Alexandre Mayran

#jobAlert We are hiring! If you like #imaging ,gene regulation and a dynamic group please apply. We are looking for a research assistant with a master degree and prior experience in academia.

Brain Surfaces of 70 primate species

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To predict the behaviour of a primate, would you rather base your guess on a closely related species or one with a similar brain shape? We looked at brains & behaviours of 70 species, you’ll be surprised!

🧵Thread on our new preprint with @r3rt0.bsky.social , doi.org/10.1101/2025...

So excited to share my 1st paper !!🌞
Co-authored with @jules-vanaret.bsky.social @dunsingvalentin.bsky.social, we developped an integrated pipeline for imaging, segmenting and analysing cell-scale patterns in gene expression + tissue properties in complex 3D tissues
elifesciences.org/reviewed-pre...

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...

Finally out! 🥳 Our paper showing how a transposable element (TE) insertion can cause developmental phenotypes is now published @natgenet.nature.com 🧬🦠🐁
Below is a brief description of the major findings. Check the full version of the paper for more details: www.nature.com/articles/s41588-025-02248-5

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...

A dream come true: my first first-author publication! 🧬 🎉 Working to unravel the mysteries of long-range gene regulation has been an incredible journey. Endless gratitude to Evgeny, the lab, and all of the amazing collaborators who helped make this happen 🙌

Range extender mediates long-distance enhancer activity - Nature The REX element is associated with long-range enhancer–promoter interactions.

Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/

Congrats Jean Leon!

Congrats! Happy to see it out!

Checkout the full story online now at Dev Cell, the product of a team effort with the help of our fantastic collaborators including @da-bar.bsky.social @borislenhard.bsky.social @mpercharde.bsky.social

Article link:
doi.org/10.1016/j.de...

Sham Tlili, winner of the CNRS 2025 bronze medal - IBDM | Institut de Biologie du Développement de Marseille A distinction that rewards a promising and already fruitful scientific career.

🥇Sham Tlili has been awarded the CNRS 2025 Bronze Medal! She studies how physical forces shape living tissues by using mouse stem cell models known as gastruloids. A unique blend of physics & biology.

🔗 Read more: www.ibdm.univ-amu.fr/sham-tlili-w...

We are looking for a research assistant to join our lab and support ongoing projects with genome engineering in mouse embryonic stem cells! Please get in touch if you are interested.
www.fmi.ch/education-ca...

A major KI initiative to recruit new assistant professors with outstanding proposals in all areas of medicine, biomedicine and public health. We offer an amazing research environment, great colleagues and generous startup packages. Check it out and get working on your applications! (repost please!)

Portrait photo of Dr. Juliane Glaser

We are excited to officially welcome a new group leader at the MPI-IE in #Freiburg. 🎉

Dr Juliane Glaser 🥳 – she studies epigenetic mechanisms of embryonic development, with a focus on transposable elements. 👉 Interview: www.ie-freiburg.mpg.de/6043545/2025...

Welcome, @julianeg.bsky.social!

How do non-coding variants in enhancers lead to disease? Happy to share our recent work, led by @ewholling.bsky.social, in which we discovered that poised chromatin sensitizes enhancers to aberrant activation by non-coding mutations, contributing to disease. www.biorxiv.org/content/10.1... 1/

⚠️ I am really excited to share the work of Anastasios Balaskas, an excellent PhD candidate in the lab, with the wider world. Tasos made a significant advance: generating a stem cell-based embryo model that contains both posterior and anterior neural tissues of the late-stage gastrulating embryo.

An advanced head-to-tail mouse embryo model with hypoxia-mediated neural patterning https://www.biorxiv.org/content/10.1101/2025.06.17.660116v1

A meme-style comic panel with three parts. Left: A stylized enhancer with a mutation, surrounded by colored blocks representing functional motifs, a neural network diagram, chromatin accessibility signal traces, and a sequence motif. Two cartoon mouse embryos below show different LacZ reporter activity patterns. Top right: A hand hovers anxiously between two red buttons labeled “Experiments” and “AI,” with the caption “HOW DO ENHANCERS REALLY WORK?” Bottom right: A sweating superhero wipes his forehead, looking stressed about the difficult choice.

Textbooks: “Enhancers are just a bunch of TFBSs”

But how do they REALLY work?

New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social

A 🧵 (1/n)

Free access link: rdcu.be/erD22

Save the date 📅! Our TriNational #devbio #stemcell Meeting 2025 will be held in Freiburg on Sept. 19th. As always, participation is free and talks will be selected from early career scientists. Joun us 😊
Info: devstemcell.org/home

@biozentrum.unibas.ch @uni-freiburg.de @igbmc.bsky.social

Great work from Mochulska & Francois developing a generative framework for systematically building Dynamical Landscapes of cell fate decision making using modular dynamical components

Important step to interpretable and predictive models of cellular differentiation

www.biorxiv.org/content/10.1...

If you are interested by epigenetics, early human development in excellent scientific environment in middle of Paris, we are recruiting a postdoc.
app.beetween.com/WeaselWeb/p/...
Don't hesitate to apply or share the post !

Out today in @natmethods.nature.com : Spotiflow, our transcript localization method for imaging-based spatial transcriptomics. Led by amazing PhD student @albertdm.bsky.social, joint work w @gioelelamanno.bsky.social at EPFL / @scadsai.bsky.social
www.nature.com/articles/s41...
rdcu.be/epIB7

Conservation of regulatory elements with highly diverged sequences across large evolutionary distances Nature Genetics - Combining functional genomic data from mouse and chicken with a synteny-based strategy identifies positionally conserved cis-regulatory elements in the absence of direct sequence...

How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...

Dual DNA demethylation mechanisms implement epigenetic memory driven by the pioneer factor PAX7 Pioneer factor PAX7 highjacks control of DNA methylation maintenance, leading to enhancer demethylation and epigenetic memory.

TF binding is usually anticorrelated with DNA methylation, but there are very few studies that actually investigate why. This is really nice work from Jacques Drouin's lab showing PAX7 physically interacts with UHFR1, blocking DNMT1 recruitment ‪@ircm.bsky.social‬ www.science.org/doi/10.1126/...

New preprint of @trono-lab.bsky.social and my PhD work!
By modulating SWI/SNF remodeling at ancient transposable elements - LINE/L2s and SINE/MIRs, a "noncanonical" KZFP called ZNF436 protects cardiomyocytes from losing their identity.
🫀heartbeat on 🔁 repeat
www.biorxiv.org/content/10.1... #TEsky

In preprints: exploring developmental robustness and timing with gastruloids How developmental processes are coordinated in time and space to ensure the robust formation of complex, functional patterns during embryogenesis remains an outstanding question. Investigating this in...

For an update on a set of recent preprints using gastruloids to investigate the interplay between morphogenesis, gene expression and physical parameters, on the robustness of patterning:

journals.biologists.com/dev/article/...

Chromatin loops are an ancestral hallmark of the animal regulatory genome - Nature The physical organization of the genome in non-bilaterian animals and their closest unicellular relatives is characterized; comparative analysis shows chromatin looping is a conserved feature of ...

I’m very excited to share our work on the early evolution of animal regulatory genome architecture - the main project of my postdoc, carried out across two wonderful and inspirational labs of @arnausebe.bsky.social and @mamartirenom.bsky.social. www.nature.com/articles/s41...

Our recent paper reports extremely long-range (up to 5.1 Mb 😲) regulation of certain genes in fly neurons and provides new insights into how they form (see short thread below 👇).
genesdev.cshlp.org/gca?gca=gene...

📢 Fresh off the press and featuring new exciting experiments! 🧪
We show how glycolytic activity instructs germ layer proportions through regulation of Nodal and Wnt signaling - happy to finally share this 😊
doi.org/10.1016/j.st...

B2B with @jesseveenvliet.bsky.social lab: doi.org/10.1016/j.st... 🤩

Symposium on ‘Enhancer Sequences’ at beautiful @collegedefrance.bsky.social in Paris, by April 11th. Open and free, no registration. Come to relax listening to facts #TherapeuticEffects #VillageGauloix Final programme below. Tell your friends! 🙏🤘