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Reposted by Martin Franke

Denis Duboule @denisduboule.bsky.social · 22d

Out today. 🙏 again to everyone for this wonderful piece of work, in particular to Aurelie @aurhin.bsky.social Chase @chasebolt.bsky.social and Brent @homeobox.bsky.social. 🙏 also to the Harris lab @fish4walking.bsky.social and @neilshubin.bsky.social @biology-unige.bsky.social @college-de-france.fr

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Aurelie Hintermann @aurhin.bsky.social · 22d

Are digits modified fins, or evolutionary innovations? Read how we tackled this old question from a new angle🧪
A story with @chasebolt.bsky.social, @homeobox.bsky.social and myself, coordinated by @denisduboule.bsky.social from @college-de-france.fr and published in @nature.com today!
#InHoxWeTrust

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Rada-Iglesias Lab @radaiglesiaslab.bsky.social · Aug 13

#Preprint alert! 📣

We are thrilled to share the work led by Lara Zorro-Shahidian and Lucio di Filippo, in which we show that #MLL2 controls gene expression in both #ESC and upon #differentiation by facilitating the #enhancer like activity of #LINE1 elements

www.biorxiv.org/cgi/content/...

MLL2 facilitates long-range gene regulation through LINE1 elements

Transcriptional regulation is tightly linked to chromatin organization, with H3K4me3 commonly marking both active and bivalent promoters. In embryonic stem cells (ESC), MLL2 is essential for H3K4me3 d...

www.biorxiv.org

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Centro Andaluz de Biología del Desarrollo @cabd-upo-csic.bsky.social · Jul 29

Great work from the #CABD researchers in this call of @ageinves.bsky.social for the ‘Proyectos de generación de conocimientos’!

The provisional resolution proposes funding for:

🟢 13 projects
🟢 3 PhD contracts
🟢 ~ 3,5 million €

Way to go!!!

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Axel Visel @axelvisel.bsky.social · Jul 16

No new genes needed to fly - just rewire what you have! 🦇🧬

Great new paper from the labs of @fany-real.bsky.social @stemundi.bsky.social @dariloops.bsky.social

doi.org/10.1038/s415...

#EvoDevo #SingleCell #BatWings

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Guillaume Andrey @guandrey.bsky.social · Jul 9

Our work bridging enhancer-promoter proximity to phenotypic outcomes in vivo is out! Shout out to @olimpiabompadre.bsky.social, to Marie Kmita's lab, and to all the co-authors. www.nature.com/articles/s41...

Liebenberg syndrome severity arises from variations in Pitx1 locus topology and proportion of ectopically transcribing cells - Nature Communications

Here the authors show that reducing enhancer-promoter distance at the Pitx1 locus increases proportion of Pitx1 forelimb expressing cells, worsening skeletal defects in Liebenberg syndrome. They also ...

www.nature.com

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Martin Franke @martinfranke.bsky.social · Jul 10

Congratulations, Julian @julianeg.bsky.social! It was an exciting project, and I am happy to have contributed. Wonderful to see the paper in its final form.

Nature Genetics @natgenet.nature.com · Jul 10

🎉ONLINE @natgenet.nature.com

📰Enhancer adoption by an LTR retrotransposon generates viral-like particles, causing developmental limb phenotypes.

By @julianeg.bsky.social, Giulia Cova, Stefan Mundlos and colleagues.

⬇️

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

Enhancer adoption by an LTR retrotransposon generates viral-like particles, causing developmental limb phenotypes - Nature Genetics

Activation of an LTR retrotransposon inserted upstream of the Fgf8 gene produces viral-like particles in the mouse developing limb, triggering apoptosis and causing limb malformation. This phenotype c...

www.nature.com

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Martin Franke @martinfranke.bsky.social · Jul 9

3/3
Fantastic teamwork with Víctor Sánchez Gaya @sanchezgaya.bsky.social, Álvaro Rada Iglesia, and long-time collaborators Adrian Daly and Giampaolo Trivellin @gp83.bsky.social. Grateful to be part of it! 🙌‬

Original POSTRE paper - a powerful tool for clinical genetics!
🔗 tinyurl.com/3ys78kvc

POSTRE: a tool to predict the pathological effects of human structural variants

Abstract. Understanding the pathological impact of non-coding genetic variation is a major challenge in medical genetics. Accumulating evidences indicate t

academic.oup.com

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Martin Franke @martinfranke.bsky.social · Jul 9

2/3
In collaboration with @radaiglesiaslab.bsky.social, we applied and expanded POSTRE, a bioinformatics tool that rapidly classifies structural variants in the pituitary, distinguishing pathogenic duplications from benign ones in diagnostic settings.
#SVs #GPR101 #enhancers #TADs #TADopathies

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Martin Franke @martinfranke.bsky.social · Jul 9

🧵1/3
Our new preprint is out! Proud to have contributed to this collaborative study. We identified the enhancer cluster responsible for GPR101 overexpression in X-linked acrogigantism (X-LAG) - a key step toward understanding this rare pituitary disorder 🧠🧬
🔗 www.medrxiv.org/content/10.1...

Distinguishing benign from pathogenic duplications involving GPR101 and VGLL1-adjacent enhancers in the clinical setting with the bioinformatic tool POSTRE

Background Structural variants (SVs) that disrupt topologically associating domains (TADs) can cause disease by rewiring enhancer-promoter interactions. Duplications involving GPR101 are known to caus...

www.medrxiv.org

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Martin Franke @martinfranke.bsky.social · Jul 9

Happy birthday, UCSC genome browser!

www.nature.com/articles/d41...

’We couldn’t live without it’: the UCSC Genome Browser turns 25

After a quarter of a century, the website remains an essential tool for navigating the genome and understanding its structure, function and clinical impact.

www.nature.com

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Martin Franke @martinfranke.bsky.social · Jul 2

I am very proud of you, Marta. You did outstanding work in the lab, and your defence was spotless. I am also very happy to now know an expert in gene compensation between paralogous genes!

Centro Andaluz de Biología del Desarrollo @cabd-upo-csic.bsky.social · Jul 1

Congratulations to the new PhD at #CABD: Marta Moreno Oñate!

Dr. Moreno did an amazing job explaining the projects of her PhD work! Marta's thesis was done with @pablodeolavide.upo.es’s PhD program and was co-supervised by @martinfranke.bsky.social and Juan Tena!

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Nadav Ahituv @nadavahituv.bsky.social · May 24

Comparison between a neuronal massively parallel reporter assay for 50,000 sequences and 20,000 variants with mouse enhancer assays provide complimentary information. Great work by Michael Kosicki, Dianne Laboy Cintrón, Len Pennacchio, Martin Kircher lab & many others.
www.nature.com/articles/s41...

Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity - Nature Communications

MPRAs and in vivo transgenic mouse assays are two potentially complementary ways to assay the impact of noncoding variants. Here, authors find a strong and specific correlation between the assays in n...

www.nature.com

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Reposted by Martin Franke

Konrad Chudzik @konrad-chudzik.bsky.social · May 8

🚨 Preprint 🚨
Ever wondered how cells prepare their genomes to enable new cell-fates? In this team up with the Kind lab, we show that genes are repositioned in the nucleus to get ready for future activation and tissue formation. Read 🧵👇 to find out how and when this happens!

doi.org/10.1101/2025...

Reconfiguration of genome-lamina interactions marks the commissioning of limb cell-fates

Diverse forms of heterochromatin block inappropriate transcription and safeguard differentiation and cell identity. Yet, how and when heterochromatin is reconfigured to facilitate changes in cell-fate...

www.biorxiv.org

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Reposted by Martin Franke

Stefan Mundlos @stemundi.bsky.social · May 6

Our BAT paper is accepted in Nature Ecology & Evolution! Single cell, gene regulation, TADs and key TFs that shape the bat wing. Genomics goes Evodevo 😍

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Jesse Veenvliet @jesseveenvliet.bsky.social · Apr 19

😱 A very hungry #PacManoid ate the original post 🍬🍬🍬

Here’s the 🧵 on our latest in @cp-cellstemcell.bsky.social again!

Gastruloids w/ a sweet tooth better model natural embryos: doi.org/10.1016/j.st...

Spearheaded by @cryaaa.bsky.social & Alba Villaronga-Luque @mpi-cbg.de @poldresden.bsky.social

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Konrad Chudzik @konrad-chudzik.bsky.social · Apr 14

🚨 Preprint alert 🚨
Excited to share our work on "Ab-trapping," an antibody artifact causing misleading peripheral ("rim") staining in imaging & genomics (IF, CUT&Tag, CUT&RUN). Antibodies fail to penetrate structures, accumulating at the periphery. A 🧵👇
doi.org/10.1101/2025...

Ab-trapping - a peripheral staining artifact in antibody-based microscopy and genomics

Antibodies (Ab) are essential for detecting specific epitopes in microscopy and genomics, but can produce artifacts leading to erroneous interpretations. Here, we characterize a novel artifact, Ab-tra...

doi.org

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Fany M. Real @fany-real.bsky.social · Mar 19

We’ve just launched our new website! 🚀

Check it out and stay tuned for updates! 🖥️ 🧬 🧫 🐁

fmreallab.github.io/website/

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Pedro Rocha @pedroprocha.bsky.social · Feb 26

Here is the peer-reviewed version of our study showing how some TAD borders are essential for gene regulation and development.

Loss of a single CTCF motif is sufficient to cause embryonic lethality.

www.sciencedirect.com/science/arti...

Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development

Chromatin domains delimited by CTCF can restrict the range of enhancer action. However, disruption of some domain boundaries results in mild gene dysr…

www.sciencedirect.com

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Martin Franke @martinfranke.bsky.social · Feb 27

Martin Franke @martinfranke.bsky.social · Feb 13

Wow, Google... #GeographyFun or just going the extra mile to keep someone happy?

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Nadav Ahituv @nadavahituv.bsky.social · Feb 4

Tumors need a lot of nutrients to grow. By engineering and implanting fat cells to outcompete cancers for nutrients we can suppress them. Novel cancer therapy called Adipose Manipulation Transplantation (AMT). AMAZING work led by and dedicated to Hai Nguyen.
www.nature.com/articles/s41...

Implantation of engineered adipocytes suppresses tumor progression in cancer models - Nature Biotechnology

Adipose manipulation transplantation can reduce tumor growth and proliferation in vitro and in mouse models.

www.nature.com

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Martin Franke @martinfranke.bsky.social · Jan 22

X account deactivated. Rest in peace, Twitter.

"Ich kann nicht so viel fressen, wie ich kotzen möchte." Max Liebermann, 1933

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Ivana Jerkovic @ivana-jerkovic.bsky.social · Dec 1

Ever wondered how 3D chromatin rewires during differentiation? We wanted to understand this process better & distinguish if different processes or elements drive this rewiring. To do so, we used mESC=>NPC differentiation and focused on a single locus. biorxiv.org/content/10.110… 1/17

https://biorxiv.org/content/10.110…

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Reposted by Martin Franke

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · Dec 1

Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes https://www.biorxiv.org/content/10.1101/2024.11.30.626178v1

Despite the growing abundance of sequenced animal genomes, we only have detailed knowledge of regula

www.biorxiv.org

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