Fig. 6From: Chromatin topology reorganization and transcription repression by PML-RARα in acute promyeloid leukemiaNative PML-RARα in patient-derived APL cells behaved the same as induced PML-RARα. a Schematic design for comparison of transcription (RNA-seq) and 3D genome organization (ChIA-PET of PML-RARα, RNAPII, and CTCF) between patient-derived APL cells (NB4, with native PML-RARα) and PR9 cells by ZnSO4 induction (PR9+Zn, with induced PML-RARα), as well as for comparison of transcription (RNA-seq) between NB4 cells under ATRA treatment (NB4+ATRA, with native PML-RARα depleted) and PR9 cells without PML-RARα. b Contour plots for the correlation of gene expression (RPKM) between NB4 vs. PR9+Zn cells (left) and NB4+ATRA vs. PR9 cells (right). c Contour plots for the correlation of gene expression (RPKM) of the 146 PML-RARα target genes between NB4 and NB4+ATRA cells. d Integrated 2D contact maps of PML-RARα (up, purple) and CTCF (low, green) ChIA-PET data in NB4 (left), PR9+Zn (middle), and PR9 (right) cells. e A screenshot of browser view for chromatin loops and peaks by CTCF (green) and PML-RARα (purple) showing a high similarity between NB4 (top) and PR9+Zn (middle) cells. Chromatin loops and peaks by CTCF (green) and RARα (blue) in PR9 cells are included as a reference for normal myeloid cells. f An example for comparison at the BHLHE40 locus of chromatin loops peaks by CTCF (green), PML-RARα (purple) or RARα (blue), and RNAPII (red) in cells of NB4 (orange box), PR9+Zn (purple box), and PR9 (blue box) cells. It indicated that the chromatin structures mediated by CTCF, and PML-RARα, and RNAPII in NB4 cells and PR9+Zn cells were highly comparable. When compared to the data in PR9 cells, both NB4 and PR9+Zn cells exhibited high levels of PML-RARα chromatin interactions, but basal levels of RNAPII occupancy. g At the same BHLHE40 locus, the expression (RPKM) of gene BHLHE40 as measured in PR9 were significantly reduced in PR9+Zn and NB4 cells but recovered in NB4 cells after ATRA treatmentsBack to article page