Functional anatomy of the immunoglobulin heavy chain 3’ super-enhancer needs not only core enhancer elements but also their unique DNA context

Cis-regulatory elements feature clustered sites for transcription factors, defining core enhancers and with inter-species homology. The IgH 3' regulatory region (3'RR), a major B-cell super-enhancer, consists into 4 of such core enhancers, scattered within more than 25 kb of packaging 'junk DNA", the sequence of which is not conserved but follows a unique palindromic architecture, itself conserved in all mammalian species. The 3'RR promotes long-range interactions and potential IgH loops with upstream promoters, controlling class switch recombination (CSR) and somatic hypermutation (SHM). It is thus of interest to explore if this functional architecture also involves a specific functional structure of the super-enhancer itself, potentially promoted by its symmetric DNA shell. After many reports of transgenic 3'RR model completely lacking this shell, it was also important to compare in the real endogenous IgH context, such a miniaturized "c3'RR" (simply piling up all 3'RR core enhancers) with the intact 3'RR. Packaging DNA between 3''RR core enhancers proved in fact instrumental for optimal SHM, CSR and IgH locus expression in plasma celles. This reveals that "junk" DNA can matter in the functional anatomy of a super-enhancer, and that precise evalutation of such elements requires full consideration of their global architecture.