Akis (Argyris) Papantonis

Great news for @uam-ibmib.bsky.social! Three @ncn.gov.pl OPUS grants to our researchers: @juliadluzewska.bsky.social, Wojciech Szlachcic and a collaborative Polish-German OPUS-LAP grant to @michal-gdula.bsky.social & @akispapantonis.bsky.social from @uni-goettingen.de. Big congrats to everyone!

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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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.

Interested in #3DGenomics #4Dnucleome? Like #Barcelona? Would like to enjoy doing #science and to have fun during your #PhD?

Apply now to La Caixa Foundation Doctoral #INPhINIT fellowships with us. DM or email in case of interest... 👇🏼👍🏼

lacaixafoundation.org/en/doctoral-...

Please, repost... 🔄🙏🏼

Are you being pleasantly sarcastic????

Last day of the @spp2202.bsky.social Closing Retreat in Goettingen ending in a high note with Stavros Lomvardas discussing the peculiar 3D attributes of the OR chromatin landscape!

@karsten-rippe.bsky.social rocking down memory lane and along single cell genomics data in Day 2 of the @spp2202.bsky.social Closing Retreat in Goettingen!

The Closing Scientific Retreat of @spp2202.bsky.social is under way in Goettingen with Gerd Blobel delivering the first Keynote lecture on LDB11-mediated looping of chromatin.

OFERTA DE EMPLEO (por favor difundir):

Ofrecemos un contrato predoctoral de 4 años asociado a nuestro proyecto PID2024-157249OB-I00. El objetivo del proyecto es evaluar un nuevo mecanismo patológico según el cual la competición entre promotores puede llegar a ocasionar enfermedades congénitas
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Happy to share our latest publication, in which we show that the arrangement of nucleosomes around CTCF sites contributes to higher-order organisation of chromatin into TADs: www.embopress.org/doi/full/10....

Characterization of induced cohesin loop extrusion trajectories in living cells Nature Genetics - This study introduces a system called TArgeted Cohesin Loader (TACL) that recruits cohesin complexes at defined genomic regions and induces loop extrusion events in living cells,...

The TArgeted Cohesin Loader (TACL) paper was just published. Happy that we were able to contribute to this really exciting project!

If you want to learn how targeting cohesin to defined loci in the genome affects the local chromatin environment and transcription, look no further!

rdcu.be/eLiT5

Only two days left to apply for the open tenure track professorship in Computational Biology here in @uni-goettingen.de
uni-goettingen.de/en/700631.html

Thanks, Maria!

Merci merci!

Thank you, Sandra — hope a German version appears soon!

Science-peripheral post (ignore unless you read in Greek or French): I was surprised and truly honored to receive the Aix-Marseille Metropolitain for the French translation of my novel ‘The last bear of the woods’ (Kichli 2023)—a great thanks to my translators M. Volkich and H. Zervas.

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.