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Ufuk Günesdogan

@guenesdoganlab.bsky.social

150 followers 140 following 4 posts

Developmental and Stem Cell Biology lab at the University of Goettingen

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Ufuk Günesdogan @guenesdoganlab.bsky.social · Jun 3

🚨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. 👇

Stefan Schoenfelder @stefanschoenfelder.bsky.social · Jun 2

Delighted & excited to share our latest preprint on non-canonical enhancers in human pluripotent stem cells, the result of a fantastic and fun collaboration with @guenesdoganlab.bsky.social‬:
www.biorxiv.org/content/10.1...

🧵 below

Non-canonical enhancers control gene expression and cell fate in human pluripotent stem cells

Enhancers are key gene regulatory elements that ensure the precise spatiotemporal execution of developmental gene expression programmes. However recent findings indicate that approaches to identify en...

www.biorxiv.org

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Jesse Engreitz @jengreitz.bsky.social · 21d

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

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Gurdon Institute, University of Cambridge @gurdoninstitute.bsky.social · 21d

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.

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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 29d

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

Annual Reviews @annualreviews.bsky.social · Sep 9

The latest Annual Review of Genomics and Human Genetics is now online 🧬 Most read article so far is "Mechanisms of Enhancer-Mediated Gene Activation in the Context of the 3D Genome" @akispapantonis.bsky.social @mariekeoudelaar.bsky.social Check it out arevie.ws/47BZEJp
Full TOC: arevie.ws/4plCaPe

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Mark Peifer (He, him) @peiferlabunc.bsky.social · Aug 23

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

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

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Vallier Lab @vallierlab.bsky.social · Aug 22

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...

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...

www.bihealth.org

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Bluma Lesch @ambystoma22.bsky.social · Aug 20

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...

H3K4me3 amplifies transcription at intergenic active regulatory elements

A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields

genesdev.cshlp.org

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stadtfeldlab.bsky.social @stadtfeldlab.bsky.social · Aug 19

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...

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...

www.cell.com

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Schuh Lab @schuhlab.bsky.social · Aug 14

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.

MPI for Multidisciplinary Sciences @mpi-nat.bsky.social · Aug 14

Keeping our fingers crossed for you, Melina @schuhlab.bsky.social!
We are thrilled that our director has been nominated for the Falling Walls Foundation Science Breakthroughs of the Year 2025 in the Life Sciences category with her project “Breaking the Wall of Invisible Ovulation”. 🥂

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Rada-Iglesias Lab @radaiglesiaslab.bsky.social · Aug 11

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...

www.biorxiv.org

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Marta Shahbazi @marta-shahbazi.bsky.social · Aug 9

🤩 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….

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Sara Wickstrom @sarawickstrom.bsky.social · Aug 1

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

EMBL Events @events.embl.org · Jul 31

📢 Abstract submission deadline reminder for 'Cell biology of the nucleus'!

Before packing your bags and leaving for your summer vacation, there is one important task left to do: submit your abstract for #EESNucleus ✍️

Deadline is 26 August: https://s.embl.org/ees25-07-bl

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Eileen Furlong @eileen-furlong.bsky.social · Jul 30

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...

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...

embl.wd103.myworkdayjobs.com

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Ufuk Günesdogan @guenesdoganlab.bsky.social · Jul 30

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

Stefan Schoenfelder @stefanschoenfelder.bsky.social · Jul 22

🚨 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

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Development @dev-journal.bsky.social · Jul 11

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...

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

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Ina Sonnen @sonnenlab.bsky.social · Jul 10

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!! 👇

Hubrecht Institute @hubrechtinstitute.bsky.social · Jul 10

🧬 Looking for a PhD position in molecular or developmental biology? 🔬

✉️ The Hubrecht Institute now has its very own PhD program! Applications are open and will be accepted until September 15th. Read more here 👉 www.hubrecht.eu/hipp/

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Virtual Gastrulation Zoom Talks @vgzt2021.bsky.social · Jul 8

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

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German Stem Cell Network GSCN @gscnoffice.bsky.social · Jul 7

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

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Evgeny Kvon @evgenykvon.bsky.social · Jul 2

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.

www.nature.com

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Aydan Bulut-Karslioglu @bulutkarslioglu.bsky.social · Jun 23

⚠️ 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.

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Gurdon Institute, University of Cambridge @gurdoninstitute.bsky.social · Jun 20

🌟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

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Rob Schneider @robertife.bsky.social · Jun 19

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/...

Development @dev-journal.bsky.social · Jun 18

Histone modifications in development

Read this 'Development at a Glance' article by Yu-Hao Liu and @robertife.bsky.social, summarising the role of selected histone modifications during development.
journals.biologists.com/dev/article/...

A panel of the 'Histone modifications in development' poster, showing 'histone globular domain modifications in mouse and human development;.

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Akis (Argyris) Papantonis @akispapantonis.bsky.social · Jun 19

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

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Axel Visel @axelvisel.bsky.social · Jun 18

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

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.

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FragileNucleosome @fnucleosome.bsky.social · Jun 14

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...

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Alex Gould Lab @alexgouldlab.bsky.social · Jun 4

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

FlyBase @flybase.bsky.social · Jun 3

We currently have a call for support that has gone out to European labs, to support FlyBase-UK. We are asking our colleagues from labs in the US and other countries to wait for a similar call to them that will go out in the near future, to support the US sites. We thank you for your patience.

Mark A. Hanson @hansonmark.bsky.social · Jun 3

URGENT: FlyBase has lost practically all its funding overnight; even user fees are tied up in denied grant funding. 🤬🤯

Any lab using @flybase.bsky.social please donate using the link in post below.

This incredible community, on whose backs our #Drosophila labs depend, can't be left out to dry.

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