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Reposted by Akis (Argyris) Papantonis

Merriam-Webster @merriam-webster.com · 7d

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

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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 13d

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

Gesellschaft für Genetik @gfgenetik.bsky.social · 14d

What a great first day at the GfG symposium on epigenetics & chromatin. Fantastic talks by @akispapantonis.bsky.social , @apombo1.bsky.social, @marcusbuschbeck.bsky.social and Philipp Korber. And Peter Becker giving the Max-Delbrueck lecture. A real treat for the audience!

Juri Kazakevych @juri-epigenomics.bsky.social · 14d

Looking forward to exciting talks at the GfG Symposium in Gießen.

Already found a poster, featuring my favourite gene: SMARCAD1, by Jacqueline Mermoud

#epigenomics @diagenode.bsky.social @gfgenetik.bsky.social

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Reposted by Akis (Argyris) Papantonis

Dr. Sedona Murphy @sedonamurphy.bsky.social · 19d

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/...

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...

www.science.org

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Reposted by Akis (Argyris) Papantonis

Sarah Hainer @hainerlab.bsky.social · 20d

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...

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...

www.biorxiv.org

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Reposted by Akis (Argyris) Papantonis

Anders Sejr Hansen @andersshansen.bsky.social · 21d

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

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.

www.nature.com

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Reposted by Akis (Argyris) Papantonis

Sara Wickstrom @sarawickstrom.bsky.social · 26d

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...

Computational image analyst (m/f/d)

The Max Planck Institute for Molecular Biomedicine in Münster, Germany, has an opening for a

jobs.mpi-muenster.mpg.de

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Reposted by Akis (Argyris) Papantonis

Karim-Jean Armache @kjarmache.bsky.social · 22d

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...

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!

keysym.us

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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 22d

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!

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 ...

www.biorxiv.org

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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 22d

…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.

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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 22d

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…

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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 22d

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

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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 28d

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

Annual Reviews @annualreviews.bsky.social · 29d

The latest Annual Review of Genomics and Human Genetics is now online 🧬 Most read article so far is "Mechanisms of Enhancer-Mediated Gene Activation in the Context of the 3D Genome" @akispapantonis.bsky.social @mariekeoudelaar.bsky.social Check it out arevie.ws/47BZEJp
Full TOC: arevie.ws/4plCaPe

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Akis (Argyris) Papantonis @akispapantonis.bsky.social · Sep 8

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

Kurianlab @kurianlab.bsky.social · Sep 8

Many conserved exons in the heart and brain utilize weak 5 ′ splice sites, yet they are accurately spliced. But how? We show that splicing fidelity is actively enforced through a QKI-U6 checkpoint at the U1→U6 handover in essential cardiac genes during organogenesis.
www.biorxiv.org/content/10.1...

QKI ensures splicing fidelity during cardiogenesis by engaging the U6 tri-snRNP to activate splicing at weak 5ʹ splice sites

During organogenesis, precise pre-mRNA splicing is essential to assemble tissue architecture. Many developmentally essential exons bear weak 5'splice sites (5'SS) yet are spliced with high precision, ...

www.biorxiv.org

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Akis (Argyris) Papantonis @akispapantonis.bsky.social · Aug 22

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

Ali Shaib @alishaib.bsky.social · Aug 20

Excited to host my friend and collaborator Leo for the #SFB Seminar in #Göttingen on September 18, 2025, at 12:00 PM in the Center for Biostructural Imaging of Neurodegeneration seminar room. He will discuss #RNA-driven mechanisms that shape embryonic cell fate and identity.

@kurianlab.bsky.social

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Akis (Argyris) Papantonis @akispapantonis.bsky.social · Aug 19

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.

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...

www.biorxiv.org

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Reposted by Akis (Argyris) Papantonis

Rada-Iglesias Lab @radaiglesiaslab.bsky.social · Aug 11

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...

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...

www.biorxiv.org

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Reposted by Akis (Argyris) Papantonis

Christophe Chapard @christophechapard.bsky.social · Aug 9

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!

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...

www.cell.com

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Reposted by Akis (Argyris) Papantonis

Sara Wickstrom @sarawickstrom.bsky.social · Aug 1

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

EMBL Events @events.embl.org · Jul 31

📢 Abstract submission deadline reminder for 'Cell biology of the nucleus'!

Before packing your bags and leaving for your summer vacation, there is one important task left to do: submit your abstract for #EESNucleus ✍️

Deadline is 26 August: https://s.embl.org/ees25-07-bl

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Akis (Argyris) Papantonis @akispapantonis.bsky.social · Jul 31

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

Eileen Furlong @eileen-furlong.bsky.social · Jul 30

To all post-docs: The Genome Biology dept ‪@embl.org
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Group Leader - Genome Biology Unit

Are you ready to lead groundbreaking research in Genome Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group addressing exciting and original biological...

embl.wd103.myworkdayjobs.com

Reposted by Akis (Argyris) Papantonis

Lennart Hilbert @lennarthilbert.bsky.social · Jul 26

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...

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Akis (Argyris) Papantonis @akispapantonis.bsky.social · Jul 17

Be there or be square!

Gesellschaft für Genetik @gfgenetik.bsky.social · Jul 16

🎉 Join us at the upcoming GfG Symposium "Epigenetics & Chromatin" in Giessen, Sept 24–26, 2025!
Amazing speakers, low registration fee, € 300 prizes for best poster & short talk, + free GfG membership for non-members.

Please RT!

express.converia.de/frontend/ind...

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Reposted by Akis (Argyris) Papantonis

CRC1678 @crc1678.bsky.social · Jul 11

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

About CRC 1678 - CRC1678 - Collaborative Research Center

CRC 1678 investigates how age and stress-driven declines in the accuracy of mRNA and protein production affect cellular and organismal health. By taking an

crc1678.uni-koeln.de

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Reposted by Akis (Argyris) Papantonis

Anthony Mathelier @amathelier.bsky.social · Jul 3

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.

Norwegian Centre for Molecular Biosciences and Medicine (NCMBM) @ncmbm.bsky.social · Jun 30

📣 We’re recruiting 1-2 Group Leaders! NCMBM is looking for early-career researchers ready to establish their independent research groups!

🧬 With an attractive start-up package, help us shape the future of molecular biosciences and medicine in 🇳🇴 and be part of the @nordicembl.bsky.social!

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Reposted by Akis (Argyris) Papantonis

Stefan Schoenfelder @stefanschoenfelder.bsky.social · Jul 3

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

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Reposted by Akis (Argyris) Papantonis

Jonas Paulsen @jonnings.bsky.social · Jul 1

🧬 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

StripePy: fast and robust characterization of architectural stripes

AbstractMotivation. Architectural stripes in Hi-C and related data are crucial for gene regulation, development, and DNA repair. Despite their importance,

doi.org

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