Fig. 2

Reorganization of chromatin topology by PML-RARα-mediated chromatin interactions. a Chromatin domains and genomic coverages by CTCF (combined data in PR9 and PR9+Zn cells), RARα (PR9), and PML-RARα (combined data in PR9+Zn). The summary table shows domain numbers and size of interaction domains. CTCF data from B-lymphoblastoid cells (GM12878) was given as a reference. b Schematic of RARα and PML-RARα binding sites detected in PR9 and PR9+Zn cells detected by RARα and PML ChIA-PET experiments. RARα-specific (I), RARα and PML shared (II), and PML-RARα-specific binding sites were identified based on the combination patterns of the data in both PR9 and PR9+Zn cells. c Characterized RARα and PML-RARα binding sites in relation to TSS of genes. d Identification and classification of RARα- and PML-RARα-associated chromatin interactions in PR9 and PR9+Zn cells. Three types of RARα and PML-RARα binding sites (b) involved in interactions are indicated as circles. The interactions between two sites are indicated with lines. The thickness of the lines corresponds to the number of interactions. Numbers of chromatin interactions in each category are given alongside the lines. e Screenshot of genome browser view of chromatin interaction loop, binding peak, and chromatin interaction domain for CTCF (green), RARα (blue), and PML-RARα (purple) at the ID1-HCK locus. Binding and looping signals for each protein factor were normalized. f Integrated 2D chromatin contact maps for the genomic segment (the same as in e) on chr20 for CTCF, RARα, and PML-RARα ChIA-PET data from PR9 and PR9+Zn cells. The red signals in the contact maps were from the combined CTCF and RARα data (left, PR9 cells) and the combined CTCF, RARα, and PML data (right, PR9+Zn cells). Light green and dark green triangles depict CTCF loop and CCD, respectively; light blue and dark blue triangles depict RARα loops and domains; light and dark purple depict PML-RARα loops and domains. Red triangles indicate RNAPII-mediated loops and domains. g 3D DNA-FISH validation. Two probes (red and blue) were designed at the corresponding position in the two separated CTCF domains as shown in e. Left panel: example 3D DNA-FISH images of separated and merged views for the two probes (“a” in red, “b” in green) were shown in both PR9 and PR9+Zn cells. Right panel: boxplot of spatial distance between the two probes measured microscopically from 300 nuclei in each of the PR9 and PR9+Zn cells. Mann-Whitney U test was used to test the difference. **p < 0.01. h 3D chromatin folding rendering. Simulated 3D models of average structure and ensemble cloud in PR9 (left) and PR9+Zn (middle) using the data in the corresponding region in f. Boxplot of the radial diameter of simulated 3D models. K-S test was used to test the differences. **p < 2.2e−16