Yad Ghavi-Helm

biorxiv.orgPromoter-proximal gatekeepers restrict pleiotropic enhancer inputs to achieve tissue specificityDevelopmental enhancers are central regulatory elements that can activate multiple genes, yet how they selectively regulate one gene over its neighbours remains unclear. Using the Drosophila twist E3 ...

Ever wondered what drives enhancer-promoter specificity? Why would an enhancer activate one gene rather than another neighboring one? Check our latest preprint, led by @mmasoura.bsky.social, to find out! www.biorxiv.org/content/10.1...

Yad Ghavi-Helm reposted

Michalis Averof

@michalis-averof.bsky.social

Call for a group leader in Evolutionary Biology The IGFL @igflyon.bsky.social in Lyon, France, is recruiting a group leader in Evolutionary Biology. An exciting place for exploring the interfaces of evolution with physiology and development. #EvolBiol #ecoevo #evodevo tinyurl.com/evolbiol

@emiliapsantos.bsky.social

Come join us in Lyon for a cool collaborative project between the teams of @michalis-averof.bsky.social and mine!

Michalis Averof@michalis-averof.bsky.social

6-month internship to explore (genome-wide) enhancer-promoter interactions in the crustacean Parhyale – Hosted by the Averof and Ghavi-Helm teams at IGFL Lyon – Early 2027 – Student (any level) with some prior experience in mol biol – Stipend 695 €/month

Yad Ghavi-Helm reposted

Emília Santos

14 July

🎨 job alert 🐠 Come join us! We have two positions open! These are part of our @erc.europa.eu funded project on the mechanisms underpinning convergence of colour patterns in cichlid fishes! Closing date: 16th August. Postdoc: www.cam.ac.uk/jobs/researc... Technician: www.cam.ac.uk/jobs/researc...

spatial-cell-id.github.ioRegistration & FeesFirst Spatial-Cell-ID Summer Schools

13 July

Due to a few last minute cancellations we have a limited number of places left. Please register before July 19th: spatial-cell-id.github.io/scid2026/reg...

Yad Ghavi-Helm@yghavi.bsky.social

Extended deadline until June 14th. Registration is totally free of charge for CNRS employees (including PhDs and postdocs!) Special features: time for hiking around Aussois! Bring your own data to get advice from our expert bioinformaticians!

@muscleflylab.bsky.social

13 July

Having a great time with past, current and future PhD students! A bitter sweet feeling as we say farewell to @baalberti.bsky.social and @mmasoura.bsky.social who will soon join @halloulab.bsky.social and @nvastenhouw.bsky.social labs and welcome Emeline Gallo who was just awarded a PhD fellowship!

Yad Ghavi-Helm reposted

Hadi Boukhatmi

2 July

he early bird registration deadline for DrosoFrance 2026 has been extended until July 6th. Registration remains open until September 15th, but only a limited number of places are left. So if you're planning to join us for the french Fly meeting (Trégastel), don't wait too long!

Roland Le Borgne@leborgne.bsky.social

Dear colleagues, The 36th French Drosophila Meeting (Trégastel, Oct 5–8, 2026) website is now online! drosofrance26.sciencesconf.org We look forward to welcoming you in Brittany! Best wishes, The Organizing Committee Hadi Boukhatmi, Régis Giet, Roland Le Borgne

spatial-cell-id.github.io SCID 2026Using Spatial OMICs to uncover cell identity during developmental processes 13-18 September 2026 Aussois, France

2 June

Yad Ghavi-Helm@yghavi.bsky.social

📢Join us for the Spatial-Cell-ID #spatialOMICs Summer School, September 13-18th 2026, at the Centre Paul-Langevin in Aussois, in the French Alps! You can find the full scientific program, our speakers, and the application form on our website: spatial-cell-id.github.io/scid2026/ Please share!

2 June

Relevant both for wet lab biologists who want to learn more about spatial OMICs and get initiated to data analysis and for bioinformaticians who want to learn about the latest developments in spatial OMICs data analysis.

spatial-cell-id.github.io SCID 2026Using Spatial OMICs to uncover cell identity during developmental processes 13-18 September 2026 Aussois, France

26 May

Only few days left to apply! This event is relevant both for wet lab biologists who want to learn more about spatial OMICs and get initiated to data analysis and for bioinformaticians who want to learn about the latests developments in spatial OMICs.

Yad Ghavi-Helm@yghavi.bsky.social

spatial-cell-id.github.io SCID 2026Using Spatial OMICs to uncover cell identity during developmental processes 13-18 September 2026 Aussois, France

- Call for Posters: we encourage applicants to submit a poster abstract alongside their motivation letter during the application process.

Speakers include @cantinilab.bsky.social @pascual-reguant.bsky.social @hildenelissen.bsky.social @hilsawh.bsky.social @thomas-walter.bsky.social Hands-on workshops on different aspects of sequencing-based and imaging-based spatial OMICs data analysis.

spatial-cell-id.github.io SCID 2026Using Spatial OMICs to uncover cell identity during developmental processes 13-18 September 2026 Aussois, France

Designed to bridge the gap between wet-lab innovation and advanced bioinformatics analysis, this Summer School offers a deep dive into the rapidly expanding field of Spatial OMICs with a mix of lectures from experts in the field and hands-on training sessions.

Key Information: - Only 50 places are available. - Application until May 31st, 2026. - Accommodation and meals are included in the registration fee. - Registration is free for all CNRS employees (including PhD students and Post-Doc).

sciencedirect.comCurrent Opinion in Genetics & Development | Genome Architecture and Expression (2026) | ScienceDirect.com by ElsevierThis collection summarizes key aspects of our current experimental and theoretical understanding of eukaryotic genome folding and its relationship with the molecular processes governing cell fate. Ove...

18 Feb

Don't miss this great opportunity!

IGFL@igflyon.bsky.social

L’IGFL recrute un•e Professeur•e des Universités en biologie moléculaire (CNU 64), UCBL Lyon 1. Enseignement L2-M2 (Biochimie et Biologie Moléculaire) + projet en biologie moléculaire des eucaryotes au sein de l’IGFL. Détails: shorturl.at/K5Dno #Recrutement #BiologieMoleculaire

Yad Ghavi-Helm reposted

IGFL

@igflyon.bsky.social

17 Feb

Yad Ghavi-Helm reposted

Alexis Verger 🧬🧫🧪

@alexis-verger.cpesr.fr

16 Jan

There is a special Current Opinion in Genetics & Development issue about genome architecture and expression and it looks great including reviews by @lennarthilbert.bsky.social @yghavi.bsky.social and @wbickmor.bsky.social www.sciencedirect.com/special-issu...

Yad Ghavi-Helm reposted

Roland Le Borgne

@leborgne.bsky.social

6 Jan

Happy New Year 2026! This year, Hadi Boukhatmi, Régis Giet and I are delighted to be organising the 36th French Droso Meeting in Brittany, from 5 to 8 October. A great line-up of speakers Mark the date in your diaries ! The meeting website containing all the details will be opening very soon.

@danielibrahim.bsky.social

10 Nov 2025

Congratulations to Dr @baalberti.bsky.social !! 🎉 And many thanks to his jury members @randersson.bsky.social @arnausebe.bsky.social @olivier-gandrillon.mastodon.social.ap.brid.gy Marie Sémon Anouck Necsulea and co-supervizor @paulvilloutreix.bsky.social

Yad Ghavi-Helm reposted

Daniel Ibrahim

a really cool work! everyone check it out! congratulations 🎉👏🏽

Yad Ghavi-Helm@yghavi.bsky.social

Yad Ghavi-Helm reposted

Christa Buecker

@chribue.bsky.social

super cool to see this out! looking forward to now read the details! Congratulations, Yad and @mmasoura.bsky.social

Yad Ghavi-Helm@yghavi.bsky.social

biorxiv.orgEnhancer-promoter compatibility is mediated by the promoter-proximal regionGene promoters induce transcription in response to distal enhancers. How enhancers specifically activate their target promoter while bypassing other promoters remains unclear. Here, we find that the p...

A must read! Check out @blanka-majchrzycka.bsky.social and @danielibrahim.bsky.social 's latest work

Daniel Ibrahim@danielibrahim.bsky.social

What is a promoter? And how does it work? We very happy to share our latest work trying to understand enhancer-promoter compatibility. I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters www.biorxiv.org/content/10.1...

Yad Ghavi-Helm reposted

Deevitha Balasubramanian

@deevithab.bsky.social

@danielibrahim.bsky.social

Check out our new story on how broad enhancer inputs are restricted into tissue-specific gene expression 🧬 Hint: Promoter-proximal regions are the key!

Yad Ghavi-Helm@yghavi.bsky.social

Yad Ghavi-Helm reposted

Daniel Ibrahim

Replying to @danielibrahim.bsky.social

you must check out @yghavi.bsky.social and @mmasoura.bsky.social's story, who found a similar mechanism in Drosophila. it's so cool if two works align!! www.biorxiv.org/content/10.1...

To finish, I would like to acknowledge all the members of the lab who made this work possible, in particular @mmasoura.bsky.social, soon to be graduating and on the job market!

Special thanks also to the continuous support of @erc.europa.eu @agencerecherche.bsky.social @frm-officiel.bsky.social @fondationarc.bsky.social @igflyon.bsky.social @ensdelyon.bsky.social @cnrs.fr

Altogether, we believe that these promoter-proximal gatekeepers belong to an emerging class of non-canonical regulatory elements that, together with facilitators and other similar elements, can modulate enhancer activity without acting as enhancers themselves.

Finally, we believe that these elements are not unique to the E3 enhancer or to Drosophila as beautiful work from @blanka-majchrzycka.bsky.social in @danielibrahim.bsky.social lab arrives to similar conclusions at the mouse Sox9 locus. www.biorxiv.org/content/10.1...

While the "generic" hsp70 core promoter can fully respond to E3's input, the expression of the reporter is restricted when combined with the minimal promoter of each of E3's target genes. This minimal promoter includes a ~100bp region upstream of the core promoter.

Importantly, this promoter-proximal region does not drive enhancer activity on its own. It only seems to restrict the input of the enhancer. We therefore called it a "gatekeeper".

If E3 can drive such complex expression, how is each target gene expressed only in a very specific spatio-temporal window then?? We discovered that the answer does not lie in the sequence of the enhancer or in its ability to form enhancer-promoter loops.

Instead, we found that the promoter-proximal region of each target gene plays a critical role. Indeed, the ability of a reporter gene to respond to E3's input varies drastically depending on the promoter.

However, to our surprise, we realized that in reporter assays, the activity of E3 is actually much more complex! The enhancer seemed to be active in tissues and stages when twist is not expressed, including non-mesodermal tissues!

In fact, we realized that E3 is a pleiotropic enhancer that is driving the expression of at least 3 other genes, each expressed in a very different spatio-temporal context.

Various hypotheses suggested that specificity might have to do with 3D genome organization, the sequence of the core promoter, etc... We now provide evidence that the answer instead lies upstream of the core promoter, in the promoter-proximal region!

To reach this conclusion, we first had to study an enhancer in great detail. We did this using the E3 enhancer of twist in Drosophila melanogaster embryos. E3 was previously characterized as a mesodermal enhancer driving the expression of the twist gene during early embryogenesis.

25 Sept 2025

In the starting blocks for #EDRC2025! Come see our work at posters 100 and 155 and during the Gene expression in the 3D nuclear space workshop!

EDRC2025@edrc2025.bsky.social

Only a few hours left before our meeting starts! Are you travelling to #EDRC2025 now? Let us know by using the oficial #EDRC2025 hashtag!

25 Sept 2025

Actually it’s poster 151 and 241!

buff.lyUn embryon virtuel pour cartographier l’activité des régions régulatrices du génomeDans un article publié dans Nucleic Acids Research, des scientifiques décrivent spatial-scERA, une méthode combinant biologie moléculaire, séquençage

28 July 2025

Merci au @cnrsbiologie.bsky.social de mettre en avant notre travail! @baalberti.bsky.social @paulvilloutreix.bsky.social @igflyon.bsky.social @ensdelyon.bsky.social

CNRS Biologie@cnrsbiologie.bsky.social

Un embryon virtuel pour cartographier l’activité des régions régulatrices du génome 🤝 @yghavi.bsky.social @cnrs-rhoneauvergne.bsky.social 👉 Lire l'article dans @narjournal.bsky.social buff.ly/e41cZQD

📢 We are recruiting! Several projects are available and can be tailored to the candidate's profile. Most include confocal imaging/spatial OMICs technologies. Please share and RT 🙏

Yad Ghavi-Helm reposted

Baptiste Alberti

@baalberti.bsky.social

doi.orgSpatial-scERA: a method for reconstructing spatial single-cell enhancer activity in multicellular organismsAbstract. Enhancers play an essential role in developmental processes by regulating the spatiotemporal expression of genes. Characterizing their spatiotemp

🚨 Our paper is out! 🚨 Check how spatial-scERA can predict enhancer activity in a virtual Drosophila embryo. Very proud of this first step in the research world published in @narjournal.bsky.social Thanks to @yghavi.bsky.social, @paulvilloutreix.bsky.social and all the scientists who made it real!

Yad Ghavi-Helm@yghavi.bsky.social

Now available in its final form @narjournal.bsky.social ! doi.org/10.1093/nar/... Find out how we can reconstruct enhancer activity in vivo in the Drosophila embryo using scRNAseq data and Optimal Transport.

tinyurl.comSpatial reconstruction of single-cell enhancer activity in a multicellular organismEnhancers play an essential role in developmental processes by orchestrating the spatial and temporal regulation of gene expression. However, mapping the location of these regulatory elements in the g...

Yad Ghavi-Helm@yghavi.bsky.social

🚨Preprint alert! tinyurl.com/2zkmynsd Did you ever dream of reconstruction #spatial single-cell #enhancer activity in a multicellular organism using massively parallel enhancer-reporter assays? Then Spatial-scERA is the method for you! #spatialOMICs

This is the work of a talented PhD student @baalberti.bsky.social (on the job market!) together with Séverine Vincent, and a great collaboration with @paulvilloutreix.bsky.social 🙌 @igflyon.bsky.social @cnrsbiologie.bsky.social @ensdelyon.bsky.social

Yad Ghavi-Helm reposted

Bon Pote

@bonpote.com

19 July 2025

300 000 signatures dont plus de 200000 en moins de 48h ! L’objectif des 500 000 signatures est possible d’ici dimanche soir, afin d’obtenir un vrai débat à l’Assemblée nationale sur la loi Duplomb.

2 Apr 2025

Honored and extremely grateful to see our project in collaboration with @hilaryashe.bsky.social and @hilsawh.bsky.social awarded an #HFSPReseachGrant @hfspo.bsky.social Stay tuned for exciting job offers!

Human Frontier Science Program@hfspo.bsky.social

🥳Congratulations to the 104 pioneering scientists from 30 nations awarded 2025 #HFSPResearchGrants! 🎉Your frontier research is shaping the future of #LifeSciences! 🌍🔬🧪 🏆 Meet the awardees & their projects: www.hfsp.org/bookletRG202... #ScienceDiplomacy #HFSP #FrontierScience #sts

23 Jan 2025

Thanks @evodevogenomeub.bsky.social @criscanestro.bsky.social for having us and showing us all the secrets of beautiful Oikopleura!! 😍