The inflammatory response is the first line of defense against infectious agents or tissue damage. Innate immune cells are the crucial effectors regulating the different phase of inflammation. Their ability to timely develop an immune response is tightly controlled by the interplay of transcriptional and epigenetic mechanisms. The immunological imprinting elicited by exposure to different concentrations and types of infectious agents determine the functional fate of immune cells, forming the basis of innate immune memory. In this review we highlight the best-characterized examples of gene reprogramming occurring during different phases of inflammation with particular emphasis on the epigenetic marks that determine the specificity of the immune response. We further review the potential of cutting edge experimental techniques that have recently helped to reveal the deep complexity of epigenetic regulation during the inflammatory response.
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