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Fig. 4 | Genome Biology

Fig. 4

From: OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries

Fig. 4

Hub-boundaries are highly active in gene regulation. a An illustration of the TAD boundary levels. The boundary levels are defined as the maximum number of TADs that use a boundary on either its left or right side. The yellow, purple, and red dots refer to the boundaries of levels 1, 2, and 3, respectively. b Enrichment of epigenetic states at different levels of TAD boundaries. Hub-boundaries (i.e., boundaries with level = 5) are enriched in active epigenetic states (marked in orange), especially the states associated with Tss (e.g., TssF, Tss, and TssCtcf). c Distribution of gene expression levels for genes whose transcription start sites overlap with TAD boundaries. Genes are classified by the level of TAD boundaries. d Illustration of hierarchical TAD and asymmetric loop extrusion. The red boundary denotes the “anchor” site that starts the loop extrusion in the asymmetric loop extrusion model. Boundaries in other colors are the stopping sites of the loop extrusion. The hierarchical TADs are formed by multiple stops of the loop extrusion which share the same start site. e TFs enriched (fold change > 2) at hub-boundaries in GM12878 and K562 cell lines. The fold change of ChIP-seq TF peaks at hub-boundaries (level = 5) against level 1 boundaries is shown

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