@danielibrahim.bsky.social
Group Leader @ BIH Berlin and MPI Molecular Genetics. I play around with DNA because I‘d like to know how the genome functions.
After a huge amount of work w/ @alex-stark.bsky.social's group, a new version of our Ledidi preprint is now out!
In an era of AI-designed proteins, the next leap will be controlling when, where, and how much of these proteins are expressed in living cells.
www.biorxiv.org/content/10.1...
Together, these approaches create a uniquely powerful platform for exploring how transcription factors interpret the genome.”
📰 Read the full story: www.med.uio.no/ncmbm/englis...
Congrats to the entire JASPAR community for driving this resource forward to shape the future of regulatory genomics!
🔬 Hot #PhD topic: Single-molecule fluorescence and super-resolution microscopy! Use quantitative nanoscale imaging to map nuclear organization. Apply by Jan 7 to join Johannes Stein’s Lab @jmstein.bsky.social & #IMPRS-BAC #gradschool!
👉 www.molgen.mpg.de/5098010/stei...
i’m intrigued - sounds like a niche arms race that I want to follow.
if the user would in the end just do it themselves….*sigh*
I 100% subscribe to this post!
I really do not want to read a paraphrased version of whatever is written on my website. Just write me a nice email if you're interested.
Very proud of our new paper! Great job @mweilert.bsky.social, our experimentalists and modeling collaborator Rosa Martinez-Corral. It was fun to see the story grow and get feedback from various experts. Thank you all!
19.11.2025 23:38 — 👍 22 🔁 7 💬 1 📌 0
IMPRS-BAC #gradschool: Our new groupleader @sedonamurphy.bsky.social has an open PhD project in her lab. Topic: Spatial feedback between epigenetic regulation and chromatin regulation. Apply by Jan 7, 2026!
👉 www.molgen.mpg.de/5091778/Murp...
1. We start a major consortium programme funded by the sLoLa of BBSRC (shorturl.at/aUbnt) to decipher the semantic rules of enhancer arrangements driving regulator genes of development (shorturl.at/6qcjW).
18.11.2025 12:48 — 👍 25 🔁 7 💬 2 📌 4
This mural has gone up in Kingston, ostensibly for Christmas but AI has ensured it's actually to celebrate the return of our dark lord Cthulhu
18.11.2025 09:43 — 👍 3882 🔁 1403 💬 234 📌 470
🚨Reposts appreciated‼️If I had read this PhD offer five years ago, I wouldn’t have hesitated for a second to apply 😉
Passionate about gene regulation, chromatin, and developmental biology? Just contact @radaiglesiaslab.bsky.social at @ibbtec.bsky.social 🧬✨
#PhD #3DGenome
We recently reported that promoter competition can contribute to the robust insulation of gene regulatory domains (www.nature.com/articles/s41...).
We now offer a 4-years PhD contract to investigate whether the dirsuption of this regulatory mechanism can lead to congenital defects. More details 👇
Job announcement: The image has a solid dark blue background with a clean, minimal layout. In the top left corner, the word “JOBS” appears in all-capital red sans-serif text. Below, large white sans-serif text spans several lines and reads: “Three Independent Group Leaders in Bioengineering Approaches to Human Health m/f/d.” Near the bottom left, smaller white sans-serif text reads: “Apply by November 16, 2025,” followed by “Max Delbrück Center (Berlin-Buch)” in lighter gray. In the bottom right corner is the Max Delbrück Center logo in white and blue.
🚀 WE ARE HIRING 3️⃣ Independent Group Leaders for #mdcBerlin's new cutting-edge Bioengineering Cluster within our Biomedical Engineering Program.
Lead cutting-edge research at the interface of biology, engineering, and medicine in Berlin.
👉 Apply now: www.mdc-berlin.de/career/jobs/...
Happy to share our latest publication, in which we show that the arrangement of nucleosomes around CTCF sites contributes to higher-order organisation of chromatin into TADs: www.embopress.org/doi/full/10....
27.10.2025 11:49 — 👍 71 🔁 31 💬 0 📌 2Thanks! Obvsly, I have many thoughts on that. I think enhancer-reporters tell you a lot about what expr. the enhancer might be driving, but that could be quite different from what it does endogenously.
And pairing the same enhancer with different core promoters in vivo - could be another story 😉
What happens when you change the promoter of my favorite gene? Sox9?
25.10.2025 08:04 — 👍 3 🔁 2 💬 1 📌 0My new lab at the @molgen.mpg.de will be following up on some of the nuclear organization aspects of ecDNA so please do reach out if this is of interest :)
21.10.2025 09:43 — 👍 27 🔁 9 💬 1 📌 0Our publication is out today!Big Thanks go to my amazing collaborators: @sedonamurphy.bsky.social for her imaging brilliance and @mattjones.bsky.social for his computational support.They both saw the potential in this project and helped me to explore what turned out to be an exciting discovery.
21.10.2025 13:34 — 👍 18 🔁 6 💬 0 📌 0
📢 We are hiring!
👩🏾⚕️Research technician/Lab manager
📍 @cabd-upo-csic.bsky.social , Sevilla, Spain
🧬 Gene regulation in animal development & evolution
Check the details 👇 & join us!
drive.google.com/file/d/1cZJi...
#ResearchTechnician #Zebrafish #GeneRegulation #DevelopmentalBiology
Out now! 🎉 Check the thread & preprint to see why we think E–P specificity is real in mammals — and, well, a few other interesting things popped up too 👀
Huge thanks to @danielibrahim.bsky.social, @arnaudkr.bsky.social & @stemundi.bsky.social and fantastic people in their labs — what a journey! 🧪🔬
super cool to see this out! looking forward to now read the details! Congratulations, Yad and @mmasoura.bsky.social
16.10.2025 18:31 — 👍 11 🔁 2 💬 1 📌 0What mediates enhancer-promoter compatibility? Get some answers & learn about the important of the promoter-proximal
region here 👇
Congratulations @blanka-majchrzycka.bsky.social @danielibrahim.bsky.social on this beautiful work!!!!🥂🥂
Yay! Congratulations @blanka-majchrzycka.bsky.social and @danielibrahim.bsky.social ! Good to see this beautiful dissection out !
16.10.2025 16:34 — 👍 6 🔁 2 💬 0 📌 0A genetic engineering tour de force by @blanka-majchrzycka.bsky.social. Systematic dissection of promoter function in relevant genomic context! Spoiler, promoter matters! Happy we could help on this!
16.10.2025 16:05 — 👍 12 🔁 3 💬 0 📌 0This project started when I was a postdoc in @stemundi.bsky.social lab and supported all the way. Thanks also to @molgen.mpg.de and @bihatcharite.bsky.social for an inspiring work environment
16.10.2025 15:06 — 👍 3 🔁 0 💬 0 📌 0@blanka-majchrzycka.bsky.social did an absolutely amazing job!! created everything from scratch, set up #RMCE with the fantastic help from @arnaudkr.bsky.social and saw this thing through.
She'll be looking for a #postdoc position very soon. I'd ask her if I were you!!!
you must check out @yghavi.bsky.social and @mmasoura.bsky.social's story, who found a similar mechanism in Drosophila. it's so cool if two works align!!
www.biorxiv.org/content/10.1...
even more results in the #preprint!
Our interpretation (TL;DR)
We think that the promoter-proximal cis-regulatory element acts like a #facilitator that helps to filter and relay long-range enhancer activity to the core promoter!
More questions! If Sox9 has so many long-range enhancers - Can core promoters alone be activated without #promoter-proximal-region-proximalenhancer-cis-regulatory-element?
So we tested only core promoters in our assay
FACT3: No - core promoters alone are not activated by Sox9 long-range enhancers
We then wondered: Can any other promoter be activated?
So we generated a library of 18 promoters from various genes and measured if they're activated in NPCs.
FACT2: Full promoters show differential activity in NPCs. So there is enhancer-promoter specificity in mammals!!!
Blanka developed Promoter-RMCE, an elaborate method to exchange the Sox9 FULL promoter with libraries of other promoters in mESCs. Sox9 is OFF in mESCs but ON in NPCs. So... Are truncated Sox9 promoters activated by long-range enhancers?
FACT1: Sox9 needs its proximal region to be activated in NPCs
