Figure 3.

Two distinct classes of anchors establish the pro-B cell interactome. (a) Potential anchors associated with the pro-B cell interactome are indicated. The enrichment for E2A, PU.1, CTCF, Rad21, Ebf1, c-Myc and p300 occupancy at loop attachment regions are shown. (b) Distinct putative anchors across the pro-B cell interactome are visualized in Cytoscape. The relative frequency by which putative anchors were associated with loop attachment points is indicated by node size. The significance/reproducibility of tethering, in terms of P-values, is visualized by the edge width of connecting paired marked elements. The color (red-blue) is representative of the ratio of observed frequencies relative to expected frequencies (i.e. the strength of the association). (c) Structured Interaction Matrix Analysis (SIMA) identifies distinct classes of anchors acting at different length scales across the pro-B cell interactome. Binding sites within domains were pooled and examined for interactions across the domains to binding sites in other domains (left and middle). These values were compared to peak positions that were randomized 10,000 times and P-values associated with enrichment for interactions were calculated (middle and right). (d) Distinct classes of anchors act at the different length scales. Compartmental interactions across the transcriptionally permissive compartment were examined for enrichment of interactions at sites exhibiting CTCF and E2A occupancy. One independent Hi-C experiment was performed to generate the data presented here. ChIP-Seq experiments were performed in two independent experiments for CTCF and one experiment for p300 and c-myc.