Chromatin folding principles underlying the generation of antibody diversity

Effective adaptive immunity requires generation of a diverse repertoire of antigen receptors via V(D)J recombination. To illuminate the underlying mechanisms, we combined biophysical simulations with experimental data to model chromatin folding and dynamics of the mouse immunoglobulin heavy chain gene (Igh) locus. Simulations that best recapitulated experimental data on locus structure and recombination of Igh alleles identified three novel chromatin folding principles. First, we found that prominent structural features of the Igh locus, such as the 3'-anchored stripe, required cohesin loading throughout the locus. Second, the Eμ enhancer was best modeled as a bi-directional loop extrusion blocker, though it does not bind CTCF. Third, we found that utilization of V_H genes to obtain maximum diversity required both widespread cohesin loading as well as long-range associations between H3K27ac-marked regions. Our findings provide a conceptual framework to understand chromatin folding principles that enable antibody diversity and reveal mechanisms of long-range genome communication.