Vostok: A looping factor for the organization of the regulatory genome in the Drosophila brain

Drosophila tethering elements mediate long-range enhancer-promoter interactions and connect the promoters of distant paralogous genes. Micro-C maps identified 645 such loops in the Drosophila larval brain, spanning distances of 25 to 250 kb. Here, we demonstrate that the MADF-containing Vostok protein acts as a looping factor. It binds to GCAACA motifs that are overrepresented in brain tethering elements. There is a loss of 47 (7%) of the loops in Vostok mutants, resulting in diminished expression of associated genes. Vostok is largely independent of another looping factor, GAGA-associated factor (GAF). Only 9 loops are disrupted in both Vostok and GAF mutants, raising the possibility of a combinatorial code for tether-tether interactions. This is supported by the reliance of two previously identified meta-loops spanning 6 Mb on both GAF and Vostok. We discuss the prospects of using different combinations of looping factors to engineer 3D associations in animal genomes.