Lightnews — Scholar-powered news

Reposted by Mathias Boulanger

Ewan Birney @ewanbirney.bsky.social · Aug 18

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).

kasitc.bsky.social @kasitc.bsky.social · Aug 18

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...

1 2 20

Reposted by Mathias Boulanger

Arnaud Krebs @arnaudkr.bsky.social · Aug 18

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👇

10 34 110

Mathias Boulanger @mathias-boulanger.bsky.social · Aug 18

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!

1 5

Mathias Boulanger @mathias-boulanger.bsky.social · Aug 18

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

1

Mathias Boulanger @mathias-boulanger.bsky.social · Aug 18

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.

1

Mathias Boulanger @mathias-boulanger.bsky.social · Aug 18

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).

1

Mathias Boulanger @mathias-boulanger.bsky.social · Aug 18

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.

1

Mathias Boulanger @mathias-boulanger.bsky.social · Aug 18

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.

1

Mathias Boulanger @mathias-boulanger.bsky.social · Aug 18

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!

1 1

Mathias Boulanger @mathias-boulanger.bsky.social · Aug 18

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

2 4 19

Mathias Boulanger @mathias-boulanger.bsky.social · Aug 18

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.

Mathias Boulanger @mathias-boulanger.bsky.social · Aug 18

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!

1