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. 2020 Sep 16;39(21):e99520. doi: 10.15252/embj.201899520

Figure 3. Two advanced replicons separated by 30 kb cooperate to form a synthetic early‐replicated region that is more associated with A compartments.

Figure 3

  1. Distribution of –ΔL + ΔE values for clonal cell lines containing one advanced replicon (β A ‐globin + β‐actin) inserted at site 1 (i, N = 8) or 3 (iii, N = 3) or at both sites on the same chromosome with one GFP reporter construct composed of the GFP reporter gene under the control of the β A ‐globin promoter/origin linked to a 1.6 kb fragment of human chromosome 7 (h.K7) inserted at site 2, either on the same chromosome as 1 and 3 (1 + 2 + 3), or on the other chromosome (1 + 3) (ii, N = 5). Blue and black triangles represent reactive loxP sites and recombined inactive loxP sites, respectively. Black vertical bars represent insertion sites. Rectangle edges correspond to the 0.25 and 0.75 quartiles, the thick black lines represent the median, the white triangles represent the mean and the whiskers extend to the smallest and largest –ΔL + ΔE values. Statistical analysis was performed with Wilcoxon nonparametric two‐tailed tests (**P < 0.01).
  2. Schematic representation of alleles 1 + 3 and 2. Blue and black triangles represent reactive loxP sites and recombined inactive loxP sites, respectively. Black vertical bars represent insertion sites.
  3. Interaction profiles of allele 1 + 3/2 with chr1 for combined Hi‐C libraries: distance‐corrected interactions, i.e., observed/expected (OE), binned at 500 kb with corresponding compartment (EV1) tracks. Red arrows represent the loci that show preferred interactions with allele 1 + 3 and that coincide with A compartment.
  4. OE interactions of allele 1 + 3 (orange rectangles) and allele 2 (blue rectangles) averaged over A and B compartments for p and q arms at 100 kb bin size. A random compartment status permutation test was made, and then, we calculated the one‐sided P‐value for the observed value of “difference allele 1 + 3/2 A − B”. Values corresponding to OE interactions of allele 1 + 3 and allele 2 averaged over shuffled A (red circles, N = 1,000) and B compartments (blue circles, N = 1,000) for p and q arms. ns, not significant; **P < 0.01; ***P < 0.001.
  5. Scatterplot of density of interactions between allele 1 + 3 and allele 2 with chromosomes larger than 5,000,000 bp.