Martin Franke

Our most recent work on the “function and evolution” of #nuclear-speckles is now online at Cell @cp-cell.bsky.social
doi.org/10.1016/j.ce...
Read the thread👇 for the highlights of our findings.

🚨 1/ Preprint Alert!

Sex determination outcome is conserved across vertebrates (i.e. generating 2 compatible sexes) ♀️♂️

But are the cell types and gene programs behind them conserved too? 🧬

Spoiler: not really 👀

Find out in our new preprint ⬇️

www.biorxiv.org/content/10.6...

🧬 We’re #Hiring a #Bioinformatician/ Computational Biologist!
#Single-cell genomics, #Epigenomics & #3Dgenome biology in #Zebrafish #DevBio 🐟
📍 @cabd-upo-csic.bsky.social, CABD, Seville (Spain)
🕒 Full-time, 3-year position (start March 2026)
📅 Apply by Feb 15, 2026
👉 drive.google.com/file/d/1M8rp...

Woohoo! Congratulations, Fany!

📢 We are hiring!
👩🏾‍⚕️Research technician/Lab manager
📍 @cabd-upo-csic.bsky.social , Sevilla, Spain
🧬 Gene regulation in animal development & evolution

Check the details 👇 & join us!
drive.google.com/file/d/1cZJi...

#ResearchTechnician #Zebrafish #GeneRegulation #DevelopmentalBiology

We’re looking for a research technician to join our teams with @christinapaliou.bsky.social
Passionate about Zebrafish and gene regulation? 🐟🧬
Apply now and dive into exciting research with us! ✨
See the job offer below 👇

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

hoxd13a reporter in a zebrafish larva

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

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...

#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/...

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!!!

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

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 ...

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...

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.

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

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

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

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...

🧵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...

’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.

Happy birthday, UCSC genome browser!

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

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!

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...

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...

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...

🚨 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...

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 😍

😱 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

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...

🚨 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...

We’ve just launched our new website! 🚀

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

fmreallab.github.io/website/

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…

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...

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

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.

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...

X account deactivated. Rest in peace, Twitter.

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

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