Comparative epigenomics of NADs and inter-NAD regions (iNADs) reveals specific heterochromatic features of NADs.

(A) Distribution of different chromatin states in NADs and iNADs. Bar graphs show total and relative amounts of ChromHMM states in NADs and iNADs on the left and right, respectively. The chromatin states and their colour code correspond to the Primary Core Marks segmentation 15-state ChromHMM model of the Roadmap Epigenomics Project [41]. Chromatin states specifically enriched in NADs are indicated. Red: Active Transcriptional Start Site (TSS), OrangeRed: Flanking Active TSS, LimeGreen: Transcription at gene ends, Green: Strong transcription, DarkGreen: Weak transcription, GreenYellow: Genic enhancers (Enh), Yellow: Enh, MediumAquamarine: ZNF genes & repeats, PaleTurquoise: Heterochromatin, IndianRed: Bivalent/Poised TSS, DarkSalmon: Flanking Bivalent TSS/Enh, DarkKhaki: Bivalent Enh, Silver: Repressed PolyComb, Gainsboro: Weak Repressed PolyComb, White: Quiescent/Low. (B) Boxplot of DNaseI accessibility in NADs (n = 1646) and iNADs (n = 1669). The average accessibility per base and segment were calculated from GSM468792. (C) Boxplot of RNA-seq read densities. For each NAD (n = 1646) and iNAD (n = 1669) the average number of reads per base in GSM438363 were calculated. (D) Replication timing profiles around NAD borders. Average percentage-normalized signals of different replication domains within a distance of 500 kb from aligned 5’ and 3’ NAD borders are shown. Repli-Seq signals from five different time points of the cell cycle (S1-S4 and G2) were taken from Pope et al.,[42] and averaged over 1 kb windows. Only NADs with a width >500 kb were considered (n = 652). The arrows drawn at the bottom show away from the aligned NAD/iNAD borders.