Akis (Argyris) Papantonis

We are thrilled to announce that our NEW Large Language Model will be released on 11.18.25.

Just half a day in and it’s been a blast, with really incredible talks here on Giessen!

Kinetic organization of the genome revealed by ultraresolution multiscale live imaging Genome function requires regulated genome motion. However, tools to directly observe this motion in vivo have been limited in coverage and resolution. Here we introduce an approach to tile mammalian c...

Congrats to my friends in the Boettiger lab for this really beautiful live imaging work. A big leap forward in understanding the dynamic side of genome organization. www.science.org/doi/10.1126/...

esBAF and INO80C fine-tune subcompartments and differentially regulate enhancer-promoter interactions The genome is compacted in the nucleus through a hierarchical chromatin organization, ranging from chromosome territories to compartments, topologically associating domains (TADs), and individual nucl...

New preprint is up, led by former postdoc Braulio Bonilla.
We know these remodelers regulate nucleosome positions and occupancy, but do they have a role in regulating higher order chromatin structure? We take a peek for BAF and INO80C.
www.biorxiv.org/content/10.1...

Is enhancer-driven gene regulation all wrapped up? - Nature Reviews Genetics In this Comment, Wendy Bickmore discusses mechanistic models of how 3D genome organization facilitates communication between distant enhancers and their target promoters to regulate gene expression.

Very interesting new @wbickmor.bsky.social commentary on the mechanistic mystery that is very distal enhancer-promoter interactions www.nature.com/articles/s41...

Computational image analyst (m/f/d) The Max Planck Institute for Molecular Biomedicine in Münster, Germany, has an opening for a

My lab @mpi-muenster.bsky.social is looking for a computational biologist with a passion for imaging and spatial biology. A staff scientist position with long-term perspective! Apply and spread the word 🙏 jobs.mpi-muenster.mpg.de/jobposting/0...

Epigenetics and Gene Regulation in Health and Disease: Linking Basic Mechanisms with Therapeutic Opportunities | Keystone Symposia Join us at the Keystone Symposia on Epigenetics and Gene Regulation in Health and Disease: Linking Basic Mechanisms with Therapeutic Opportunities, March 2026, in Geneva, with field leaders!

On behalf of @ckadoch.bsky.social and myself, we are pleased to present our upcoming @KeystoneSymposia, #KSEpigenetics26 Epigenetics and Gene Regulation in Health and Disease, March 2-5, in Geneva, Switzerland. keysym.us/KSEpigenetic...

Variant U1 snRNAs contribute to cell cycle and differentiation control of human iPS cells Maintenance of stem cell identity as well as differentiation of stem cells into the various lineages requires intricate regulation of gene expression. Despite intensive research, our understanding of ...

The KO effects were far more pronounced than what the relative vU1 abundance (relative to canonical U1) would predict, and uncover an additional layer in stem cell identity regulation.

Please read here: www.biorxiv.org/cgi/content/...

Feedback more than welcome!

…so Kostas generated vU1-specific KOs using CRISPR-Cas9 in hiPSCs of the two most expressed variants, and Yajie analyzed their effects via total RNA-seq data, while @carmeloferrai.bsky.social provided undirected differentiation tests.

3/n

We were motivated by my old @dunnschool.bsky.social neighbors, Shona Murphy and Dawn O’Reilly, who showed that these (falsely presumed) U1 pseudo genes may actually be functional in their 2013 Genome Res paper…

2/n

In our latest preprinted work, Yajie and Kostas combine computational analysis with precision KO of single variant U1 snRNA genes in human iPSCs to find pronounced deregulation of both gene expression and splicing that seem to affect the cell cycle and the differentiation potency of stem cells. 1/n

Most read, I hear!
Here is your chance to read what @mariekeoudelaar.bsky.social and I had in mind when writing this together.

This is an incredible mechanistic dissection by the @kurianlab.bsky.social and Van Nostrand labs linking splicing choice to cardiac development!

Soon at a Goettingen amphitheater near us! Do join, folks! Leo always has very cool data to share.

Two distinct chromatin modules regulate proinflammatory gene expression Various mechanisms have been proposed to explain gene activation and co-regulation, including enhancer-promoter interactions via chromatin looping and the enrichment of transcription factors into hubs...

Looks pretty intriguing, Arnaud! May I suggest you take a look at the preprint from the Rippe lab (with some help by us)?
www.biorxiv.org/content/10.1...

Here, some very complementary observations are made using scATAC and compared against Hi-C structures.

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!