Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells (H3K27me3 CUT&RUN of SMC3KO FL-BMDCs +/- activation)

The cohesin protein complex extrudes chromatin loops between CTCF-bound sites to organize chromosomes into topologically associated domains, yet biological implications of this process remain obscure. We show that cohesin is required for the post-mitotic differentiation and function of antigen-presenting dendritic cells (DCs), particularly for antigen cross-presentation and IL-12 secretion by type 1 conventional DCs (cDC1s) in vivo. The chromatin organization of DCs was shaped by cohesin and the DC-specifying transcription factor IRF8, which controlled chromatin looping and chromosome compartmentalization, respectively. Notably, optimal expression of IRF8 itself required CTCF/cohesin-binding sites demarcating the Irf8 gene. During DC activation, cohesin was required for the induction of a subset of genes with distal enhancers. Accordingly, the deletion of CTCF sites flanking the Il12b gene reduced IL-12 production by cDC1s. Our data reveal an essential role of cohesin-mediated chromatin regulation in cell differentiation and function in vivo, and its bi-directional crosstalk with lineage-specifying transcription factors. Overall design: CUT&RUN for H3K27me3 was performed on cDCs purified from 4-OHT-treated FL-BMDC cultures from Rosa26CreER/+ or Rosa26CreER/+ Smc3fl/fl mice, after cultures were either unstimulated or stimulated with CpG-B for 6 hours (2 replicates per genotype/stimulation condition).