Differential gene regulation by NUP98-FOs. (A) Integrative Genome Viewer (IGV) tracks of the HOXA-B clusters from CUT&RUN using HA, H3K4me3, and H3K27ac antibodies in HA-tagged NUP98r cbCD34 models (top: empty vector control, gray; HA-NUP98::KDM5A, red; HA-NUP98::NSD1, blue; HA-NUP98::HOXA9, black), and heat map showing expression levels of HOXA-B genes (bottom). N-terminal NUP98 antibody was applied for the empty vector control. (B) IGV tracks of differentiation-related gene loci (top: RUNX1, GFI1B, and the HOXC cluster) and Venn diagram showing overlap of protein-coding genes with annotated peaks (bottom: false-discovery rate <0.00001). (C) CUT&RUN strategy from primary patient samples or NUP98::KDM5A cell lines (CHRF-288-11 and ST1653). (D) Counts of peaks from the N-terminus NUP98 antibody in primary samples (top) and overlaps of target genes among non-NUP98::KDM5A and NUP98::KDM5A (bottom). NUP98::KDM5A AMKL-specific 21 target genes are highlighted. Colors indicate peak annotations. (E) IGV tracks of the HOXA-B cluster from CUT&RUN using N-terminal NUP98, H3K4me3, and H3K27ac antibodies in primary leukemia samples and NUP98::KDM5A cell lines. (F) Principal component analysis of genome-wide PBS (probability of being signals) scores of H3K27ac (left) and H3K27me3 (right) from primary samples. Colors indicate expression clusters, and shapes indicate fusion partners. (G) Differential signal analysis using H3K27ac PBS scores between NUP98::KDM5A and other (NUP98::NSD1 and NUP98::RAP1GDS1) samples (left) and NUP98::KDM5A AMKL and non-AMKL (right) calculated by limma, followed by the Benjamini-Hochberg adjustment. Only regions with significant enrichment (adjusted P < .05) are shown. (H) IGV tracks of the MECOM and MEIS2 gene loci from CUT&RUN using N-terminal NUP98, H3K4me3, and H3K27ac antibodies in primary leukemia samples and NUP98::KDM5A cell lines. IgG, immunoglobulin G.
Figure 5.

Differential gene regulation by NUP98-FOs. (A) Integrative Genome Viewer (IGV) tracks of the HOXA-B clusters from CUT&RUN using HA, H3K4me3, and H3K27ac antibodies in HA-tagged NUP98r cbCD34 models (top: empty vector control, gray; HA-NUP98::KDM5A, red; HA-NUP98::NSD1, blue; HA-NUP98::HOXA9, black), and heat map showing expression levels of HOXA-B genes (bottom). N-terminal NUP98 antibody was applied for the empty vector control. (B) IGV tracks of differentiation-related gene loci (top: RUNX1, GFI1B, and the HOXC cluster) and Venn diagram showing overlap of protein-coding genes with annotated peaks (bottom: false-discovery rate <0.00001). (C) CUT&RUN strategy from primary patient samples or NUP98::KDM5A cell lines (CHRF-288-11 and ST1653). (D) Counts of peaks from the N-terminus NUP98 antibody in primary samples (top) and overlaps of target genes among non-NUP98::KDM5A and NUP98::KDM5A (bottom). NUP98::KDM5A AMKL-specific 21 target genes are highlighted. Colors indicate peak annotations. (E) IGV tracks of the HOXA-B cluster from CUT&RUN using N-terminal NUP98, H3K4me3, and H3K27ac antibodies in primary leukemia samples and NUP98::KDM5A cell lines. (F) Principal component analysis of genome-wide PBS (probability of being signals) scores of H3K27ac (left) and H3K27me3 (right) from primary samples. Colors indicate expression clusters, and shapes indicate fusion partners. (G) Differential signal analysis using H3K27ac PBS scores between NUP98::KDM5A and other (NUP98::NSD1 and NUP98::RAP1GDS1) samples (left) and NUP98::KDM5A AMKL and non-AMKL (right) calculated by limma, followed by the Benjamini-Hochberg adjustment. Only regions with significant enrichment (adjusted P < .05) are shown. (H) IGV tracks of the MECOM and MEIS2 gene loci from CUT&RUN using N-terminal NUP98, H3K4me3, and H3K27ac antibodies in primary leukemia samples and NUP98::KDM5A cell lines. IgG, immunoglobulin G.

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