Eva D'haene

👇 Highly recommend applying if you want to join a great team and work on a high-profile, inter-university project! #postdocjobs

Epigenetic priming of mammalian embryonic enhancer elements coordinates developmental gene networks - Genome Biology Background Embryonic development requires the accurate spatiotemporal execution of cell lineage-specific gene expression programs, which are controlled by transcriptional enhancers. Developmental enha...

🚨 New paper alert 🚨
I am excited to share our new work on epigenetic enhancer priming in early mammalian development
genomebiology.biomedcentral.com/articles/10....
Fantastic collaboration with Wolf Reik’s team, with key contributions from many others, led by the excellent Chris Todd.
Short 🧵

📣 Join us at the Genetics of Ocular Development (GoOD) Meeting in Ghent, Belgium, 8-9/09/25 🧬

Abstract submission until 16/07/25 goodsoc.org
✨ Exciting line-up ✨

Supported by GoOD @vlaamseoverheid.bsky.social @ds-ugent.bsky.social Lucid

#eyegenetics #development #models #diagnosis #therapy

Structural variants in the 3D genome as drivers of disease - Nature Reviews Genetics Disruption of the 3D genome caused by structural variation contributes to developmental disorders and cancer. The authors review the causes and molecular and clinical consequences of position effects ...

🚀 Thrilled to share our new review on how structural variants reshape 3D genome architecture and cause disease! 🧬🔀
Out now in Nature Reviews Genetics: www.nature.com/articles/s41...
#3D-Genome #StructuralVariants #uksh

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/

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

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...

Excellent poster talks from all Ghent PhD students at #eshg25! Well done 👏🏻👏🏻

Excellent talk by my colleague @elfridedebaere.bsky.social on cis regulatory elements in eye diseases at #eshg25. If you did not attend her session, I highly recommend to watch it on the virtual platform. Enhanceropathies research at Ghent University is on 🔥

@lisahamerlinck.bsky.social kicking ass at #eshg2025

Sharing work on non-coding regulatory disruptions of FOXG1.

#FunGen @svergult.bsky.social @eedhaene.bsky.social

If you're interested and happen to be at #eshg2025, look up @svergult.bsky.social to chat!

We're looking for a new colleague! If you're excited by 2D and 3D neural models for neurodegenerative disease and want to join a fantastic lab, apply!!! 👇

Sharing would be great as well 🙏

#postdoc #jobs #neurogen #neurogenomics

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...

On my way to #eshg25!
If you are interested in the work we do at the FunGen lab, check out the flash talk on Sunday and poster on Monday by @lisahamerlinck.bsky.social or come and have a coffee with team members @michael-b-vaughan.bsky.social, @eedhaene.bsky.social or me. Hope to see you there!

Scalable automated reanalysis of genomic data in research and clinical rare disease cohorts Reanalysis of genomic data in rare disease is highly effective in increasing diagnostic yields but remains limited by manual approaches. Automation and optimization for high specificity will be necess...

🤗 Hugely excited to share our work on automating iterative reanalysis in #raredisease, preprint out: www.medrxiv.org/content/10.1... 🤖🧬

github.com/populationge...

A superb collaboration with @dgmacarthur.bsky.social @cassimons.bsky.social @heidirehm.bsky.social @ksamocha.bsky.social and many more!

Congrats Jasper!

Looking forward to exciting science and to connect with colleagues in Milan at the Neurogenomics conference @humantechnopole.bsky.social Presenting our research ( @svergult.bsky.social @lisahamerlinck.bsky.social ) on noncoding variants in the FOXG1 locus during the poster session (#88) #neurogen25

Very happy to share the peer-reviewed version of our paper in which we study the formation and function of pair-wise and multi-way enhancer-promoter interactions in gene regulation (see thread below): www.nature.com/articles/s41...

Check out our latest work on the evolution of animal genome regulation out today in @nature.com. Nicely summarized below by @ianakim.bsky.social.
www.nature.com/articles/s41...

This is a major output from our ERC-StG project Evocellmap @erc.europa.eu at @crg.eu

Dissecting regulatory syntax in human development with scalable multiomics and deep learning Transcription factors (TFs) establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility, and regulating gene expre...

Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️

Saturation genome editing of RNU4-2 reveals distinct dominant and recessive neurodevelopmental disorders Recently, de novo variants in an 18 nucleotide region in the centre of RNU4-2 were shown to cause ReNU syndrome, a syndromic neurodevelopmental disorder (NDD) that is predicted to affect tens of thous...

🚨I could not be more excited to share our new preprint on saturation genome editing of the small nuclear RNA (snRNA) RNU4-2:
www.medrxiv.org/content/10.1...

A super fun collaboration with incredible duo @gregfindlay.bsky.social @joachimdejonghe.bsky.social from @crick.ac.uk
🧬🖥️🩺

🧵1/12

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! 🙏🤘

Only one week left to submit your abstract to the @embo.org workshop on "Enhancer mechanics and Enhanceropathies". Submit now and present your latest work in one of our short talks.

Happy to share our review with @akispapantonis.bsky.social in which we summarise and discuss our current understanding of enhancer-mediated gene activation in the context of the 3D genome:

www.annualreviews.org/content/jour...

This multi-year, multi-PhD project was made possible by financial support from the Research Foundation Flanders (FWO) and the Marguerite-Marie Delacroix research fund. @deciphergenomics.bsky.social was instrumental in gathering clinical information.

To sum it up, we identified and characterized regulatory elements essential for proper FOXG1 transcription. Our findings provide new insights into chromatin architecture and gene regulation at the FOXG1 locus, improving SV interpretation in individuals with FOXG1 syndrome-like characteristics.

Finally, CRISPR-Cas9 deletion of the enhancer cluster and TAD boundary in NPCs resulted in decreased FOXG1 transcription.

As FOXG1 plays a crucial role in differentiation and proliferation of neural progenitor cells (NPCs), we performed sequential UMI-4C and CUT&RUN assays during NPC differentiation. We found dynamic activation of, and FOXG1 interaction with, our enhancer cluster.

Integrating epigenomics data, 3D chromatin interaction profiles (Hi-C, UMI-4C), and in vivo enhancer assays in zebrafish, we uncovered multiple regulatory elements within this CARR, including a neuronal enhancer cluster and a conserved boundary of the FOXG1 TAD.

We identified a de novo non-coding deletion in an individual with FOXG1 syndrome, allowing us to delineate a ~124 kb commonly affected regulatory region (CARR). Deletion of this region resulted in reduced FOXG1 expression and TAD fusion in patient cells.