Figure 2.
Single-cell integrative multiomics analysis highlights chromatin genes as responsible for RA resistance in PLZF-RARA–expressing cells. (A) UMAP visualization of integrated scRNA-seq (11 900 cells) and scATAC-seq (7367 cells) data set colored by cluster. (B) Donut plots showing the distribution of scRNA- and scATAC-seq cells in each cluster for NT and RA d7 conditions. (C) (Left) Heat map showing the ATAC signal in the NT condition on the differentially accessible peaks between ReP and Prom2-3 clusters. Hierarchical clustering is done according to the ReP data set. (Right) Coverage plot of ATAC signal at selected genes. (D) Coverage plot of ATAC signal per condition in each cluster associated with Ipcef1, Sox6, and Prdx6b genes. (E) Computational scheme to identify key regulon targets in the ReP cluster. The first filtering consists to select TFs with high activity in the ReP cluster by considering the accessibility of their DNA motifs in this cluster. TF motif accessibility scores are calculated with Signac,17 and TF motif markers are identified for each cluster (supplemental Table 2A). Selected ReP TFs are cross-referenced with master transcriptional regulators identified from scRNA-seq data using SCENIC18 (supplemental Table 2B). After this filtering, 3 TFs remain. Target genes shared at least by 2 TFs are taken into account for further filtering (second filtering). Target genes considered are: (i) found in all pySCENIC run, (ii) linked with positive regulons, and (iii) filtered based on the sum of normalized importance (>0.35). One hundred seventy-six genes are conserved (supplemental Table 3). (F) Box plots showing E2f1, E2f4, and Tfdp1 (TFs obtained after the first filtering) regulon activity in each cluster. ∗P < .05. (G) Heat map showing the mRNA expression (left), the promoter accessibility (middle, ±3 kb from the TSS), and the enhancer accessibility (right, ±50 kb from the TSS minus the ±3-kb promoter region) of the 176 target genes in the ReP cluster (obtained after the second filtering). Results are expressed as normalized log (mean gene activity). Hierarchical clustering is done according to the NT data set.

Single-cell integrative multiomics analysis highlights chromatin genes as responsible for RA resistance in PLZF-RARA–expressing cells. (A) UMAP visualization of integrated scRNA-seq (11 900 cells) and scATAC-seq (7367 cells) data set colored by cluster. (B) Donut plots showing the distribution of scRNA- and scATAC-seq cells in each cluster for NT and RA d7 conditions. (C) (Left) Heat map showing the ATAC signal in the NT condition on the differentially accessible peaks between ReP and Prom2-3 clusters. Hierarchical clustering is done according to the ReP data set. (Right) Coverage plot of ATAC signal at selected genes. (D) Coverage plot of ATAC signal per condition in each cluster associated with Ipcef1, Sox6, and Prdx6b genes. (E) Computational scheme to identify key regulon targets in the ReP cluster. The first filtering consists to select TFs with high activity in the ReP cluster by considering the accessibility of their DNA motifs in this cluster. TF motif accessibility scores are calculated with Signac,17 and TF motif markers are identified for each cluster (supplemental Table 2A). Selected ReP TFs are cross-referenced with master transcriptional regulators identified from scRNA-seq data using SCENIC18 (supplemental Table 2B). After this filtering, 3 TFs remain. Target genes shared at least by 2 TFs are taken into account for further filtering (second filtering). Target genes considered are: (i) found in all pySCENIC run, (ii) linked with positive regulons, and (iii) filtered based on the sum of normalized importance (>0.35). One hundred seventy-six genes are conserved (supplemental Table 3). (F) Box plots showing E2f1, E2f4, and Tfdp1 (TFs obtained after the first filtering) regulon activity in each cluster. ∗P < .05. (G) Heat map showing the mRNA expression (left), the promoter accessibility (middle, ±3 kb from the TSS), and the enhancer accessibility (right, ±50 kb from the TSS minus the ±3-kb promoter region) of the 176 target genes in the ReP cluster (obtained after the second filtering). Results are expressed as normalized log (mean gene activity). Hierarchical clustering is done according to the NT data set.

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