Establishment of loop domains during medaka development. (A) An example of establishment of large loop and small loop, and contact domain N10 statistics over stages are shown. Normalized observed Hi-C contacts are shown as a heat map at 10-kb (upper portion) and 5-kb (middle portion) resolution. Higher N10 values mean that larger contact domains cover longer intervals of genome (see Methods for detail). (B) Loops are established during gastrulation. Representative Hi-C contact map (normalized observed Hi-C contacts at 10-kb resolution) of a loop domain is shown in upper portion. Normalized APA plots in middle portion show that loops become evident during gastrulation. APA scores (loop signal enrichment compared to lower-right signal of APA plot) across the developmental stages are shown in lower portion. Values greater than 1 indicate the presence of loops. Hi-C contacts around loops identified in fibroblast cells were aggregated for each stage.
