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...