Chromatin folding principles underlying the generation of antibody diversity

Achieving a diverse repertoire of antigen receptors for effective adaptive immunity requires rearrangement of gene segments into unique combinations via V(D)J recombination. To illuminate precise mechanisms underlying this process, 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 wild-type and mutated 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 rather than at the stripe anchor. Second, the Eµ enhancer was best modeled as a bi-directional loop extrusion blocker though it does not bind the known extrusion blocker CTCF. Third, we found that utilization of VH 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. Overall design: Capture Hi-C of the Igh locus in an IGCR1-deleted pro-B cell line