Fig. 1. Inference and characterization of chromatin subcompartments using Calder.

a Main steps of Calder: Step 1) identifying compartment domains from whole-chromosome contacts (top left); Step 2) deriving sequence-independent hierarchy of compartment domains (right); Step 3) finding nested domains from short-range contacts (bottom left). b Maximum number of subcompartments among which significant differences between mean ChiP-seq intensities of the domains were found for different histone marks (rows) and cell lines (columns). c Enrichment of histone marks (rows) in each subcompartment (columns) of IMR90 cell line. Log₂ fold-changes between the median value within a compartment and the expected median value is color coded. Histone modification names are color coded based on the regulatory element they mark. d Enrichment of ChromHMM states (rows) in each subcompartment (columns) for GM12878. Ratios between the distribution of compartment labels for each ChromHMM state and their expected distribution is color coded and reported. e Representative examples of subcompartments inferred by Calder and SNIPER (colored tracks at the bottom) in two regions of Chr.1. of the GM12878 cell line. ChIP-seq tracks for H3K27me3 (blue), H3K4me3 (green), and H3K27ac (red) are shown in these regions. The bivalent/poised promoter (marked by both H3K4me3 and H3K27me3) of the ASAP3 gene is marked.