American Society of Hematology

Figure 1

$Figure 1. Characterization of putative enhancer regions marked by cell stage–specific H3K4me1 during macrophage differentiation. (A) H3K4me1 ChIP-seq tag counts for peak regions are compared between macrophage differentiation stages (HSC, CD133+ HSCs; MO, monocytes; MAC, macrophages) in a density plot. The colors represent the relative density of peaks in each location within the density plot. Numbers in corners refer to the number of cell type–specific promoter-distal H3K4me1 sites (± 3 kb from RefSeq-annotated TSS). (B) Genome browser tracks for 3 transcription factors genes with cell stage–specific expression patterns. Boxes indicate promoter distal (based on RefSeq gene annotation), cell stage–specific H3K4me1-marked regions representing putative enhancer regions. Bar charts on the right show microarray-based mean expression values (log10 scale) for each gene in each cell type. Coloring indicates cell types (HSCs, purple; MOs, dark red; MACs, blue). (C) Box plots showing the distribution of mRNA expression levels (HSC, CD34+ HSCs; MO, monocytes; MAC, macrophages; and lymphoid cell types as indicated) for RefSeq genes adjacent to differentiation stage-specific promoter distal H3K4me1 peak regions. Cell types showing cell-stage specificity are indicated by colored boxes (HSCs, green; MOs, blue; MACs, 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 < .001 by Student t test, paired, 2-sided). (D-F) De novo–extracted sequence motifs associated with differentiation stage–specific H3K4me1 peak regions. Motifs were assigned to transcription factors or transcription factor families based on similarity with known motif matrices. In addition, the fraction of H3K4me1 regions (1 kb) 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.$

Characterization of putative enhancer regions marked by cell stage–specific H3K4me1 during macrophage differentiation. (A) H3K4me1 ChIP-seq tag counts for peak regions are compared between macrophage differentiation stages (HSC, CD133⁺ HSCs; MO, monocytes; MAC, macrophages) in a density plot. The colors represent the relative density of peaks in each location within the density plot. Numbers in corners refer to the number of cell type–specific promoter-distal H3K4me1 sites (± 3 kb from RefSeq-annotated TSS). (B) Genome browser tracks for 3 transcription factors genes with cell stage–specific expression patterns. Boxes indicate promoter distal (based on RefSeq gene annotation), cell stage–specific H3K4me1-marked regions representing putative enhancer regions. Bar charts on the right show microarray-based mean expression values (log₁₀ scale) for each gene in each cell type. Coloring indicates cell types (HSCs, purple; MOs, dark red; MACs, blue). (C) Box plots showing the distribution of mRNA expression levels (HSC, CD34⁺ HSCs; MO, monocytes; MAC, macrophages; and lymphoid cell types as indicated) for RefSeq genes adjacent to differentiation stage-specific promoter distal H3K4me1 peak regions. Cell types showing cell-stage specificity are indicated by colored boxes (HSCs, green; MOs, blue; MACs, 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 < .001 by Student t test, paired, 2-sided). (D-F) De novo–extracted sequence motifs associated with differentiation stage–specific H3K4me1 peak regions. Motifs were assigned to transcription factors or transcription factor families based on similarity with known motif matrices. In addition, the fraction of H3K4me1 regions (1 kb) 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.

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