Specialized cell state and spatial compartments within the germinal center dark zone

Within germinal centers (GCs), complex and highly orchestrated molecular programs must balance proliferation, somatic hypermutation (SHM), class switch recombination (CSR) and selection to both provide effective humoral immunity and to protect against genomic instability and neoplastic transformation. In contrast to this complexity, GC B cells are canonically divided into two principal populations, dark zone (DZ) and light zone (LZ) cells. We now demonstrate that following selection in the LZ, B cells migrate to microniches within the canonical DZ that are sites of ongoing cell division. These proliferating DZ (DZp) cells then transit into the larger DZ to become differentiating DZ (DZd) cells before re-entering the LZ. Multidimensional analysis revealed distinct molecular programs in each population commensurate with observed compartmentization of non-compatable functions. These data provide a new three cell zone model that both orders critical GC functions and reveals essential molecular programs of humoral adaptive immunity. Overall design: 32 samples from mouse: 10 ATAC-Seq samples; 9 ChIP-Seq (ChIP-Tagmentation-Sequencing [ChIP-Tag-Seq]) samples, including GCB cell input; 10 bulk RNA-Seq samples; and 3 Drop-Seq captures for single cell RNA-Seq.