Figure 3.
NFIA-ETO2 expression alters chromatin accessibility and binds to gene loci encoding regulators of erythroid differentiation. (A) Comparative motif enrichment in primary EBs expressing NFIA-ETO2 or CTRL of ATAC-seq peaks via HOMER. Motifs were ranked according to the variation of normalized P values calculated for peaks detected in the CTRL (negative values) and the NFIA-ETO2 expressing EBs (positive values). (B) Comparative motif enrichment in primary EBs expressing NFIA-ETO or ETO2 from ATAC-seq peaks via HOMER. Motifs were ranked based on the variation of normalized P values calculated for peaks detected in the ETO2- (negative values) and NFIA-ETO2–expressing primary EBs (positive values). Waterfall plot was made after substraction of the peaks detected in control conditions of both experiments.9 (C) Heatmaps representing ChIPseq read intensities of the NFIA-ETO2-HA (red), H3K4me1 (blue), H3K27ac (green), H3K27me3 (orange), and H3K9me1 (yellow). Each heatmap corresponds to the sum of reads mapped to the region focused on NFIA-ETO2-HA peak centers with ±5 kb. (D) Waterfall plot showing enriched motifs associated with NFIA-ETO2-HA peaks in MEL cells expressing NFIA-ETO2-HA built using HOMER. Motifs are ranked according to their P values. (E) Barplot representing DEGs (obtained in the RNA-seq analysis of NFIA-ETO2 and vector-transduced MEL cells) located in the vicinity of NFIA-ETO2-HA peaks. DEGs related to erythropoiesis were acquired through literature-based search (Erythroid DEGs). (F) Genome browser snapshots of ChIPseq tracks showing the binding of NFIA-ETO2-HA (red), H3K27ac (green), H3K4me1 (blue), H3K9me1 (yellow,) and H3K27me3 (orange) to the Gypc and Alas2 loci, and their RNA-seq tracks (dark green) showing their normalized expression in MEL cells. The known cis-regulatory element in the mm10 mouse genome from ENCODE data are indicated in the yellow track. (G) Bargraph representing NFIA-ETO2-HA peaks containing NFIA motif and/or overlaping with ETO2 peak, which were located in the vicinity of DEGs (obtained via the RNA-seq analysis of NFIA-ETO2 and vector-transduced MEL cells). HA, hemagglutinin.

NFIA-ETO2 expression alters chromatin accessibility and binds to gene loci encoding regulators of erythroid differentiation. (A) Comparative motif enrichment in primary EBs expressing NFIA-ETO2 or CTRL of ATAC-seq peaks via HOMER. Motifs were ranked according to the variation of normalized P values calculated for peaks detected in the CTRL (negative values) and the NFIA-ETO2 expressing EBs (positive values). (B) Comparative motif enrichment in primary EBs expressing NFIA-ETO or ETO2 from ATAC-seq peaks via HOMER. Motifs were ranked based on the variation of normalized P values calculated for peaks detected in the ETO2- (negative values) and NFIA-ETO2–expressing primary EBs (positive values). Waterfall plot was made after substraction of the peaks detected in control conditions of both experiments.9 (C) Heatmaps representing ChIPseq read intensities of the NFIA-ETO2-HA (red), H3K4me1 (blue), H3K27ac (green), H3K27me3 (orange), and H3K9me1 (yellow). Each heatmap corresponds to the sum of reads mapped to the region focused on NFIA-ETO2-HA peak centers with ±5 kb. (D) Waterfall plot showing enriched motifs associated with NFIA-ETO2-HA peaks in MEL cells expressing NFIA-ETO2-HA built using HOMER. Motifs are ranked according to their P values. (E) Barplot representing DEGs (obtained in the RNA-seq analysis of NFIA-ETO2 and vector-transduced MEL cells) located in the vicinity of NFIA-ETO2-HA peaks. DEGs related to erythropoiesis were acquired through literature-based search (Erythroid DEGs). (F) Genome browser snapshots of ChIPseq tracks showing the binding of NFIA-ETO2-HA (red), H3K27ac (green), H3K4me1 (blue), H3K9me1 (yellow,) and H3K27me3 (orange) to the Gypc and Alas2 loci, and their RNA-seq tracks (dark green) showing their normalized expression in MEL cells. The known cis-regulatory element in the mm10 mouse genome from ENCODE data are indicated in the yellow track. (G) Bargraph representing NFIA-ETO2-HA peaks containing NFIA motif and/or overlaping with ETO2 peak, which were located in the vicinity of DEGs (obtained via the RNA-seq analysis of NFIA-ETO2 and vector-transduced MEL cells). HA, hemagglutinin.

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