Graphical Abstract Highlights d Atlas of 512,595 cis-regulatory elements active in 86 immunologic cell types d Two classes of loci, controlled by either promoter-or enhancer-driven logic d Inference of enhancer elements that activate each gene across differentiation d Context-specificity of enhancer activation by transcription factors Pile-up traces of ATAC-seq signals in Itgax locus. Blue bars in the first row indicate the positions of identified peaks (Pval % 0.05) and the graph in the 2 nd row conservation score among vertebrates. RNA expression for Itgax (Cd11c) gene are indicated by barplots with * where RNA-seq data was not acquired.

Mast cells (MC) and basophils (Ba) share expression of the high affinity receptor for IgE (FcεRI) but can be distinguished by their divergent expression of KIT and CD49b. In BALB/c mice, MC lineage cells expressing high levels of FcεRI by flow cytometry were seen only in bone marrow (BM) while those expressing intermediate levels of FcεRI were present in BM and spleen of naïve mice and in mesenteric lymph nodes (mLN) of Trichinella spiralis-infected mice. These FcεRI+KIT+CD49b− cells had a membrane phenotype like intraperitoneal connective tissue-type MC, but were smaller and hypogranular by flow cytometry forward and side scatter profiles, respectively. Consistent with this, they lacked the prominent secretory granules identified by histochemistry and immunodetection for the MC-specific granule proteases that are readily seen in mature jejunal mucosal MC (MMC) that also are induced by the infection and present at the same time. The concentration of these MC lineage cells in mLN determined by flow cytometry was comparable to that of MC progenitors (MCp) measured by limiting dilution and clonal expansion with maturation. We observed upregulation of IL-4 mRNA levels by MCp in mLN and spleens of helminth-infected 4get mice, and demonstrated by intracellular cytokine staining production of IL-4 and IL-6 by the mLN MCp in helminth-infected mice. Furthermore, treatment of helminth-infected mice with anti-FcεRI mAb, a protocol known to deplete Ba, also depleted mLN MCp. Thus, this study identifies a hypogranular subset of MCp recruited to mLN by helminth infection that may be an important unrecognized source of cytokines.

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