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? ⬇️

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....

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! 🧪🔬

Daniel Ibrahim@danielibrahim.bsky.social · 10mo ago

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...

Really excited to share our latest work led by @mattiaubertini.bsky.social and @nesslfy.bsky.social: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication. www.biorxiv.org/content/10.1... A🧵👇

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.

1/ First preprint from @jdemeul.bsky.social lab 🥳! We present our new multi-modal single-cell long-read method SPLONGGET (Single-cell Profiling of LONG-read Genome, Epigenome, and Transcriptome)! www.biorxiv.org/content/10.1...

We're super excited to announce the entire lineup for the Fall season of Fragile Nucleosome Seminars, starting on Sept 10th at 1200 EDT / 1600 UTC with @gracebower.bsky.social and @creminslab.bsky.social! register here for the entire series: us06web.zoom.us/webinar/regi...

Excited / nervous to share the “magnum opus” of my postdoc in Andreas Wagner’s lab! "De-novo promoters emerge more readily from random DNA than from genomic DNA" This project is the accumulation of 4 years of work, and lays the foundation for my future group. In short, we… (1/4)

De-novo promoters emerge more readily from random DNA than from genomic DNA

Promoters are DNA sequences that help to initiate transcription. Point mutations can create de-novo promoters, which can consequently transcribe inactive genes or create novel transcripts. We know lit...

biorxiv.org

New paper @natrevcancer.nature.com on the evolutionary interplay between ageing and cancer 🚨 www.nature.com/articles/s41...

The evolution of cancer and ageing: a history of constraint - Nature Reviews Cancer

In this Perspective, de Magalhães explores the evolutionary relationship between cancer and ageing, proposing that the need to minimize cancer risk early in life may contribute to tissue degeneration ...

nature.com

Please RP. We are thrilled to announce that our lab’s first preprint is out! ”Whole-genome single-cell multimodal history tracing to reveal cell identity transition” We report HisTrac-seq, a multiomic single-cell molecular recording platform. www.biorxiv.org/content/10.1...

Activity of most genes is controlled by multiple enhancers, but is there activation coordinated? We leveraged Nanopore to identify a specific set of elements that are simultaneously accessible on the same DNA molecules and are coordinated in their activation www.biorxiv.org/content/10.1... @embl.org

Activity of most genes is controlled by multiple enhancers, but is there activation coordinated? We leveraged Nanopore to identify a specific set of elements that are simultaneously accessible on the same DNA molecules and are coordinated in their activation. www.biorxiv.org/content/10.1...

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....

🚨 New preprint from our labs (STOP lab @stoplab.bsky.social & Nojima lab @pol2rna.bsky.social @pyrolyn.bsky.social)! We've been digging into how chromatin remodeler SETD2 controls the start and end of transcription 👇 www.biorxiv.org/cgi/content/... (1/5)

Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/

Range extender mediates long-distance enhancer activity - Nature

The REX element is associated with long-range enhancer–promoter interactions.

nature.com

Join us next Wed, for three amazing ECR researchers_ @fueyoraquel.bsky.social, @kaiamattioli.bsky.social and Laura talk about their work in #FragileNucleosome seminar series! In case you haven't joined any of the previous 2025 sessions, here is registration link: us06web.zoom.us/webinar/regi...

How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭 Check out our paper - fresh off the press!!! We find widespread functional conservation of enhancers in absence of sequence homology Including: a bioinformatic tool to map sequence-diverged enhancers! rdcu.be/enVDN github.com/tobiaszehnde...

Conservation of regulatory elements with highly diverged sequences across large evolutionary distances

Nature Genetics - Combining functional genomic data from mouse and chicken with a synteny-based strategy identifies positionally conserved cis-regulatory elements in the absence of direct sequence...

rdcu.be

🚨 New preprint out! Do you think Single Molecule Footprinting and Fiber-seq are super cool but aren't sure how to unlock their full potential? HiddenFoot can help you: www.biorxiv.org/content/10.1...

Join us on Wednesday next week for two exciting talks on transcription regulation from @kasitc.bsky.social and @davidsuter.bsky.social! You can register at: us06web.zoom.us/webinar/regi...

5/2025 Issue ➡️ www.embopress.org/toc/17444292... tissue-specific huntingtin interactomes, gene product diversity evolution Cover: mammalian promoters characterised by low RNA pol II occupancy and high turnover @kasitc.bsky.social @molinalab.bsky.social @arnaudkr.bsky.social

New research by @kasitc.bsky.social @molinalab.bsky.social @arnaudkr.bsky.social reveals limited RNA polymerase II pausing at mouse promoters compared to flies ➡️ www.embopress.org/doi/full/10....

Pol II Pausing on LSD on the MSB cover! Credits to the amazing creative team @kasitc.bsky.social (right) and Roos (left)! Pleasure to work with this bunch of talented people, here at our Belgian retreat. Paper: doi.org/10.1038/s443...

Don't forget to checkout our annex pre-print bit.ly/3EkRqJh for a sense on our new 💻 tool FootprintCharter, for the unsupervised footprint quantification from single molecule data. Available on Bioconductor at bit.ly/3XLe8RC.

FootprintCharter: unsupervised detection and quantification of footprints in single molecule footprinting data

Single molecule footprinting profiles the heterogeneity of TF occupancy at cis-regulatory elements across cell populations at unprecedented resolution. The single molecule nature of the data in princi...

bit.ly

Valentina Baderna@valentinabaderna.bsky.social · last yr.

We developed FootprintCharter to classify molecules into accessible or nucleosome-occupied at TF motifs by unsupervisedly detecting TF and nucleosome footprints. FootprintCharter is distributed on Bioconductor at bit.ly/3XLe8RC. For more details, read our annex preprint at bit.ly/3EkRqJh. 3/11

Having a stressful day? Lay back, crack a beer open and read about how chromatin accessibility responds to perturbations of TF binding at the single molecule level bit.ly/3XQMFxN. I'm incredibly thankful to my PhD mentors @arnaudkr.bsky.social and Judith Zaugg for these super productive years!!

Cumulative TF binding and H3K27 Acetylation drive enhancer activation frequency

In eukaryotes, transcription factors (TFs) must continuously compete with nucleosomes to access their binding sites, leading to cell-to-cell variability in chromatin accessibility at regulatory region...

bit.ly

Valentina Baderna@valentinabaderna.bsky.social · last yr.

Happy to share the latest story from @arnaudkr.bsky.social's lab @embl.org! With @guidobarzaghi.bsky.social, we used Single Molecule Footprinting to quantify how often chromatin is accessible at enhancers after TF and chromatin environment changes! Check our preprint bit.ly/3XQMFxN + thread ⬇️ 1/11

Happy to share the latest story from @arnaudkr.bsky.social's lab @embl.org! With @guidobarzaghi.bsky.social, we used Single Molecule Footprinting to quantify how often chromatin is accessible at enhancers after TF and chromatin environment changes! Check our preprint bit.ly/3XQMFxN + thread ⬇️ 1/11

Excited to see this out! Using single-molecule footprinting, we showed that Pol II occupancy is lower at mouse than fly promoters. This low Pol II occupancy is explained by high Pol II turnover and low transcription initiation at mouse promoters.

Arnaud Krebs@arnaudkr.bsky.social · last yr.

The importance of moving away from bulk! Occupancy of Pol II at promoters is dramatically different between fly and mouse cells! When looking single molecule! Proud of the team! @kasitc.bsky.social @molinalab.bsky.social doi.org/10.1038/s443...

Terrifying 😭😭

The New York Times@nytimes.com · last yr.

This is the moment when a 30-story skyscraper under construction collapsed in Bangkok, when a 7.7-magnitude earthquake struck central Myanmar hundreds of miles away on Friday. Myanmar’s military government said that 144 people had been killed and 732 injured. Follow live updates. nyti.ms/3QSKjuw