Figure 5
Chromatin looping and activation status of regulatory elements are Notch1- and Tcf1-dependent. (A) Three-way quantitative comparison of identified chromatin loops for condition-specific and shared loops for Controls, N1IC, and N1IC Tcf7Δ/Δ. (B) Overrepresentation analysis (ORA) for N1IC-specific loop-associated genes for phenotype catalog. Top 10 pathways are shown. P values were calculated with Fisher's exact test. (C) Association of gene expression differences (adjusted P value ≤ .05) for genes within dynamic condition-specific loops (from panel A). Left and right panels show log2 fold-change for condition-specific loop-associated genes from RNA-seq analysis. (D) Induced CD45.2+ BM cells from Controls (black, n = 3), N1IC (red, n = 3), or N1IC Tcf7Δ/Δ (blue, n = 3) mice were FACS purified for lineage-, cKit+ (CD117), and Sca1+ BM progenitors (LSK) for histone mark ChIP-seq analysis with H3K27ac antibody. (E) H3K27ac ChIP-seq signal at the non-TSS loop anchor. Shown at 5 kb windows around the center of a peak or loop anchor. Enrichment for H3K27ac is scaled. Quantification of the global signal for non-TSS loop anchors is depicted on the right. Data are shown from left to right for Controls, N1IC, and N1IC Tcf7Δ/Δ. (F) Gene-annotated scatterplot for differential EPI (x-axis) for differentially expressed genes (log2FC, y-axis) in comparison N1IC vs Controls. Dots for genes with differential EPI >1 are shown in red. (G) ORA for genes with differential EPI in comparison N1IC vs Controls for gene ontology biological processes (GOBP) catalog. Top 20 pathways are shown. P values were calculated with Fisher's exact test. (H) Expression of Bcl11b measured as transcripts per million (TPM) from RNA-seq on LSK cells. Data are represented as mean ± standard error of the mean. One-way ANOVA, ***P value < .001. (I) Representation of 5 kb interacting regions between the indicated genomic coordinates color-coded based on their EPI strength value (top). Identified enhancer (gray line) and promoter (yellow line) interaction is enlarged in the top left corner. Integrative genomics viewer CTCF, chromatin accessibility, and H3K27ac profiles are shown for all experimental conditions (bottom). Tracks were group-scaled. Schematic representation of genetic loci is depicted below the profiles.

Chromatin looping and activation status of regulatory elements are Notch1- and Tcf1-dependent. (A) Three-way quantitative comparison of identified chromatin loops for condition-specific and shared loops for Controls, N1IC, and N1IC Tcf7Δ/Δ. (B) Overrepresentation analysis (ORA) for N1IC-specific loop-associated genes for phenotype catalog. Top 10 pathways are shown. P values were calculated with Fisher's exact test. (C) Association of gene expression differences (adjusted P value ≤ .05) for genes within dynamic condition-specific loops (from panel A). Left and right panels show log2 fold-change for condition-specific loop-associated genes from RNA-seq analysis. (D) Induced CD45.2+ BM cells from Controls (black, n = 3), N1IC (red, n = 3), or N1IC Tcf7Δ/Δ (blue, n = 3) mice were FACS purified for lineage-, cKit+ (CD117), and Sca1+ BM progenitors (LSK) for histone mark ChIP-seq analysis with H3K27ac antibody. (E) H3K27ac ChIP-seq signal at the non-TSS loop anchor. Shown at 5 kb windows around the center of a peak or loop anchor. Enrichment for H3K27ac is scaled. Quantification of the global signal for non-TSS loop anchors is depicted on the right. Data are shown from left to right for Controls, N1IC, and N1IC Tcf7Δ/Δ. (F) Gene-annotated scatterplot for differential EPI (x-axis) for differentially expressed genes (log2FC, y-axis) in comparison N1IC vs Controls. Dots for genes with differential EPI >1 are shown in red. (G) ORA for genes with differential EPI in comparison N1IC vs Controls for gene ontology biological processes (GOBP) catalog. Top 20 pathways are shown. P values were calculated with Fisher's exact test. (H) Expression of Bcl11b measured as transcripts per million (TPM) from RNA-seq on LSK cells. Data are represented as mean ± standard error of the mean. One-way ANOVA, ***P value < .001. (I) Representation of 5 kb interacting regions between the indicated genomic coordinates color-coded based on their EPI strength value (top). Identified enhancer (gray line) and promoter (yellow line) interaction is enlarged in the top left corner. Integrative genomics viewer CTCF, chromatin accessibility, and H3K27ac profiles are shown for all experimental conditions (bottom). Tracks were group-scaled. Schematic representation of genetic loci is depicted below the profiles.

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