Figure 5
Figure 5. EGR2 is associated with the macrophage-specific epigenetic enhancer signature. (A) De novo–extracted consensus motif for EGR2-bound sites and genomic distribution of total transcription factor–bound sites depicted as a pie chart. (B) Box plots showing the distribution of mRNA expression levels for genes adjacent to the 1800 EGR2 peak regions that also gained PU.1 or C/EBPβ in macrophages (indicated by orange). Solid bars of boxes display the interquartile ranges (25%-75%) with an intersection as the median; whiskers, 5th and 95th percentiles. Pairwise comparisons of mRNA expression levels for the indicated cell types are significant (**P < .01 by Student t test, paired, 2-sided). (C) Pie chart depicting the overlap of EGR2, PU.1, and C/EBPβ peaks within 200 bp of centered EGR2 ChIP-seq peaks. (D) Histograms for genomic distance distributions of tag counts for macrophage (MAC) EGR2 and monocyte (MO) and MAC PU.1, C/EBPβ, H3K4me1, H3K27ac, and H2AZ centered across macrophage-specific EGR2-bound sites across a 4-kb genomic region. (E) Promoter distal (according to RefSeq annotation) EGR2 peaks were subdivided into groups that showed induced binding for PU.1 and C/EBPβ, were already preoccupied by 1 of the 2 factors in monocytes, or were not co-bound by PU.1 or C/EBPβ. Regions (6-kb-wide, 500 of each group) centered on EGR2-bound peaks were clustered according to their C/EBPβ, PU.1, H3K4me1, H2AZ, and H3K27ac ChIP-seq profiles in monocytes and macrophages and results are presented as heat maps.

EGR2 is associated with the macrophage-specific epigenetic enhancer signature. (A) De novo–extracted consensus motif for EGR2-bound sites and genomic distribution of total transcription factor–bound sites depicted as a pie chart. (B) Box plots showing the distribution of mRNA expression levels for genes adjacent to the 1800 EGR2 peak regions that also gained PU.1 or C/EBPβ in macrophages (indicated by orange). Solid bars of boxes display the interquartile ranges (25%-75%) with an intersection as the median; whiskers, 5th and 95th percentiles. Pairwise comparisons of mRNA expression levels for the indicated cell types are significant (**P < .01 by Student t test, paired, 2-sided). (C) Pie chart depicting the overlap of EGR2, PU.1, and C/EBPβ peaks within 200 bp of centered EGR2 ChIP-seq peaks. (D) Histograms for genomic distance distributions of tag counts for macrophage (MAC) EGR2 and monocyte (MO) and MAC PU.1, C/EBPβ, H3K4me1, H3K27ac, and H2AZ centered across macrophage-specific EGR2-bound sites across a 4-kb genomic region. (E) Promoter distal (according to RefSeq annotation) EGR2 peaks were subdivided into groups that showed induced binding for PU.1 and C/EBPβ, were already preoccupied by 1 of the 2 factors in monocytes, or were not co-bound by PU.1 or C/EBPβ. Regions (6-kb-wide, 500 of each group) centered on EGR2-bound peaks were clustered according to their C/EBPβ, PU.1, H3K4me1, H2AZ, and H3K27ac ChIP-seq profiles in monocytes and macrophages and results are presented as heat maps.

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