Sign in

Schubeler Lab

@schubelerlab.bsky.social
440 followers 50 following 24 posts
PostsRepliesMedia
Schubeler Lab @schubelerlab.bsky.social · 07/05/2026
Congrats Angelika. Well deserved!
140
Reposted by Schubeler Lab
Grand Lab @grandlab.bsky.social · 07/05/2026
Excited to share our first story led by @martinacapriati.bsky.social! How do cells control the expression of viability genes? We find that single transcription factors can drive both chromatin opening and gene activation from densely co-bound CpG island promoters, including at essential genes
25127
Schubeler Lab @schubelerlab.bsky.social · 07/05/2026
Also take a look at the great and complementary work from Ralph’ Grand's lab @grandlab.bsky.social identifying the transcriptional dominance of individual TFs for regulating essential genes by CGIs using a sophisticated combinatorial degradation and recovery approach. 9/9
biorxiv.org
040
Schubeler Lab @schubelerlab.bsky.social · 07/05/2026
Much more in the preprint. doi.org/10.64898/202... Thanks to all authors (Fumiya, Murat, Sevi, Christiane, Leslie, Sébastien, Lukas) Schübeler lab and FMI genomics facility @FMIscience, and our funders. Looking forward to feedback. 8/9
doi.org
120
Schubeler Lab @schubelerlab.bsky.social · 07/05/2026
Even distal enhancers follow this logic. Remarkably, placing a coding sequence next to an enhancer TSS turns it into a functional promoter. 💡 This suggests a “minimal promoter” may be as simple as binding site for a chromatin-opening TF. 7/9
150
Schubeler Lab @schubelerlab.bsky.social · 07/05/2026
What about TATA-box containing promoters? Same principle applies. Chromatin-opening TFs expose the TATA box, enabling focused initiation. 6/9
120
Schubeler Lab @schubelerlab.bsky.social · 07/05/2026
We tested this directly using synthetic promoters at a defined genomic site. Result: 👉 The most downstream chromatin-opening TF sets the TSS position. A simple, modular rule! 5/9
140
Schubeler Lab @schubelerlab.bsky.social · 07/05/2026
We mapped transcriptional start sites (TSS) using CAGE revealing that TF removal shifts the TSS to an adjacent secondary TF position. ➡️ The TF closest to a TSS dominates where transcription starts and its output. 4/9
130
Schubeler Lab @schubelerlab.bsky.social · 07/05/2026
Profiling with ChIP-seq, ATAC-seq, and RNA-seq gave us our first surprise: Each TF triggered highly specific transcriptional changes. This motivated us to dig deeper into how CGI promoters are controlled. 3/9
120
Schubeler Lab @schubelerlab.bsky.social · 07/05/2026
Using deep learning, we identified a set of chromatin-opening TFs. To test their function, we generated degron cell lines for 12 TFs—allowing us to acutely deplete each one. 2/9
130
Schubeler Lab @schubelerlab.bsky.social · 07/05/2026
Excited to share our new study on CpG islands (CGIs) regulation by transcription factors (TFs)! CGIs drive most transcription initiation with unclear regulation. We find that chromatin-opening TFs are key players—following a surprisingly simple rule. 🧵 www.biorxiv.org/content/10.6... 1/9
biorxiv.org
18641
Schubeler Lab @schubelerlab.bsky.social · 18/09/2025
Congrats Francesca !
010
Reposted by Schubeler Lab
FMI science @fmiscience.bsky.social · 28/08/2025
Our Open Day for Novartis was a great success! 🎉 Many @novartis.bsky.social colleagues joined us today to explore our science, meet our researchers & enjoy food trucks. Huge thanks to all volunteers and everyone who stopped by — here’s to more connections and collaborations!
072
Schubeler Lab @schubelerlab.bsky.social · 27/08/2025
Iconic!
040
Reposted by Schubeler Lab
Alexandra Bendel @alexbendel.bsky.social · 25/08/2025
I am happy to finally share this preprint of my PhD project in @guillaumediss.bsky.social lab at the FMI in Basel. We used ddPCA to map the genetic architecture of the entire human bZIP interaction network. www.biorxiv.org/content/10.1... Thanks to all our co-authors for the great collaboration!
biorxiv.org
The genetic architecture of the human bZIP family
Generative biology holds the promise to transform our ability to design and understand living systems by creating novel proteins, pathways, and organisms with tailored functions that address challenge...
13213
Schubeler Lab @schubelerlab.bsky.social · 26/08/2025
We all look forward to the Batki lab at FMI !!!!
120
Schubeler Lab @schubelerlab.bsky.social · 12/08/2025
Using this definition leads to the observed continuum of chromatin sensitivities across TFs. Thanks to all authors and all the helpful input from lab members and members of the computational biology platform. Looking forward to feedback.
000
Schubeler Lab @schubelerlab.bsky.social · 12/08/2025
The framework quantifies chromatin sensitivity as the degree to which binding is determined by the motif sequence, i.e. the motif affinity, versus the flanking sequence around the motif, likely indicating the presence of additional motifs bound by other TFs.
100
Schubeler Lab @schubelerlab.bsky.social · 12/08/2025
To circumvent this problem, we developed a deep-learning-based framework which assesses chromatin sensitivity via an evaluation of predicted binding at a balanced set of in silico sequence constructs.
110
Schubeler Lab @schubelerlab.bsky.social · 12/08/2025
However, as we show, genomic motifs are biased in terms of their occurrence relative to chromatin features, making it difficult to quantitatively assess chromatin sensitivity from binding profiles at genomic motifs.
100
Schubeler Lab @schubelerlab.bsky.social · 12/08/2025
We started by characterizing TF binding at genomic motifs and found a large variety in binding behaviours, indicating both differential sensitivity to chromatin for different TFs and a general dependence of chromatin sensitivity on motif affinity.
100
Schubeler Lab @schubelerlab.bsky.social · 12/08/2025
Key finding is that chromatin sensitivity is not binary, but a continuum across TFs, clearly arguing against a purely hierarchical model involving chromatin-insensitive TFs (pioneers) that open the chromatin for other chromatin-sensitive TFs to bind.
120
Schubeler Lab @schubelerlab.bsky.social · 12/08/2025
Excited to share our latest preprint. www.biorxiv.org/content/10.1.... Lead by Lukas, we investigated multiple ways of assessing a TF's sensitivity to chromatin based on genome-wide binding profiles. The developed methods allowed us to quantify chromatin sensitivity across tested TFs.
biorxiv.org
A novel deep learning-based framework reveals a continuum of chromatin sensitivities across transcription factors
The genome-wide binding of many transcription factors (TFs) depends not only on the presence of their recognition motifs, but also on the surrounding chromatin context. This raises the question of how...
14312
Schubeler Lab @schubelerlab.bsky.social · 07/08/2025
Demonstrates how a combination of opportunistic binding and context-specific chromatin-opening underpin TF specificity, driving differentiation trajectories.
070
Schubeler Lab @schubelerlab.bsky.social · 07/08/2025
Excited to see this published with additional data following our preprint a while back. Cool combination (in our biased view) of controlled TF expression and machine learning to decode chromatin sensitivity. www.sciencedirect.com/science/arti....
211549
Schubeler Lab @schubelerlab.bsky.social · 16/12/2024
Great colleagues in a vibrant and supportive community. We are looking forward to your application !!!
020
Reposted by Schubeler Lab
FMI science @fmiscience.bsky.social · 10/12/2024
What a night! The FMI year-end party had it all: an inspiring speech from our director, a delicious dinner buffet, a hilarious meme contest, and our traditional cake showdown. Here's to a fantastic 2025 ahead! 🥂🎉
081
Schubeler Lab @schubelerlab.bsky.social · 04/12/2024
congrats Pia. Well deserved
110