Immune response diversity originates from differences in cellular programming mediated by genetic and epigenetic mechanisms, yet the interplay between these factors in innate immune cells is only partly understood. Dendritic cells (DCs) are critical regulators of innate and adaptive immunity, driving immune activation and peripheral tolerance in a context-specific manner. DCs respond rapidly to environmental stimuli, therefore they must be primed at the molecular level. We hypothesized that chromatin state specifically accessibility and histone post-translational modifications (PTMs) drives heterogeneity in DC immune responses and can predict their responsiveness to stimulation.

From C57BL/6J mice, we isolated three conventional DC subsets including cDC1s, cDC2As, and cDC2Bs at steady state and following LCMV immune challenge. We used low-input ATAC-seq optimized for ex vivo splenic DCs to determine how DC subsets are primed for stimulation based on differentially accessible chromatin regions. Low input bulk RNA-seq revealed that gene expression often but not always correlated with changes in chromatin accessibility. Complementary CUT&RUN mapping of histone PTMs including key methylation and acetylation marks distinguished active, poised, and repressed promoters and enhancers across DC subsets and how these states contributed to DC responsiveness. Integrated analysis of chromatin accessibility, histone PTM, and transcriptomic data established regulatory networks governing DC function and revealed the extent of gene and enhancer priming in functionally distinct DC populations.

These studies generated the first comprehensive epigenomic atlas of ex vivo DC subsets, providing a predictive framework linking chromatin state to immune responsiveness and laying the groundwork for understanding how environmental factors such as inflammation, obesity, and cancer reshape DC programming.