Tethering elements link distant DNA sequences in the Drosophila genome. They facilitate long-range enhancer-promoter interactions, as well as promoter-promoter associations connecting distant paralogous genes within topological operons. Tethering elements are GAGA-rich and bind to several different proteins, including Trithorax-like (Trl), also known as GAGA-associated factor (GAF). Previous in vitro assays documented multimerization and prion-like behaviors of Trl/GAF, including formation of DNA loops. In this study we observe losses of long-range loops in early embryos upon targeted proteasome degradation of Trl/GAF. We also show that deletions in the N-terminal POZ/BTB (BR-C, ttk and bab / Pox virus and Zinc finger) domain disrupt looping behavior in wing imaginal discs. Strikingly, Trl/GAF depletion and POZ mutants disproportionately disrupt long-range focal contacts within topological operons, resulting in reduced levels of gene expression. We propose that Trl/GAF works in concert with loop extrusion mechanisms to refine the specificity of enhancer-promoter and promoter-promoter interactions within complex topological associating domains.