Ufuk Günesdogan

bioRxiv - An unbiased survey of distal element-gene regulatory interactions with direct-capture targeted Perturb-seq

New preprint from our lab!

What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?

Find out here: www.biorxiv.org/content/10.1...

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Thrilled to share that our Group Leader Prof. Azim Surani, together with Prof. Davor Solter, has been awarded the 2026 Paul Ehrlich & Ludwig Darmstaedter Prize 🎉 for discovering genomic imprinting—a breakthrough that reshaped genetics and launched modern epigenetics.

Most read, I hear!
Here is your chance to read what @mariekeoudelaar.bsky.social and I had in mind when writing this together.

Dear Fly Community, In May 2025, the NIH terminated all grant funding to Harvard University, including the NHGRI grant that supported FlyBase. This grant also funded FlyBase teams at Indiana University (IU) and the University of Cambridge (UK), and as a result, their subawards were also canceled. The Cambridge team has secured support for one to two years through generous donations from the European fly community, emergency funding from the Wellcome Trust, and support from the University of Cambridge. At IU, funding has been secured for one year thanks to reserve funds from Thom Kaufman and a supplement from ORIP/NIH to the Bloomington Drosophila Stock Center (BDSC). Unfortunately, the situation at Harvard is far more critical. Harvard University had supported FlyBase staff since May but recently denied a request for extended bridge funding. As a result, all eight employees (four full-time and four part-time) were abruptly laid off, with termination dates ranging from August to mid-October depending on their positions. In addition, our curator at the University of New Mexico will leave her position at the end of August. This decision came as a shock, and we are urgently pursuing all possible funding options. To put the need into perspective: although FlyBase is free to use, it is not free to make. It takes large teams of people and millions of dollars a year to create FlyBase to support fly research (the last NHGRI grant supported us with more than 2 million USD per annum). To help sustain FlyBase operations, we have been reaching out to you to ask for your support. We have set up a donation site in Cambridge, UK, to which European labs have and can continue to contribute, and a new donation site at IU to which labs in the US and the rest of the world can contribute. We urge researchers to work with their grant administrators to contribute to FlyBase via these sites if at all possible, as more of the money will go to FlyBase. However, we appreciate that some fu…

https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase Our immediate goals are: 1. To maintain core curation activities and keep the FlyBase website online 2. To complete integration with the Alliance of Genome Resources (The Alliance). Integration with the Alliance is essential for FlyBase’s long-term sustainability. For nearly a decade, NHGRI/NIH has supported the unification of Model Organism Databases (MODs) into the Alliance, which we aim to achieve by 2028. Therefore, securing bridge funding to sustain FlyBase over the next three years is crucial for successful integration and the long-term access to FlyBase data. At present, our remaining funds will allow us to keep the FlyBase website online for approximately one more year. Beyond that, its future is uncertain unless new funding is secured. We will, of course, continue pursuing additional grant opportunities as they arise. Given the uncertainty of future NIH or alternative funding sources, we are relying on the Fly community for support. Your contributions will directly help us retain the staff needed to complete this transition and to secure ongoing fly data curation into the Alliance beyond 2028. We at FlyBase are incredibly grateful for the outpouring of support from the community during this challenging time. Your encouragement has strengthened our resolve and underscores how vital this resource remains to Drosophila research worldwide. Sincerely, The FlyBase Team

The community of Drosophila researchers is amazing, mutually supportive and collaborative. Right now a key resource for our community, @flybase.bsky.social , is threatened by the cancellation of its NIH grant and is seeking community help in raising short term funds 1/n 🧪 please share

Berlin Organoid Symposium - News - BIH at Charité The Berlin Organoid Symposium will highlight recent advances in the field, covering topics from fundamental organoid biology to translational applications. By uniting scientists from various instituti...

So, we (Dylan Liabeuf and Anastasiia Maksiuk) are organising the first Berlin symposium on organoids. The objective is to bring together the Berlin organoid community and to develop further interactions.

Info:
www.bihealth.org/en/notices/b...

Free registration:
www.bihealth.org/en/news/even...

New paper on the role of H3K4me3 at enhancers! We (led by Haoming Yu) used dCas9 epigenome editing to add H3K4me3 to intergenic enhancers. This was (1) sufficient to turn up transcription at open, active regions and (2) has no effect on target gene transcription. genesdev.cshlp.org/content/earl...

Enhancer remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm Correct patterning of emerging tissues in the developing embryo is essential for the formation of functional organ systems. Using genetic tools for controlled protein depletion, Ee et al. identify the...

Excited to share our new study in @cp-devcell.bsky.social dissecting how the brain-associated transcription factor OTX2 drives anteriorization of the mammalian gut by enhancer remodeling using stem cell-based models. #development #enhancers #patterning #stemcells

www.cell.com/developmenta...

Great honor to be nominated as one of the top 10 Falling Walls Foundation Science Breakthroughs of the Year 2025 in the Life Sciences. A big thank you to @ovarylab.bsky.social & @tabeamarx.bsky.social for their outstanding contributions, & to everyone else who helped move this project forward.

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...

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...

🤩 Very excited to share our new work! We have derived euploid and aneuploid trophoblast organoids and extra-embryonic mesoderm cell lines from early human embryos. In doing so, we have characterised the tissue requirements for their specification. If you want to know more, continue reading….

Check out this exciting meeting and register! Fantastic line-up of speakers on cell biology of the nucleus and a great venue 🔥

Group Leader - Genome Biology Unit Are you ready to lead groundbreaking research in Genome Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group addressing exciting and original biological...

To all post-docs: The Genome Biology dept ‪@embl.org
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Delighted to see this work published! Congrats to Chris Todd and everyone involved - happy to have been part of the team.

Human Development: Stem Cells, Models, Embryos. 7 - 9 September 2026 University of Warwick, UK. Resgiter your interest. #HumanDev26. Image credit: Susanna Narkilahti, Tampere University, Finland

Save the Date!

Development has teamed up with the Wellcome-funded consortium the Human Developmental Biology Initiative to co-organise a meeting on #HumanDevelopment.

📅7 - 9 Sep 2026
📍University of Warwick, UK

Register your interest for #HumanDev26: www.biologists.com/meetings/dev...

Please pread the word.

We have just launched the Hubrecht International PhD Program (HIPP).

Are you looking for a PhD position in molecular and developmental biology or related subject in an international, very supportive and collaborative environment?

Then apply to the HIPP!! 👇

Join the VGZT Eastern KEYNOTE lecture ☀️☕ TOMORROW

🗓️ Wednesday July 09
⏰ 13:30 IST / 17:00 JST / 8:00 UTC / 10:00 CET

Featuring:
1) Maithreyi Narasimha
👉Positioning tissues during Drosophila morphogenesis

Jose Silva @josesilvalab.bsky.social
👉From founder cells to organogenesis-stage embryo model

GSCN Conference (15. - 17. Oct 2025 in Munich)! Extended Deadline: 21 July 2025. Submit your abstract for an oral presentation & get an early bird ticket by 21.7.! Save on registration and secure your spot in the scientific program. Register and submit your abstract here: ➙ gscn-conferences.org

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/

⚠️ 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.

🌟Congratulations to Azim Surani @gurdoninstitute.bsky.social @cam.ac.uk for receiving the 2025 Kyoto Prize - Basic Sciences. Azim's research fundamentally advanced our understanding of developmental biology🔬🧬 www.gurdon.cam.ac.uk/kyoto-prize-...
#KyotoPrize #AzimSurani #DevelopmentalBiology

Our review on ➡️"Histone modifications in development" is out 🍾 in 🔖 Development @dev-journal.bsky.social urnal.bsky.social‬
Read more about histone tail and globular domain modifications during development: journals.biologists.com/dev/article/...

This is a piece that I and @karsten-rippe.bsky.social discussing a lot, and a topic that is very close to my heart. The editors @naturerevgenet.bsky.social gave us the stage to do so, and the final version of our review is now available under this link: rdcu.be/erP1u

A short thread follows 1/n

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

Join us next Wed, for three amazing ECR researchers_ @fueyoraquel.bsky.social, @kaiamattioli.bsky.social and Laura talk about their work in #FragileNucleosome seminar series!
In case you haven't joined any of the previous 2025 sessions, here is registration link:
us06web.zoom.us/webinar/regi...

Calling all European #Drosophila labs. Time for all of us, that are able, to step up to support FlyBase during this funding crisis.

Welcome! You are invited to join a webinar: The 3D Regulatory Genome: Gaining mechanistic insights into long-range gene regulation through synthetic biology approaches. After registering, you will rec... Join our guest speaker, Dr. Alvaro Rada-Iglesias, in this exciting seminar on the 3D Regulatory Genome, sponsored by Enhanced Genomics.

Really looking forward to @radaiglesiaslab.bsky.social's talk on "Gaining mechanistic insights into long-range gene regulation through synthetic biology approaches" in @enhancedgenomics.bsky.social's seminar series.

📅 June 5th 2025 tomorrow
⏰ 4pm GMT

Please join us:
us02web.zoom.us/webinar/regi...

Maternal iron deficiency causes male-to-female sex reversal in mouse embryos - Nature Iron-deficient conditions in pregnant mice can cause XY mouse embryos to develop female rather than male genitalia, revealing that iron metabolism has a role in determining male sex in mice.

www.nature.com/articles/s41...

Dev bio is amazing !!

H3.3 deposition counteracts the replication-dependent enrichment of H3.1 at chromocenters in embryonic stem cells - Nature Communications In mammals, two major non-centromeric histone H3 (H3.1/2 and H3.3) variants, display distinct nuclear distribution patterns across the genome and use distinct deposition pathways. Here the authors rev...

🔬✨ Excited to share a major milestone from my PhD research at Institut Curie, where I am a first author in a recently published paper in Nature Communications!
www.nature.com/articles/s41...

🚨Preprint alert!🚨 Great collaboration with the lab of Stefan Schoenfelder @stefanschoenfelder.bsky.social - we dissect the role of non-canonical enhancers in human pluripotent stem cells. 👇

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...