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! 🧪🔬

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

ikea-style logo of splongget

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...

Fragile Nucleosome Fall Seminars: September 10 Grace Bower, Kvon Lab @ UC Irvine, USA Jennifer Phillips-Cremins, UPenn, USA September 24 Ali Wilkening, Sanulli Lab @ Stanford, USA Juanma Schvartzman, Columbia University, USA October 8 Sanim Rahman, Greenberg Lab @ UPenn, USA Alex Federation, Talus Bio, USA October 22 Alice Laigle, Croll Lab @ University of Neuchâtel, Switzerland Seungsoo Kim, UC Irvine, USA November 5 Hannah Long, University of Edinburgh, UK Jeff Vierstra, Altius Institute, USA November 19 Ishtiaque Hossain, Pastor Lab @ McGill, Canada Sarah Teichmann, University of Cambridge, UK December 3 María Mariner Faulí, Rada Iglesias Lab @ IBBTEC, Spain Jonathan Henninger, Carnegie Mellon, USA December 17 Rebecca Berrens, Oxford University, UK Jean-Benoit Lalanne, University of Montreal, Canada

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...

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...

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)

Congrats Pedro, glad to see you write about ageing & cancer again!

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 ...

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

www.nature.com/articles/s41...

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

Huge thanks to the co-first author @mathias-boulanger.bsky.social. Also thanks to Rene, Marc Jan, Karine, Kim, and especially @arnaudkr.bsky.social @embl.org @dfg.de.
Finally, I'll be presenting the story at the @cshlnews.bsky.social #cshlmoet next week! Please stop by if you are around!

What about transcription? We could link changes in enhancer activity to the consequences at a co-accessible promoter!

Can we prove coordination in their activity? Using regulatory changes between cell types, we show that co-accessible enhancers co-vary, demonstrating the dependency between them.

What regulates co-accessibility? We found that certain TF motifs are enriched in co-accessible CREs (vs independent ones). These include several usual suspects such as Su(Hw) and Trl (GAF).

Co-accessible pairs aren't always the closest neighbours! For each pair of CREs, we tested if they are co-accessible more often than expected by chance, creating a co-accessibility map across CREs.

Here is an example locus: we can resolve chromatin accessibility for a promoter and 8 enhancers located up to 20kb away! — all on the same DNA molecules.

We used Single-molecule footprinting (SMF) to methylate accessible regions, combined with Nanopore long-read sequencing. At each locus, we collected thousands of molecules — enough to quantify coordinated accessibility across distant cis-regulatory elements (CREs) up to 30 kbs apart!

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)

Range extender mediates long-distance enhancer activity - Nature The REX element is associated with long-range enhancer–promoter interactions.

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/

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...

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...

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...

🚨 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.