Exploiting genomics and natural genetic variation to decode macrophage enhancers

•Enhancers are major determinants of cell specific gene expression.•Small sets of lineage-determining factors prime the majority of macrophage enhancers.•Tissue environment drives selective activation of macrophage enhancers.•Genetic variation can be exploited to discover mechanisms of enhancer activation.

The mammalian genome contains on the order of a million enhancer-like regions that are required to establish the identities and functions of specific cell types. Here, we review recent studies in immune cells that have provided insight into the mechanisms that selectively activate certain enhancers in response to cell lineage and environmental signals. We describe a working model wherein distinct classes of transcription factors define the repertoire of active enhancers in macrophages through collaborative and hierarchical interactions, and discuss important challenges to this model, specifically providing examples from T cells. We conclude by discussing the use of natural genetic variation as a powerful approach for decoding transcription factor combinations that play dominant roles in establishing the enhancer landscapes, and the potential that these insights have for advancing our understanding of the molecular causes of human disease.