The macrophage IRF8-IRF1 regulome is required for protection against infections, and is associated with chronic inflammation (ChIP-Seq)

IRF8 and IRF1 are transcriptional regulators that play critical roles in the development and function of myeloid cells, including activation of macrophages by pro-inflammatory signals such as interferon gamma. Loss of IRF8 or IRF1 function causes severe susceptibility to infections in mice and in humans. We used chromatin immunoprecipitation sequencing and RNA sequencing in wild type, and in IRF8 and IRF1 mutant primary macrophages to systematically catalog all the genes bound by (cistromes) and transcriptionally activated (regulomes) by IRF8, IRF1, PU.1 and STAT1 including modulation of epigenetic histone marks. Of seven binding combinations identified, two (cluster 1: IRF8/IRF1/STAT1/PU.1; cluster 5: IRF1/STAT1/PU.1) were found to have a major role in controlling macrophage transcriptional programs both at basal level and following IFNγ activation. They direct expression of a set of genes, the IRF8/IRF1 regulome, that play critical roles in host inflammatory and anti-microbial defenses in mouse models of neuroinflammation and of pulmonary tuberculosis, respectively. In addition, this IRF8/IRF1 regulome is enriched for genes mutated in human primary immuno-deficiencies, and with loci associated for several inflammatory diseases in humans. Chromatin immunoprecipitations followed by high throughput sequencing of IRF8, IRF1 and PU.1 transcription factors ChIP prior to and following 0.5h and 3h interferon gamma stimulation on wild type (B6) bone marrow derived macrophages (BMDM). Histone H3 lysine 4 mono-methylation was evaluated by ChIP-seq on untreated wild type BMDMs. H3 lysine 27 acetylation was assessed in wild type (B6) and in IRF8 or IRF1 mutant BMDM prior to and after 3h of interferon gamma stimulation.