested!

Biozentrum, University of Basel @biozentrum.unibas.ch · Sep 4

Why do some cells become neurons and others muscle?
Physicist Prof. David Brückner @davidbrueckner.bsky.social @biozentrum.unibas.ch @unibas.ch receives a prestigious #ERCStartingGrant to uncover how cells make life-shaping decisions. @erc.europa.eu
www.biozentrum.unibas.ch/news/detail/...

ERC Starting Grant for Physicist David Brückner

How do cells decide which role to take on in the body? Prof. David Brückner from the Biozentrum of the University of Basel is investigating this and similar questions. Over the next five years, a Star...

www.biozentrum.unibas.ch

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Reposted by Grosshans Lab

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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Reposted by Grosshans Lab

Society for Developmental Biology @socdevbio.bsky.social · Aug 25

🪱 C. elegans (Nematode). Every cell counts, literally. C. elegans has a fully mapped cell lineage from egg to adult. Key for understanding cell fate specification, apoptosis, nervous system wiring, aging, and stem cell regulation. Image taken by Swagata Dey #ModelMonday

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Reposted by Grosshans Lab

Alexandra Bendel @alexbendel.bsky.social · Aug 25

I am happy to finally share this preprint of my PhD project in @guillaumediss.bsky.social lab at the FMI in Basel.
We used ddPCA to map the genetic architecture of the entire human bZIP interaction network.

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

Thanks to all our co-authors for the great collaboration!

The genetic architecture of the human bZIP family

Generative biology holds the promise to transform our ability to design and understand living systems by creating novel proteins, pathways, and organisms with tailored functions that address challenge...

www.biorxiv.org

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Grosshans Lab @labgrosshans.bsky.social · Aug 26

Very thrilled to welcome Julia as our new colleague in Multicellular Systems at @fmiscience.bsky.social !

Julia Batki @juliabatki.bsky.social · Aug 25

I am excited to share that I will join the Friedrich Miescher Institute @fmiscience.bsky.social in Basel as a group leader, starting my lab in March 2026 🎉

We will explore cell fate regulation during organogenesis, with a focus on how cell elimination underlies the emergence of functional tissues.

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