Akis (Argyris) Papantonis

Synthetic engineering demonstrates that synergy among enhancers involves an increase in transcriptionally productive enhancer-gene contacts Enhancers are non-coding cis-regulatory elements that control the expression of distally located genes in a tissue- and time-specific manner. Recent studies indicate that enhancers can differ in their...

Excited to share the latest work from the lab led by @eharo84.bsky.social, in which we have used synthetic biology to explore the mechanisms by which different types of long-range enhancers ensure robust and precise developmental gene expression

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

RNA Pol II-based regulations of chromosome folding How transcription and cohesin complexes interact to regulate 3D genome organization remains unclear. Chapard et al. dissect their respective contributions and their interplay in shaping the genome arc...

Pleased to see this study out, combining experimental work from our lab at the @cbitoulouse.bsky.social, in particular by @nathaliebastie.bsky.social and @beckof.bsky.social, and from Laura Chaptal and @alengronne.bsky.social at IGH Montpellier
@cnrs.fr @cnrsbiologie.bsky.social

Congrats to all!

Check out this exciting meeting and register! Fantastic line-up of speakers on cell biology of the nucleus and a great venue 🔥

If I wasn’t this old, I would definitely apply.

How do enhancer-gene contacts relate to transcription activation? In mouse embryonic stem cells, a combo of STED, oligoFISH & RNA FISH shows that 3% of Dppa3 alleles transcribe. For these, enhancers and promoters come closer (panel E). Stumberger ... Leonhardt & Harz www.biorxiv.org/content/10.1...

Be there or be square!

Freshly launched! 🚀 Check out the new CRC 1678 website 🌐
👉 crc1678.uni-koeln.de

Fantastic opportunity to launch your research group following the @embl.org model in a great environment with a solid startup package and access to state-of-the-art resources.

Join us at the @ncmbm.bsky.social, part of the @nordicembl.bsky.social, at @uio.no

Feel free to reach out if you have Qs.

Thank you, Evgeny! I am delighted that we have a top line up of speakers confirmed for 'The 3D Regulatory Genome' for 2025:
@andersshansen.bsky.social July 3rd 2025
@mariekeoudelaar.bsky.social September 4th 2025
@axelvisel.bsky.social October 2nd 2025
@efapostolou29.bsky.social November 6th 2025

🧬 New in Bioinformatics! We’re excited to share StripePy - a Python application for fast, robust detection of architectural stripes in Hi-C & Micro-C data.
🔗 Read the paper 👉 doi.org/10.1093/bioi...
#3DGenomics #Bioinformatics #HiC #cool #hic @robomics.bsky.social @rea191.bsky.social

How to represent genomes in 3D?

In this paper (and video), we propose Geometric Diagrams of Genomes (GDG)—a visual grammar that aims at emulating the effect ribbon diagrams (Richardson et al 1981) had in protein structural biology. Time will tell.😅

👉🏼 genomebiology.biomedcentral.com/articles/10....

A CNRS Junior Professorship on RNA Modifications and Advanced… | Centre for Integrative Biology of Toulouse A CNRS Junior Professorship on RNA Modifications and Advanced Epitranscriptomic Technologies offer at CBI-Toulouse Fixed-term (3–6 years), tenure-track (Chaire de Professeur Junior) Application Dead...

www.linkedin.com/posts/centre...

Thank you — and very welcome for the throwback! :-)

Let’s make a hat out of that.

I echo the feeling!

Looking forward to your thoughts. I think we way quite some way to go still.

Finally, it is important to state that this piece was the outcome of exchanges (and funding, of course) in the framework of the amazing @dfg.de @spp2191.bsky.social and @spp2202.bsky.social Priority Programs, as well as of the SFB1565 consortium of the Göttingen Campus @uni-goettingen.de.

6/n

...and in doing so, we also discuss how formations such as "factories" and "condensates" can mediate the communication of genes with their cognate cis-regulatory elements to tune their output in different scenarios.

5/n

In our new review, we critically approach both the historical and current nomenclatures, as well as evidence from molecular and cell biology assays since the early '90s to highilght the (many) points where the two concepts align as well as those that still require further work to settle.

Transcription factories: gene expression in unions? - PubMed Transcription is a fundamental step in gene expression, yet it remains poorly understood at a cellular level. Visualization of transcription sites and active genes has led to the suggestion that trans...

An extra motivation was to revisit the 2009 @natrevgenet.nature.com piece by @wbickmor.bsky.social:
pubmed.ncbi.nlm.nih.gov/19506577/

...as well as that by Peter Cook and I in 2013: pubmed.ncbi.nlm.nih.gov/23597155/

..and integrate the state-of-the-art.

3/n

The great pace of the "condensate" field has offered frameworks that can be used to explain earlier, but still very valid experimental observations. Thus, we set out to compare and contrast (and synthesize) the "transcription factory" model with what is known about "transcriptional condensates"

2/n

This is a piece that I and @karsten-rippe.bsky.social discussing a lot, and a topic that is very close to my heart. The editors @naturerevgenet.bsky.social gave us the stage to do so, and the final version of our review is now available under this link: rdcu.be/erP1u

A short thread follows 1/n

A meme-style comic panel with three parts. Left: A stylized enhancer with a mutation, surrounded by colored blocks representing functional motifs, a neural network diagram, chromatin accessibility signal traces, and a sequence motif. Two cartoon mouse embryos below show different LacZ reporter activity patterns. Top right: A hand hovers anxiously between two red buttons labeled “Experiments” and “AI,” with the caption “HOW DO ENHANCERS REALLY WORK?” Bottom right: A sweating superhero wipes his forehead, looking stressed about the difficult choice.

Textbooks: “Enhancers are just a bunch of TFBSs”

But how do they REALLY work?

New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social

A 🧵 (1/n)

Free access link: rdcu.be/erD22

Home - Argyris Papantonis Lab The Argyris Papantonis Lab at University Medical Center Goettingen. Our research goals, team members, and where to find us.

Some more info on our lab's work here: papantonislab.eu

Do get in touch if interested!

Henriette Herz Scouting Programme By introducing the Henriette Herz Scouting Programme, the Foundation is opening up a new way of accessing the Humboldt Research Fellowship in parallel with the standard application procedure. It will ...

In a nutshell, over the next 2.5 years, I will have the responsibility (and privilege) of nomination 3 postdocs from outside of Germany to come and work with us at the University Medical Center Göttingen.

Further details on the program here: www.humboldt-foundation.de/en/apply/spo...

Hear, hear!
Since last week, I have the honor of serving as a Scout for the Henriette Herz program of the Humboldt Foundation.
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…further extending this to epitranscriptomic RNA modifications! #SIBBM2025

…and now, Maria Pelizzola (from Milan) is presenting a framework called “Nanodynamo” to chart subcellular RNA dynamics in cells.

Magda Bienko just gave an amazing talk on how long intronic RNAs generate a neuronal-specific nuclear architecture (picture missing because I was trying to take in the many data) #SIBBM2025

Will try — but I am terrible at multitasking :-)