ChIP-Seq of in vivo biotin-tagged LXRβ in the murine macrophage RAW264.7 cell line (validated in Figure S5A and S5B) identified 664 confident LXR binding sites (FDR < 0.1%), 85% of which were distally located relative to the TSS of vicinal genes (Figure 5A). Conventional, antibody-based ChIP assays for endogenous LXRβ in primary macrophages confirmed 12 of 12 representative LXR binding sites (Figure S5C). While de novo motif analysis identified the consensus LXR response element (DR4) as the most highly enriched motif, PU.1 and AP-1 motifs were also highly co-enriched in LXRβ-bound regions (Figure 5B). In line with motif enrichment, 34% of LXRβ peaks were within 100 bp of a PU.1-bound site in primary macrophages (Figure 5C), exemplified for the established LXR target gene Abcg1 (Figure 5D). Additionally, macrophage LXR binding sites exhibited a macrophage-specific H3K4me1 signature, in contrast to the H3K4me1 pattern around the same sites in liver (Robertson et al., 2008), another tissue in which LXRs play key regulatory roles (Figure 5E and 5G).
