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ecific enhancer-like regions of the genome established by PU.1 and other macrophage Aphrodine site lineage determining factors. Gain and loss of function experiments indicated that Rev-erbs function to suppress the activities of these enhancers by repressing enhancer-directed transcription. The data for this heat map is accessible in Here, we provide evidence that Rev-erbs repress the transcription and function of signal-dependent enhancers that are targets of TLR, IL4, TGFb, and DAMP signaling. Rather than exerting a pattern of repression that reinforces a particular polarization phenotype, Rev-erbs regulate subsets of signal responsive genes that span those associated with M or M, M, and M phenotypes, enriching for functions associated with wound repair. Consistent with these in vitro observations, deletion of Rev-erbs from the hematopoietic lineage in vivo results in accelerated wound repair. Unexpectedly, we found that a complex tissue injury signal directs genomic binding patterns for NF-kB p65, FBJ murine osteosarcoma viral oncogene homolog, and Smad3 that differ substantially from those observed following selective treatments with a TLR4 agonist or TGFb. In addition, by analyzing changes in enhancer signatures, we identified Nrf2 as an additional mediator of the transcriptional response to the tissue injury signal. While these transcription factors exhibit relatively little co-localization in response to single polarizing ligands, we observe substantial co-localization and enhancer activation in response to the complex tissue injury signal, resulting in transcriptional outcomes that are qualitatively different than the sum of single polarizing signals. These observations provide insights into how combinations of signals are integrated at a transcriptional level to result in context-specific patterns of gene expression. Results Rev-erb transcriptional activity varies according to polarizing signal Our previous findings that Rev-erbs regulate transcription from signal-dependent enhancers led us to PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19826300 investigate possible biological roles of Rev-erbs in influencing macrophage phenotypes. To study the phenotypic contribution of Rev-erbs to signal-dependent gene expression in macrophages, we performed RNA-Sequencing of poly mRNA isolated from wild-type macrophages and those deficient for both Rev-erba and Rev-erbb. Data are pooled from three independent experiments as described in more detail in the Materials and methods. The p-values shown reflect comparisons with a p-value less than 0.05, as determined by the linear mixed effects model. Macroscopic digital photographs of wound closure in WT and Rev-erb DKO bone marrow transplanted animals. Histological images of wound healing in WT and Rev-erb DKO bone marrow transplanted animals taken at 2.5x magnification after 2, 4, and 6 days. Arrowheads show differential re-epithelialization between WT and Rev-erb DKO bone marrow transplanted animals. Abbreviations: g=granulation tissue, d=dermis. Images representative of two independent animals. Day 4 hematoxylin and eosin, as well as F4/80 stained histological images taken at 20x magnification. Images representative of two independent animals. Day 4 hematoxylin and eosin, as well as Ly6B.2 stained histological images taken at 20x magnification. Images representative of two independent animals. Migration of WT and Rev-erb DKO macrophages through matrigel extracellular matrix for 24 hr. DOI: 10.7554/eLife.13024.006 The following figure supplement is available f