Fig. 2: Integrated analysis of ChIP-seq and RNA-seq data reveal unique genes regulated by RARG fusions compared to PML-RARA. | Nature Communications

Fig. 2: Integrated analysis of ChIP-seq and RNA-seq data reveal unique genes regulated by RARG fusions compared to PML-RARA.

From: Oncogenic role of RARG rearrangements in acute myeloid leukemia resembling acute promyelocytic leukemia

Fig. 2

a Schematic illustration of the experimental design. b Density heatmap of HA-X-RARG fusion genes binding peaks. The heatmap encompasses a region extending from −5 kb to +5 kb centered on TSS enriched by the anti-HA antibody. c Venn diagram indicating the common binding peaks of RARG fusions identified by ChIP-seq. d Venn diagram indicating the common binding peaks in both RARG fusions and PML::RARA identified by ChIP-seq. e Venn diagram indicating the genes uniquely activated and repressed by RARG fusions compared to PML-RARA based on integrated analysis of ChIP-seq and RNA-seq data. f Motif enrichment at RARG fusions binding sites by HOMER analysis. g Real-time PCR analysis of the effect of CPSF6-RARG and NUP98-RARG overexpression in hCD34+ cells on the expression of activated genes and repressed gene. h Genome browser tracks showing the binding patterns of RARG fusions and PML::RARA on ATF3 and BCL2. i hCD34+ cells overexpressing RARG fusions were analyzed by ChIP with an anti-HA antibody or IgG. Immunoprecipitated DNA was quantified using qPCR for the anti-HA antibody- or IgG- bound BCL2 and ATF3 promoter and enhancer regions. j Effect of RARG fusions on the transcriptional activity of ATF3 and BCL2. k Heat maps and density plots of ATAC-seq peaks aligned to human hg38 genome around the TSS ± 5 kb. l, m Heatmaps and histograms shown the abundant CPSF6-RARG, NUP98-RARG, H3K27ac, H3K4me1, H3K4me3, and ATAC-seq occupancy on RARG fusions binding sites. A 5 kb window is shown with the summit of RARG fusions binding in the center of each panel. n Real-time PCR analysis of the effect of p300 inhibitor C646 on the expression of BCL2 and ATF3 in hCD34+ cells with or without CPSF6-RARG or NUP98-RARG overexpression. g, i, j, n n = 3 technical replicates. Results are representative of three independent experiments. Statistical significance was calculated by (i, j) one-way ANOVA with Tukey’s multiple comparison tests; (g, n) two-tailed Student’s t test; Data are presented as means ± S.E.M. Source data are provided as a Source Data file.

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