The Murine MHC Class II Super Enhancer Contains a Functionally Redundant CTCF-Binding Component and a Novel Element Critical for Maximal Expression.

In both humans and mice, CTCF-binding elements form a series of interacting loops across the MHC class II (MHC-II) locus, and CTCF is required for maximal MHC-II gene expression. In humans, a CTCF-bound chromatin insulator termed and a super enhancer (SE) situated in the intergenic region between and play critical roles in regulating MHC-II expression. In this study, we identify a similar SE, termed located between and of the mouse that contains a CTCF site () and a novel region of high histone H3K27 acetylation. A genetic knockout of was created and its role on MHC-II expression tested on immune cells. We found that deletion did not alter MHC-II expression in B cells, macrophages, and macrophages treated with IFN-γ because of functional redundancy of the remaining MHC-II CTCF sites. Surprisingly, embryonic fibroblasts derived from -deleted mice failed to induce MHC-II gene expression in response to IFN-γ, suggesting that at least in this developmental lineage, was required. Examination of the three-dimensional interactions with and the and promoters identified interactions within the novel region of high histone acetylation within the (termed ) that contains a PU.1 binding site. CRISPR/Cas9 deletion of altered chromatin interactions across the locus and resulted in reduced MHC-II expression. Together, these data demonstrate the functional redundancy of the MHC-II CTCF elements and identify a functionally conserved SE that is critical for maximal expression of MHC-II genes.