We provide further evidence that the priming of cis-active elements by lineage-determining factors is required for the subsequent binding of a second tier of factors, exemplified by LXRs (Figure 6E) and transcription factors that are activated by TLR4 signalling. This interpretation is supported by the recent observation that recruitment of p300 to new genomic locations in macrophages in response to TLR4 activation primarily occurs at regions exhibiting pre-existing H3K4me1 (Ghisletti et al., 2010), which from our analysis largely are sites of combinatorial interactions of PU.1, C/EBP and AP-1 transcription factors. Collectively, these sequential events lead to a functionally active enhancer capable of contributing to cell type-specific and/or signal-dependent gene expression, similar to the sequential steps leading to activation of the Csf1r locus during macrophage development (Krysinska et al., 2007). This model offers an explanation for the extensive genome-wide and cell type-specific co-localization of transcription factors observed in various previous studies (Chen et al., 2008; MacArthur et al., 2009), and provides insights into how simple combinations of lineage-restricted transcription factors on a genome-wide scale can specify promoter-distal cis-regulatory elements ultimately responsible for both cell identity and cell type-specific responses to diverse signaling inputs.
