Why 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 🧪 🧵👇

ChromSMF preprint is out!🚀 tinyurl.com/ChromSMF We often piece together chromatin regulation layer by layer from separate assays. But this can be limiting! In @arnaudkr.bsky.social's lab, we developed a method to directly study multiple layers on the same DNA molecule! 🧬 What does this unlock? ⬇️

We preprinted an exiting new story, using the hopping technology to study gene regulation. This project was led by Mathias with some contributions from me. For anyone who read the original Sox2 hopping story and wondered 'but what about CTCF?', read this preprint!

@mathiaseder.bsky.social · 5mo ago

🔥 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...

✨Exciting news: the main story of my PhD is out in Science! Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation. 📖 Read the full story here: www.science.org/doi/10.1126/...

Functional maps of a genomic locus reveal confinement of an enhancer by its target gene

Genes are often activated by enhancers located at large genomic distances, and the importance of this positioning is poorly understood. By relocating promoter-reporter constructs into thousands of alt...

science.org

Have you ever wondered how the exact location of a gene affects it's activity? The main story of my PhD deals with exactly that question, and is now published in Science! ✨ www.science.org/doi/10.1126/... My amazing co-author and friend @mathiaseder.bsky.social summarized the highlights for you

Functional maps of a genomic locus reveal confinement of an enhancer by its target gene

Genes are often activated by enhancers located at large genomic distances, and the importance of this positioning is poorly understood. By relocating promoter-reporter constructs into thousands of alt...

science.org

@mathiaseder.bsky.social · 11mo ago

1/ Using a transposon-based approach, we systematically studied the positional relationship between the mouse Sox2 gene and its enhancer (SCR). In a single experiment, we can map >2000 unique genomic positions.