Characteristics of domain types. (A) Gene density in IMR90. (B) Gene expression relative to average over 33 cell types, averaged over eight annotations (t-test 95% confidence interval error bars). (C) Fraction of active genes also active in more than 15 other cell types, averaged over eight annotations (binomial test 95% confidence interval error bars). All gene expression data are from CAGE (Methods). (D–F) Histograms of (D) GC content, (E) conservation (PhyloP score) (Siepel et al. 2005), and (F) Hi-C compartment eigenvalues in IMR90. Positive PhyloP scores indicate evolutionary conservation; positive scores, accelerated evolution; and scores near zero, neutral evolution. Hi-C compartment values are computed according to the method of Lieberman-Aiden et al. (2009) (Methods). Positive values indicate open compartment; negative values indicate closed compartment. (G) Enrichment of each domain type with respect to IMR90 replication time (early vs. late) and replication time dynamics across cell types (constitutive vs. switching) (V Dileep, F Ay, J Sima, WS Noble, and DM Gilbert, unpubl.) (Methods). (H) CTCF motif density for each domain type. Dashed line indicates genome-wide average. (I) Fraction of CTCF motifs bound (overlapping a CTCF peak) in IMR90 (binomial test 95% confidence interval error bars). Dashed line indicates average over all motifs.
