Stefan Schoenfelder

Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀

Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function

now revised and journal accepted at www.science.org/doi/10.1126/...

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Welcome! You are invited to join a webinar: The 3D Regulatory Genome: Towards a quantitative understanding of long-range transcriptional regulation . After registering, you will receive a confirmation... Join our guest speaker, Dr. Luca Giorgetti, in this exciting seminar on the 3D Regulatory Genome, sponsored by Enhanced Genomics.

Very excited to host @lucagiorgetti.bsky.social for this talk 'Towards a quantitative understanding of long-range transcriptional regulation' in @enhancedgenomics.bsky.social's ‘The 3D Regulatory Genome’ seminar.

📅 04 Dec 2025 (today!)
⏰ 4 pm GMT
Please join us :
us02web.zoom.us/webinar/regi...

Hiring Senior Computational Postdoc to lead large-scale scRNAseq analysis for Project JAGUAR, one of the world’s most comprehensive single-cell immune resources from Latin American ancestries. If big data, global partnerships, human diversity and immune regulation excite you, apply! bit.ly/3XyFWrW

We are excited to share our new preprint:

SMARCA2/4-Dependent Chromatin Remodelling Establishes Gene Regulatory Programs in Early Human Embryos and Blastoids.

www.biorxiv.org/content/10.64898/2025.12.01.691499v1

Oxidative phosphorylation complexes contain subunits encoded by both the nuclear and mitochondrial genomes. How do cells coordinate the synthesis and assembly of these complexes at the inner membrane? We teamed up with Martin Ott (@mitolab.bsky.social) to address this in two recent papers.

First paper from the lab is now online
@natneuro.nature.com !
We mapped injury induced enhancers in the mouse CNS and decoded their sequence architecture. Little 🧵 rdcu.be/eSQi1

Specialized signaling centers direct cell fate and spatial organization in a mesodermal organoid model Stem cell–derived mesodermal organoids reveal how signaling centers guide cell fate and tissue organization.

🎉 Our deconstructed, stem-cell–based approach to studying signaling centers and limb-development cell types is out! 🥳 So nice to see it in its final form after the preprint— and huge thanks to the community for all the enthusiasm and interest since then!
www.science.org/doi/10.1126/...

Tomorrow!
www.varianteffect.org/seminar-seri...

Progressive coevolution of the yeast centromere and kinetochore - Nature Thousands of centromeres were identified and tracked across two major fungal clades, showing that new centromeres spread progressively and that the kinetochore acts as a filter to determine which new ...

www.nature.com/articles/s41...

Progressive coevolution of the yeast centromere and kinetochore
🤩
@helsenjana.bsky.social @gautamdey.bsky.social

Synergy between regulatory elements can render cohesin dispensable for distal enhancer function Enhancers are critical genetic elements controlling transcription from promoters, yet how they convey regulatory information across large genomic distances remains unclear. Here, we engineer pluripote...

Bah, who needs cohesin if you're at the right place (near). Grover once taught us the difference between near and far (my favourite Sesame Street piece), and now amazing work from @elphegenoralab.bsky.social led by @karissalhansen.bsky.social shows us how: www.science.org/doi/10.1126/...

📣 I hereby make my Bluesky debut to announce that our work linking DNA binding affinities and kinetics 𝘪𝘯 𝘷𝘪𝘵𝘳𝘰 and 𝘪𝘯 𝘷𝘪𝘷𝘰 for the human transcription factor KLF1 just got published in Cell! @cp-cell.bsky.social

www.cell.com/cell/fulltex...

Key findings in a thread (1/6):

Rapid compensatory evolution within a multiprotein complex preserves telomere integrity Intragenomic conflict with selfish genetic elements spurs adaptive changes in subunits of essential multiprotein complexes. Whether and how these adaptive changes disrupt interactions within such comp...

Rapid compensatory evolution within a multiprotein complex preserves telomere integrity www.science.org/doi/10.1126/... @levine-lab.bsky.social very cool work

🚨Post open in our lab! Come work on some cool themes involving metabolism, chromatin, early development 🤓. Pls RT

Join @mpercharde.bsky.social Lab at the MRC LMS! We have an 18mo postdoc position to cover a couple of projects (maternity leave and paper revisions). The projects are focussed on chromatin in early mouse embryos and metabolism in mouse embryonic stem cells and pluripotency.

Want to analyze the role of endogenous retroviruses in early human development or investigate their regulation in pluripotency and early development for your PhD?

Join the lab of @fueyoraquel.bsky.social via the IMPRS-BAC #gradschool!

👉 www.molgen.mpg.de/5094682/Fuey...

Looking for some Thanksgiving reading? 🦃🦃🦃

🚨Check out our new preprint on CRISPore-seq!🚨

Combining pooled CRISPR perturbations with single-cell sequencing has been tremendously powerful... but we are missing a lot with current approaches like Perturb-seq and ECCITE-seq.

Doctoral INPhINIT fellowships - Incoming Call 2026 We grant 30 fellowships for researchers of any nationality who wish to pursue a doctorate in a STEM discipline at research centres of excellence in Spain or Portugal.

Outstanding PhD fellowship call OPEN for excellent students.

lacaixafoundation.org/en/doctoral-...

This is for students incoming from outside Spain. And it is VERY well supported (ie at European levels).

If you’re interested in doing a PhD in our lab @irbbarcelona.org, reach out!!!!

Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs Low-affinity transcription factor (TF) motifs are an important element of the cis-regulatory code, yet they are notoriously difficult to map and mechanistically incompletely understood, limiting our a...

We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below:

(TLDR; low-affinity motifs matter as pioneers!)

Cool project with a couple of great supervisors!

RNA polymerase II coordinates histone deacetylation at active promoters Transcription initiation limits histone acetylation and H2AZ incorporation at promoters.

Unpause! I'm super happy to now be able to share the published version of our paper at Science Advances showing that:
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...

Programmable initiation of mRNA translation by trans-RNA - Nature Biotechnology Translation can be initiated from a specific start codon using trans-RNA.

Programmable initiation of mRNA translation by trans-RNA - @cornelluniversity.bsky.social @iecb.bsky.social go.nature.com/3K7SEdO

Excited to share our new study, led by @dellaVolpe_L, now out in @natcellbio.nature.com! Blocking #ferroptosis enhances human 🩸 stem cell expansion, with implications for transplantation and gene therapy. www.nature.com/articles/s41...

Today in @nature.com, in work led by @adititm.bsky.social, we report the ability to prompt Evo to generate functional de novo genes.

You shall know a gene by the company it keeps!

It's always special when you find your own paper in the table of contents of the journal 😍

"The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube" -> Now out in its final form

www.cell.com/developmenta...

Our new preprint is online! Viruses, bacteria and parasites use effector proteins to evade immunity and rewire host cell pathways. Together with @AlexanderStark8, we wondered if we could systematically map what these effectors, regardless of their origin, do in human cells. 1/8

Major new direction in the lab: hacking human cell biology with pathogen effectors (eORFs) - amazing collaboration with @miketilapia.bsky.social lab. Huge congrats to first authors Tomas & He & all co-authors! Check out the pre-print on @biorxivpreprint.bsky.social www.biorxiv.org/content/10.1...

IMPRS-BAC #gradschool: Our new groupleader @sedonamurphy.bsky.social has an open PhD project in her lab. Topic: Spatial feedback between epigenetic regulation and chromatin regulation. Apply by Jan 7, 2026!
👉 www.molgen.mpg.de/5091778/Murp...

*no longer

A rare voice of reason indeed. First the Tories and now Labour have allowed Farage et al to dictate the agenda re immigration & asylum, to the point where a grown-up and fact-based discussion seems now longer possible within either party. I suspect this will only contribute to the downfall of both.