Our paper on the effect of non-coding variants in FOXG1 syndrome is out! A substantial amount of new data over the preprint. Enhancers, TADs and much more. Great teamwork with @lisahamerlinck.bsky.social. Read about it in the thread by @svergult.bsky.social below 👇

Sarah Vergult@svergult.bsky.social · last mo.

40 individuals with the clinical picture of FOXG1 syndrome and a completely intact FOXG1 gene. So what’s going wrong then? Our new paper in @natcomms.nature.com traces the answer to a stretch of non-coding DNA 665 kb away from the gene. (1/7)

Thanks to a fellowship from @nordicembl.bsky.social I have been able to start a new chapter in the labs of @hkilpinen.bsky.social and @thomasdwkim.bsky.social. A bit more about the science to come in the article here 👇

Nordic EMBL Partnership for Molecular Medicine@nordicembl.bsky.social · 6mo ago

Welcome to Eva D'haene, new NORPOD Fellow in the Nordic EMBL Partnership for Molecular Medicine🎉! She is working with Helena Kilpinen at @fimm-uh.bsky.social and @thomasdwkim.bsky.social at @dandrite.bsky.social. Find out about Eva’s research and aspirations 👉 tinyurl.com/mrmd3chy @embl.org

Join us today at Sept 23rd2025 from 5pm to 6.30 pm (Central European Time) for our ERN ITHACA webinar on the non-coding genome and human disease by @svergult.bsky.social , @mspielmann.bsky.social , Florence Petit and @stefanbarakat.bsky.social ern-ithaca.eu/events-news/...

Excited to share the latest work from the lab led by @eharo84.bsky.social, in which we have used synthetic biology to explore the mechanisms by which different types of long-range enhancers ensure robust and precise developmental gene expression www.biorxiv.org/content/10.1...

Synthetic engineering demonstrates that synergy among enhancers involves an increase in transcriptionally productive enhancer-gene contacts

Enhancers are non-coding cis-regulatory elements that control the expression of distally located genes in a tissue- and time-specific manner. Recent studies indicate that enhancers can differ in their...

biorxiv.org

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

Sarah Vergult@svergult.bsky.social · last yr.

📣Job Alert: We are looking for a postdoctoral researcher with hands-on experience in neural tissue culture, preferably neural organoids, for a collaborative project on Alzheimer's disease and MS between KULeuven, UHasselt and UGent in Belgium. Deadline August 31: www.ugent.be/en/work/scie...

🚨 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 🧵

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...

genomebiology.biomedcentral.com

📣 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

🚀 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

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 ...

nature.com

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/

Range extender mediates long-distance enhancer activity - Nature

The REX element is associated with long-range enhancer–promoter interactions.

nature.com

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

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...

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...

rdcu.be

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

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

Sarah Vergult@svergult.bsky.social · last yr.

📣Job Alert: We are looking for a postdoctoral researcher with hands-on experience in neural tissue culture, preferably neural organoids, for a collaborative project on Alzheimer's disease and MS between KULeuven, UHasselt and UGent in Belgium. Deadline: June 23 Link: www.ugent.be/en/work/scie...

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...

nature.com

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!

🤗 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!

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...

medrxiv.org

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...

CTCF depletion decouples enhancer-mediated gene activation from chromatin hub formation - Nature Structural & Molecular Biology

Karpinska, Zhu and colleagues characterize the structure-function relationship of the genome during cellular differentiation and demonstrate a role for enhancer-promoter interactions in gene regulatio...

nature.com

Marieke Oudelaar@mariekeoudelaar.bsky.social · 2y ago

📣 Preprint alert! We have studied the formation of pair-wise and multi-way enhancer-promoter interactions in the #3Dgenome in a lymphoid-to-myeloid transdifferentiation system and learned interesting new things about their function in #GeneRegulation. 1/10 www.biorxiv.org/content/10.1...

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

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 ...

nature.com

Iana V. Kim@ianakim.bsky.social · last yr.

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...

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 🧬🖥️

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...

biorxiv.org

🚨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

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...

medrxiv.org

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.

Rada-Iglesias Lab@radaiglesiaslab.bsky.social · 2y ago

Together with @smandrup.bsky.social and Minna Kaikkonen we are happy to announce the 3rd Edition of the EMBO Workshop on #Enhancers and #Enhanceropathies. This time we will meet during the beautiful Danish summer (June 16-21). Book the dates and register soon!!! meetings.embo.org/event/25-enh...

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...

📢 New preprint from the FunGen lab @svergult.bsky.social on how non-coding structural variants disrupt FOXG1 regulation during early neurodevelopment. Great teamwork from Lisa Hamerlinck and everyone in the lab! Thread below👇 www.medrxiv.org/content/10.1... #GeneRegulation #RareDisease #Epigenomics

One of the best workshops out there if you work on #Enhancers #GeneRegulation #Epigenomics 👇

Susanne Mandrup@smandrup.bsky.social · 2y ago

Join us for this exciting @embo.org workshop to explore recent advances in our understanding of enhancer mechanisms and the critical roles of enhancers in human health! 🧬 🧪 Submit an abstract by March 17 to be considered for short talk. Register by April 1 to participate! 😊 @sdu.dk @dg.dk

Looking forward to attending this great meeting and connecting with #RareDisease colleagues!

Wellcome Connecting Science Learning and Training@eventswcs.bsky.social · 2y ago

Join leading experts working in #RareDisease research at our #GRD25 conference. 📅 Dates: 9-11 April 2025 💭 Share insights in person Explore the latest #genomics advances accelerating improvements in clinical care for rare disorders, globally. ⏰Secure your place by 11 March: bit.ly/3BpAe44

Together with @smandrup.bsky.social and Minna Kaikkonen we are happy to announce the 3rd Edition of the EMBO Workshop on #Enhancers and #Enhanceropathies. This time we will meet during the beautiful Danish summer (June 16-21). Book the dates and register soon!!! meetings.embo.org/event/25-enh...

Enhancer Mechanics and Enhanceropathies

Join us for the highly anticipated third EMBO workshop on Enhancer Mechanics and Enhanceropathies! Building on the success of our previous meetings in Santander (2021) and Marseilles (2023), this eve…

meetings.embo.org