Gene expression profiling in dendritic cell progenitors and dendritic cells

To understand the roles of Irf8 3' enhancers on Irf8 expression during cDC1 differentiation, we performed RNA-seq analysis of bone marrow cells and splenocytes from wild-type, and the Irf8 enhancer-deficient mice. Phenotypic analysis and integrated analysis of transcriptome data with genome-wide CUT&Tag data analysis for H3K27ac revealed that the +56 kb enhancer acts on other 3' enhancers via an IRF8-dependent TF program and the +32 kb enhancer acts in cis to activate other 3' enhancers. Overall design: Murine type1 classical dendritic cells (cDC1s), cDC1 subset-committed progenitors (pre-cDC1s), common DC progenitors (CDPs), and monocyte-DC progenitors (MDPs) were isolated from WT, +56 kb enhancer-heterozygous deficient (d+56het), or +32 kb enhancer-heterozygous deficient (d+32het). The IRF8-rescued cDC1s were prepared from Lin– cells from WT, +56 kb enhancer-deficient (d+56), or +32 kb enhancer-deficient (d+32). These cells were subjected to RNA-seq analysis (biological duplicates for each cell type).