Luca Braccioli Lab @ UU
@bracciolilab.bsky.social
Exploring the interplay between gene regulation and tissue-tissue interactions in stem cell-based embryo models.
🧩 What is the role of translational regulation during early tissue development? I am very grateful to have been awarded the ECR Seed Grant to answer this question together with @thejoanasilva.bsky.social ! #UtrechtLifeSciences #EarlyCareerResearchers #Gastruloids
In our latest editorial @amjeve.uk & I take on the dreaded impact factor Like Monday mornings no one likes them but you can't ignore them & they keep coming around However there are things we should all do as authors, reviewers & editors journals.biologists.com/dev/article/...
The elephant in the room: impact factor
Summary: This Editorial offers an honest look at impact factor trends in developmental biology, explains how Development serves its community, and makes the case that sustaining developmental biology ...
journals.biologists.com
Our latest: Minimal essential requirements for neural tube self-organisation How does a single cell give rise to a tissue with the right cell types in the right proportions? We deconstruct and rebuild a self-organising tissue from first principles A thread🧵 www.biorxiv.org/content/10.6...
Minimal essential requirements for neural tube self-organisation
The reliable generation of diverse cell types in precise proportions is essential for the formation of functional tissues during embryonic development. Three-dimensional organoid models derived from p...
biorxiv.org
🤯
Elphege Nora Lab at UCSF@elphegenoralab.bsky.social · 3mo agoWhy can't we explain enhancer action despite 2 decades of chromosome conformation technologies? 😬 Our new study spearheaded by Leonid Mirny's group points to a flaw in our assumptions, and to a solution from physical principles By @timothyfoldes.bsky.social 💻& @karissalhansen.bsky.social 🧪 🧵👇
🚨One week left! Applications for our Postdoctoral Fellows Program will close on 20. May! We offer numerous benefits: ✅ 3-year funded position ✅ Core research funding to cover travel, publishing, and project costs ✅Mentorship from 2+ PoL PIs ..and much more! Apply now: tud.link/y3djda
This years' edition of the International Dutch Embryo Model Meeting was truly fantastic! Thanks to all the participants and my co-organizers @moritzbauer.bsky.social and @Hendrik Marks for making this happen! #IDEMM2026 ##ZonMW @oncodeinstitute.bsky.social
Moritz Bauer@moritzbauer.bsky.social · 3mo agoIt’s a wrap! 🎉 iDEMM 2026 is done — two days, 160 scientists, the most exciting embryo model science around. Less conference, more rock festival — just with pipettes instead of guitars. 🎸🔬 Huge thanks to speakers, posters, attendees, and my co-organizers @bracciolilab.bsky.social and Hendrik Marks.
It’s a wrap! 🎉 iDEMM 2026 is done — two days, 160 scientists, the most exciting embryo model science around. Less conference, more rock festival — just with pipettes instead of guitars. 🎸🔬 Huge thanks to speakers, posters, attendees, and my co-organizers @bracciolilab.bsky.social and Hendrik Marks.
🥳 I am happy to share our latest manuscript published in @natcellbio.nature.com We use #Gastruloids to study #CellCompetition during early mammalian development and find not only that this is highly pronounced in our system but also tightly restricted in time. (1/12) www.nature.com/articles/s41...
Mosaic gastruloids reveal a temporal restriction for developmental cell competition - Nature Cell Biology
Frenster et al. utilize mosaic mouse gastruloids as a model of cell fitness and competition, identifying a temporal window between primed pluripotency and early gastrulation during which cell competit...
nature.com
Don’t forget to sign up — registration is still open for the International Dutch Embryo Model Meeting 2026 in Utrecht (7–8 May)! 🚀 Hope to see many of you there. Registration closes 24 April!
Luca Braccioli Lab @ UU@bracciolilab.bsky.social · 6mo ago🧬 We are excited to announce the INTERNATIONAL DUTCH EMBRYO MODEL MEETING 2026 — Engineering the Origins of Life 📅 7–8 May 2026 📍 Utrecht, The Netherlands Register & submit abstracts: www.oncodeinstitute.nl/internationa...
🔥 How does CTCF shape enhancer–promoter communication? In our new preprint, we systematically test how the position and orientation of CTCF binding sites (CBSs) influence gene regulation at the mouse Sox2 locus. 🧪 full paper can be found here: www.biorxiv.org/content/10.6...
biorxiv.org
New paper out! Huge congratulations to Noemí Alonso Saiz (wet-lab) and Moreno Martinovic (computational) for leading fantastic work, co-supervised by me and @dewitlab.bsky.social.
Elzo de Wit lab @ NKI@dewitlab.bsky.social · 5mo ago🧵 CTCF is essential for embryonic development, but why has remained unclear. By combining gastruloids with a temporal degron system, we uncovered a surprising dual function — and it changes how we think about CTCF's role in development. 1/8 www.biorxiv.org/content/10.6...
🧵 CTCF is essential for embryonic development, but why has remained unclear. By combining gastruloids with a temporal degron system, we uncovered a surprising dual function — and it changes how we think about CTCF's role in development. 1/8 www.biorxiv.org/content/10.6...
A dual role for CTCF in development
CTCF is an essential DNA binding protein whose absence leads to embryonic lethality. CTCF is primarily known for its role in 3D genome organization where its N-terminal domain interacts with cohesin to anchor chromatin loops. How CTCF facilitates proper embryonic development remains unclear, necessitating temporal control to resolve its stage-specific functions. By combining gastruloids, an in vitro model of embryonic development, with a degron system to rapidly deplete CTCF at defined timepoints, we show that early CTCF depletion impairs early gastruloid morphogenesis. Surprisingly, ATAC-seq and time-resolved RNA-seq revealed that differentiation was unaffected. CTCF binding is strongly enriched at promoters of downregulated genes. Re-expression of a CTCF variant with an N-terminal truncation, incapable of looping, was sufficient to rescue the expression of CTCF-promoter bound genes and the defects in morphogenesis. However, extended culture (up to 168 hours) of gastruloids reconstituted with N-terminal truncated CTCF led to their collapse. Our work shows that CTCF has a dual function in early mammalian development: at early stages CTCF regulates developmentally important genes through promoter binding, while at later stages its looping function is required for correct development. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, https://ror.org/0472cxd90, 637587, 865459 Dutch Research Council, https://ror.org/04jsz6e67, 016.161.316, VI.C.222.049 Dutch Cancer Society, https://ror.org/0368jnd28, N/A
biorxiv.org
More on enhancers at #gfe2026, with @bracciolilab.bsky.social exploring how long-distance, DNA loops are formed through CTCF and cohesin interactions in gastruloids. Removing CTCF early severely affects morphogenesis, but not differentiation, and is dependent on CTCF looping function. #gfe2026
🧬 We are excited to announce the INTERNATIONAL DUTCH EMBRYO MODEL MEETING 2026 — Engineering the Origins of Life 📅 7–8 May 2026 📍 Utrecht, The Netherlands Register & submit abstracts: www.oncodeinstitute.nl/internationa...
🧬 We are excited to announce the INTERNATIONAL DUTCH EMBRYO MODEL MEETING 2026 — Engineering the Origins of Life 📅 7–8 May 2026 📍 Utrecht, The Netherlands Register & submit abstracts: www.oncodeinstitute.nl/internationa...
Join us for two days of discussions on blastoids, gastruloids, pluripotency, gametogenesis, implantation, and the ethical dimensions of embryo models.
The International Dutch Embryo Model Meeting 2026 | Oncode Institute
oncodeinstitute.nl
🧬 We are excited to announce the INTERNATIONAL DUTCH EMBRYO MODEL MEETING 2026 — Engineering the Origins of Life 📅 7–8 May 2026 📍 Utrecht, The Netherlands Register & submit abstracts: www.oncodeinstitute.nl/internationa...
Register now for the second Hubrecht Symposium, themed Molecular Machines in Development in Utrecht on March 26, 2026. Visit hubrecht.eu/hubrecht-symposium-2026/ for registration and abstract submission. Abstract submission deadline: February 1, 2026.
Reminder: Tomorrow is VGZT day! 🚀 Don’t miss great talks from 👉 Luca Braccioli (@bracciolilab.bsky.social) 👉 Komal Makwana (on X: @Komal_Makwana4)
Virtual Gastrulation Zoom Talks@vgzt2021.bsky.social · 8mo agoJoin us next week for another round of inspiring VGZT talks! 🤩 🗓️ Thursday, December 4th ⏰ 9:30 PST / 12:30 EST / 17:30 UTC / 17:30 GMT / 18:30 CET Our speakers are 👉 Luca Braccioli (@bracciolilab.bsky.social) 👉 Komal Makwana (on X: @Komal_Makwana4) See you next week 👋
Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀 Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function now revised and journal accepted at www.science.org/doi/10.1126/... 🧵👇
🧩 What breaks when you remove DNA loop extrusion? Gastruloids show it: not lineage decisions… but morphogenesis. That’s our contribution to www.science.org/doi/10.1126/... Huge thanks to the amazing @karissalhansen.bsky.social + @elphegenoralab.bsky.social for leading this fantastic work 🙌
Elphege Nora Lab at UCSF@elphegenoralab.bsky.social · 8mo ago(5) But can embryonic cell types properly emerge even when loop extrusion is prevented? Unambiguous gastruloid experiments by @bracciolilab.bsky.social in @dewitlab.bsky.social : YES, they clearly can. Even though morphogenesis, which is normally very stereotypical, is pretty screwed up.
IT'S HAPPENING! 💥 I'm psyched to launch the collaboration between @qedscience.bsky.social & @openrxiv.bsky.social @biorxivpreprint.bsky.social! Preprint + q.e.d = your science is out there, and anyone can appreciate it. Let's care about making discoveries, and not on “getting published” (1/3) 👇
Daniel Kahneman's imaginary sabbatical in a fly lab continues...this time: The art of letting go. Have you felt the pain of stopping while standardising a new method? Or letting go of a project? When to stop, when to persist? Have a read @the-node.bsky.social thenode.biologists.com/the-kahneman...
The Kahneman Chronicles: Lessons from a Fly Lab - the Node
The Kahneman Chronicles #2: Loss Aversion and the Art of Quitting Daniel Kahneman (1934-2024) was a legendary psychologist who revolutionized our
thenode.biologists.com
Ascidians (Ciona intestinalis)🪸Our distant chordate cousins! 🌊 Simple sea squirts that reveal how vertebrate body plans evolved 🧬 A key model for notochord formation, neural induction, and cell lineage mapping 📸 Video by MBL Embryology 2019 #ModelMonday #DevBio #EvoDevo
Three short talks now at #GenBio25. @bracciolilab.bsky.social discusses the ability of cells to contribute to different lineages in a gastruloid model. Luca recently published an ‘In preprints’ article in @dev-journal.bsky.social: doi.org/10.1242/dev....
Very proud of our paper on "scrambling-by-hopping" LADs, which was just published: www.nature.com/articles/s41.... Congrats to Lise Dauban and the rest of the team – this was a real tour-de-force!
(1/14) I’m happy and proud to introduce: SpinePy – a framework to detect the "spine" of gastruloids and measure biological and physical signals in a local dynamic 3D coordinate system. www.biorxiv.org/content/10.1...
Ever wondered how to get a gastruloid to grow a head? The Bulut-Karslioğlu lab figured out that by growing different stem cell aggregates in high and low oxygen and later assembling them, you can get gastruloids with a fully formed neural tube. Check out our "In preprints": doi.org/10.1242/dev....
In preprints: gastruloids get (a)head
A major breakthrough in the field of mammalian embryology is the development of stem-cell based embryo models. Derived from pluripotent stem cells, such as embryonic stem cells or induced pluripotent ...
doi.org