Figure 5

Structurally variable regions indicate cell-type-specific biology. Regions occupying the active A nuclear compartment in one cell type, but the repressed B compartment in the other two, were selected and ranked by the number of predicted active enhancers (Figure 4). (A) The region chr5:158–159 Mb, which occupies the open A compartment in GM12878 cells, is shown as an example (top five regions for each cell type are shown in Additional file 1: Figure S10). Displayed tracks are: known genes (UCSC), compartment eigenvectors, chromHMM/Segway combined chromatin state predictions, open chromatin FAIRE peaks, and H3K27ac signal. (B) Structurally variable regions show a greater than expected proportion of contacts with other active A compartments, in the cell type in which they are active relative to those same regions in the other two cell types. Box plot notches represent 95 % confidence intervals of the median. Each variable region is also shown individually in Additional file 1: Figure S11. TSS, transcription start site.