Genome wide profiling of active enhancers and IRF8-binding sites in murine mononuclear phagocyte lineage cells

To understand the mechanism underlying monocyte and dendritic cell development through the regulation of Irf8 expression by the 56 kb downstream (+56 kb) Irf8 enhancer, we performed epigenetic profiling of bone marrow cells and splenocytes from wild-type, the Irf8 +56 kb enhancer-deficient, and IRF8-deficient mice. Taken together with the transcriptome analysis of mononuclear phagocyte lineage cells in these mice, the Irf8 +56 kb enhancer-mediated high Irf8 expression in hematopoietic progenitor cells promote type 1 classical dendritic cell (cDC1) differentiation, while low Irf8 expression in progenitors led to Ly6C+ monocyte development. In addition, IRF8 ChIP-seq of mature cDC1s and monocytes suggested that IRF8 regulates enhancers in cooperation with different transcription factors in each lineage in its expression level. Overall design: Murine Lin- Sca1+ CD117+ (LSK), lymphoid-primed multipotent progenitors (LMPP), granulocyte-monocyte progenitors (GMP), common dendritic cell progenitors (CDP), common monocyte progenitors (cMoPs), Ly6C+ monocytes (Mo), classical dendritic cells (cDC), and neutrophils (Neu) were isolated from wild-type, the +56 kb Irf8 enhancer-deficient (d+56kb), or IRF8-deficient (IRF8KO) mice, and the immunoprecipitated chromatin from these cells was subjected to ChIP-seq (biological duplicates for each cell type).