MICC-seq. Homo sapiens

Our lab has developed a technique called SCA-seq (Spatial Chromatin Accessibility sequencing), which combines pore-C and methyltransferase labeling to observe the interaction and accessibility of high-order genome fragments. We observed that open chromatin formed stripes, which could indicate loop extrusion. We hypothesize that the loop extrusion process might involve open-open interaction with CTCF sites,considering that CTCF usually binds to open chromatin and is a typical marker for loop extrusion due to its barrier function for the direction of loop extrusion. However, we have encountered a challenge where reads from nanopore are few and closed chromatin seriously affects the observation of open chromatin. To overcome this, we have decided to design an NGS-based open chromatin approach MICC-seq, with a specific focus on open-open interactions in the genome, to more clearly observe the stripes.