American Society of Hematology

Figure 4

$Figure 4. Dynamics of PU.1 and C/EBPβ binding during monocyte-to-macrophage differentiation. (A) ChIP-seq tag counts of each of the indicated transcription factors are compared for peak regions between monocytes (MO) and macrophages (MAC) in a density plot as described in the legend to Figure 1. (B) Pie charts depicting the genomic distribution of total transcription factor–bound sites or differentially bound regions (defined as having at least a 4-fold tag count difference in peak regions). For C/EBPβ, only a small fraction of monocyte-specific peaks were detected and are not included. (C) De novo–extracted consensus motifs for PU.1 and C/EBPβ bound sites. Motifs were assigned to transcription factors or transcription factor families based on similarity with known motif matrices. In addition, the fraction of transcription factor–bound regions containing at least 1 motif instance, the expected frequency of the motif in random sequences (in parentheses), and P values (hypergeometric) for the overrepresentation of each motif are given. (D) Box plots showing the distribution of mRNA expression levels for genes adjacent to differentiation stage-specific transcription factor peak regions as described in the legend to Figure 1. (E) De novo–extracted sequence motifs associated with macrophage-specific promoter-distal (according to RefSeq annotation) PU.1 peak regions. Motifs were assigned to transcription factors or transcription factor families based on similarity with known motif matrices. In addition, the fraction of PU.1-bound regions (200 bp) containing at least 1 motif instance, the expected frequency of the motif in random sequences (in parentheses), and P values (hypergeometric) for the overrepresentation of each motif are given. (F) Corresponding data for macrophage-specific C/EBPβ-bound regions are shown. (G) Histograms for genomic distance distributions of monocytes (MO) and macrophage (MAC) PU.1, C/EBPβ, H3K4me1, H3K27ac, and H2AZ tag counts centered across macrophage-specific PU.1-bound sites across a 4-kb genomic region. (H) Corresponding data for macrophage-specific C/EBPβ-bound regions.$

Dynamics of PU.1 and C/EBPβ binding during monocyte-to-macrophage differentiation. (A) ChIP-seq tag counts of each of the indicated transcription factors are compared for peak regions between monocytes (MO) and macrophages (MAC) in a density plot as described in the legend to Figure 1. (B) Pie charts depicting the genomic distribution of total transcription factor–bound sites or differentially bound regions (defined as having at least a 4-fold tag count difference in peak regions). For C/EBPβ, only a small fraction of monocyte-specific peaks were detected and are not included. (C) De novo–extracted consensus motifs for PU.1 and C/EBPβ bound sites. Motifs were assigned to transcription factors or transcription factor families based on similarity with known motif matrices. In addition, the fraction of transcription factor–bound regions containing at least 1 motif instance, the expected frequency of the motif in random sequences (in parentheses), and P values (hypergeometric) for the overrepresentation of each motif are given. (D) Box plots showing the distribution of mRNA expression levels for genes adjacent to differentiation stage-specific transcription factor peak regions as described in the legend to Figure 1. (E) De novo–extracted sequence motifs associated with macrophage-specific promoter-distal (according to RefSeq annotation) PU.1 peak regions. Motifs were assigned to transcription factors or transcription factor families based on similarity with known motif matrices. In addition, the fraction of PU.1-bound regions (200 bp) containing at least 1 motif instance, the expected frequency of the motif in random sequences (in parentheses), and P values (hypergeometric) for the overrepresentation of each motif are given. (F) Corresponding data for macrophage-specific C/EBPβ-bound regions are shown. (G) Histograms for genomic distance distributions of monocytes (MO) and macrophage (MAC) PU.1, C/EBPβ, H3K4me1, H3K27ac, and H2AZ tag counts centered across macrophage-specific PU.1-bound sites across a 4-kb genomic region. (H) Corresponding data for macrophage-specific C/EBPβ-bound regions.

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