Daniel Ibrahim
@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.
Pinned
Daniel Ibrahim
@danielibrahim.bsky.social
· Oct 16
Enhancer-promoter compatibility is mediated by the promoter-proximal region
Gene promoters induce transcription in response to distal enhancers. How enhancers specifically activate their target promoter while bypassing other promoters remains unclear. Here, we find that the p...
www.biorxiv.org
What is a promoter? And how does it work?
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
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*
if the user would in the end just do it themselves….*sigh*
November 25, 2025 at 7:28 AM
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*
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.
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.
Students applying for grad school, or reaching out to professors. I have an important piece of advice for you: STOP DOING THIS 👇 (a thread) #STEM #PhD #gradschool #academictips
November 24, 2025 at 10:23 AM
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.
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.
Reposted by Daniel Ibrahim
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!
We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below:
(TLDR; low-affinity motifs matter as pioneers!)
(TLDR; low-affinity motifs matter as pioneers!)
Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs
Low-affinity transcription factor (TF) motifs are an important element of the cis-regulatory code, yet they are notoriously difficult to map and mechanistically incompletely understood, limiting our a...
www.biorxiv.org
November 19, 2025 at 11:38 PM
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!
Reposted by Daniel Ibrahim
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...
👉 www.molgen.mpg.de/5091778/Murp...
November 18, 2025 at 4:05 PM
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...
👉 www.molgen.mpg.de/5091778/Murp...
Reposted by Daniel Ibrahim
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).
shorturl.at
November 18, 2025 at 12:48 PM
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).
Reposted by Daniel Ibrahim
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
November 18, 2025 at 9:44 AM
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
Reposted by Daniel Ibrahim
🚨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
Passionate about gene regulation, chromatin, and developmental biology? Just contact @radaiglesiaslab.bsky.social at @ibbtec.bsky.social 🧬✨
#PhD #3DGenome
November 15, 2025 at 9:53 AM
🚨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
Passionate about gene regulation, chromatin, and developmental biology? Just contact @radaiglesiaslab.bsky.social at @ibbtec.bsky.social 🧬✨
#PhD #3DGenome
Reposted by Daniel Ibrahim
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 👇
We now offer a 4-years PhD contract to investigate whether the dirsuption of this regulatory mechanism can lead to congenital defects. More details 👇
November 6, 2025 at 6:37 PM
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 👇
We now offer a 4-years PhD contract to investigate whether the dirsuption of this regulatory mechanism can lead to congenital defects. More details 👇
Reposted by Daniel Ibrahim
🚀 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/...
Lead cutting-edge research at the interface of biology, engineering, and medicine in Berlin.
👉 Apply now: www.mdc-berlin.de/career/jobs/...
October 9, 2025 at 11:00 AM
🚀 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/...
Lead cutting-edge research at the interface of biology, engineering, and medicine in Berlin.
👉 Apply now: www.mdc-berlin.de/career/jobs/...
Reposted by Daniel Ibrahim
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....
October 27, 2025 at 11:49 AM
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....
Thanks! 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 😉
And pairing the same enhancer with different core promoters in vivo - could be another story 😉
October 26, 2025 at 7:55 AM
Thanks! 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 😉
And pairing the same enhancer with different core promoters in vivo - could be another story 😉
Reposted by Daniel Ibrahim
What happens when you change the promoter of my favorite gene? Sox9?
What is a promoter? And how does it work?
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
Enhancer-promoter compatibility is mediated by the promoter-proximal region
Gene promoters induce transcription in response to distal enhancers. How enhancers specifically activate their target promoter while bypassing other promoters remains unclear. Here, we find that the p...
www.biorxiv.org
October 25, 2025 at 8:04 AM
What happens when you change the promoter of my favorite gene? Sox9?
Reposted by Daniel Ibrahim
My 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 :)
October 21, 2025 at 9:43 AM
My 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 :)
Reposted by Daniel Ibrahim
Our 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.
Here, we show that the unique regulatory landscape of ecDNA enables an ancient LINE to resurrect and act as an enhancer of Myc. This was so fun with @katerinakraft.bsky.social and @mattjones.bsky.social and others. www.nature.com/articles/s41...
Enhancer activation from transposable elements in extrachromosomal DNA - Nature Cell Biology
Kraft, Murphy, Jones et al. identify extrachromosomal DNA (ecDNA)-interacting elements (EIEs) enriched for transposable elements within ecDNA in colorectal cancer cells. They show that EIE 14 integrat...
www.nature.com
October 21, 2025 at 1:34 PM
Our 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.
Reposted by Daniel Ibrahim
📢 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
👩🏾⚕️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
October 15, 2025 at 3:00 PM
📢 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
👩🏾⚕️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
Reposted by Daniel Ibrahim
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! 🧪🔬
Huge thanks to @danielibrahim.bsky.social, @arnaudkr.bsky.social & @stemundi.bsky.social and fantastic people in their labs — what a journey! 🧪🔬
What is a promoter? And how does it work?
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
Enhancer-promoter compatibility is mediated by the promoter-proximal region
Gene promoters induce transcription in response to distal enhancers. How enhancers specifically activate their target promoter while bypassing other promoters remains unclear. Here, we find that the p...
www.biorxiv.org
October 17, 2025 at 5:50 AM
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! 🧪🔬
Huge thanks to @danielibrahim.bsky.social, @arnaudkr.bsky.social & @stemundi.bsky.social and fantastic people in their labs — what a journey! 🧪🔬
Reposted by Daniel Ibrahim
super cool to see this out! looking forward to now read the details! Congratulations, Yad and @mmasoura.bsky.social
Ever wondered what drives enhancer-promoter specificity? Why would an enhancer activate one gene rather than another neighboring one?
Check our latest preprint, led by @mmasoura.bsky.social, to find out!
www.biorxiv.org/content/10.1...
Check our latest preprint, led by @mmasoura.bsky.social, to find out!
www.biorxiv.org/content/10.1...
Promoter-proximal gatekeepers restrict pleiotropic enhancer inputs to achieve tissue specificity
Developmental enhancers are central regulatory elements that can activate multiple genes, yet how they selectively regulate one gene over its neighbours remains unclear. Using the Drosophila twist E3 ...
www.biorxiv.org
October 16, 2025 at 6:31 PM
super cool to see this out! looking forward to now read the details! Congratulations, Yad and @mmasoura.bsky.social
Reposted by Daniel Ibrahim
What 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!!!!🥂🥂
region here 👇
Congratulations @blanka-majchrzycka.bsky.social @danielibrahim.bsky.social on this beautiful work!!!!🥂🥂
What is a promoter? And how does it work?
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
Enhancer-promoter compatibility is mediated by the promoter-proximal region
Gene promoters induce transcription in response to distal enhancers. How enhancers specifically activate their target promoter while bypassing other promoters remains unclear. Here, we find that the p...
www.biorxiv.org
October 16, 2025 at 3:23 PM
What 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!!!!🥂🥂
region here 👇
Congratulations @blanka-majchrzycka.bsky.social @danielibrahim.bsky.social on this beautiful work!!!!🥂🥂
Reposted by Daniel Ibrahim
Yay! Congratulations @blanka-majchrzycka.bsky.social and @danielibrahim.bsky.social ! Good to see this beautiful dissection out !
What is a promoter? And how does it work?
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
Enhancer-promoter compatibility is mediated by the promoter-proximal region
Gene promoters induce transcription in response to distal enhancers. How enhancers specifically activate their target promoter while bypassing other promoters remains unclear. Here, we find that the p...
www.biorxiv.org
October 16, 2025 at 4:34 PM
Yay! Congratulations @blanka-majchrzycka.bsky.social and @danielibrahim.bsky.social ! Good to see this beautiful dissection out !
Reposted by Daniel Ibrahim
A 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!
What is a promoter? And how does it work?
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
Enhancer-promoter compatibility is mediated by the promoter-proximal region
Gene promoters induce transcription in response to distal enhancers. How enhancers specifically activate their target promoter while bypassing other promoters remains unclear. Here, we find that the p...
www.biorxiv.org
October 16, 2025 at 4:05 PM
A 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!
This 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
October 16, 2025 at 3:06 PM
This 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
@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!!!
She'll be looking for a #postdoc position very soon. I'd ask her if I were you!!!
October 16, 2025 at 3:06 PM
@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!!!
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...
www.biorxiv.org/content/10.1...
Promoter-proximal gatekeepers restrict pleiotropic enhancer inputs to achieve tissue specificity
Developmental enhancers are central regulatory elements that can activate multiple genes, yet how they selectively regulate one gene over its neighbours remains unclear. Using the Drosophila twist E3 ...
www.biorxiv.org
October 16, 2025 at 3:06 PM
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...
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!
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!
October 16, 2025 at 3:06 PM
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!
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
So we tested only core promoters in our assay
FACT3: No - core promoters alone are not activated by Sox9 long-range enhancers
October 16, 2025 at 3:06 PM
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
So we tested only core promoters in our assay
FACT3: No - core promoters alone are not activated by Sox9 long-range enhancers