Given the large number of transcription factors that are known to play important roles in each cell type (e.g. greater than 350 transcription factors are transcribed in macrophages and ES cells, see Figure S4D), it was surprising to find that only small numbers of transcription factor motifs were highly overrepresented in the H3K4me1 patterns in the different cell types we analyzed (Figure S4C and S4E). To explore the relationship of transcription factors whose motifs are not enriched in H3K4me1-marked regions with H3K4me1-associated factors, the global H3K4me1 pattern, and cell type-specific gene expression, we initially focused on Liver X Receptors (LXRα and LXRβ). These oxysterolresponsive nuclear receptors play numerous roles central to macrophage function by regulating target genes involved in lipid metabolism, cell survival, and immunity (Rigamonti et al., 2008).
