MLL4 prepares the enhancer landscape for Foxp3 induction via chromatin looping

MLL4 is an essential subunit of the H3K4 methylation complexes. We report that MLL4 deficiency compromised regulatory T (T(reg)) cell development and resulted in substantial decreases in H3K4me1 and chromatin interaction at putative enhancers, a remarkable portion of which were not direct targets of MLL4 but were enhancers that interact with MLL4-bound sites. The decrease in H3K4me1 and chromatin interaction at the MLL4-unbound enhancers correlated with MLL4 binding at distant-interacting regions. Deletion of an upstream MLL4 binding site reduced H3K4me1 at the Foxp3 regulatory elements looped to the MLL4 binding site and compromised both thymic T(reg) and inducible T(reg) cell differentiation. We show that MLL4 catalyzed H3K4 methylation at distant unbound enhancers via chromatin looping, thus providing a new mechanism of regulating T cell enhancer landscape and impacting T(reg) cell differentiation.