Just brilliat work by Kasit and colleagues in @arnaudkr.bsky.social's group @embl.org. This is leveraging the "everyday" length of ONT (20KB) plus exogenous modification to sort out co-occupancy between enhancers and promoters (and inter-enhancer).
This is not a HiC map! Ever wondered if multiple enhancers get activated simultaneously? We measured chromatin accessibility on thousands of molecules by nanopore to create genome-wide co-accessibility maps. Proud of @mathias-boulanger.bsky.social @kasitc.bsky.social Biology in the thread👇
Huge thanks to the co-first author @kasitc.bsky.social Also thanks to Rene, Marc Jan, Karine, Kim, and especially @arnaudkr.bsky.social @embl.org @dfg.de.
Finally, Kasit will 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 activity at enhancer 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 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... @embl.org
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 CREs up to 30 kbs apart!
